diff --git a/docs/source/conf.py b/docs/source/conf.py
index 946a89ae7..88033a488 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -90,7 +90,7 @@
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
diff --git a/mriqc/cli/parser.py b/mriqc/cli/parser.py
index 349dcfab6..907b7e43f 100644
--- a/mriqc/cli/parser.py
+++ b/mriqc/cli/parser.py
@@ -538,7 +538,7 @@ def parse_args(args=None, namespace=None):
config.execution.participant_label,
session_id=config.execution.session_id,
task=config.execution.task_id,
- group_echos=False,
+ group_echos=True,
bids_filters=config.execution.bids_filters,
queries={mod: DEFAULT_BIDS_QUERIES[mod] for mod in lc_modalities}
)
@@ -575,7 +575,7 @@ def parse_args(args=None, namespace=None):
# Estimate the biggest file size / leave 1GB if some file does not exist (datalad)
with suppress(FileNotFoundError):
config.workflow.biggest_file_gb = _get_biggest_file_size_gb(
- [i for sublist in config.workflow.inputs.values() for i in sublist]
+ config.workflow.inputs.values()
)
# set specifics for alternative populations
@@ -593,11 +593,14 @@ def parse_args(args=None, namespace=None):
def _get_biggest_file_size_gb(files):
+ """Identify the largest file size (allows multi-echo groups)."""
+
import os
- max_size = 0
+ sizes = []
for file in files:
- size = os.path.getsize(file) / (1024**3)
- if size > max_size:
- max_size = size
- return max_size
+ if isinstance(file, (list, tuple)):
+ sizes.append(_get_biggest_file_size_gb(file))
+ else:
+ sizes.append(os.path.getsize(file))
+ return max(sizes) / (1024**3)
diff --git a/mriqc/data/bootstrap-func.yml b/mriqc/data/bootstrap-func.yml
index ae07531f3..659c3b5e8 100644
--- a/mriqc/data/bootstrap-func.yml
+++ b/mriqc/data/bootstrap-func.yml
@@ -26,18 +26,14 @@
###########################################################################
packagename: mriqc
-title: '{filename} :: Functional MRIQC report'
+title: "{filename} :: MRIQC's BOLD fMRI report"
sections:
- name: Summary
reportlets:
- bids: {datatype: figures, desc: summary, extension: [.html]}
-- name: Basic visual report
+- name: Basic echo-wise reports
+ ordering: echo
reportlets:
- - bids: {datatype: figures, desc: zoomed}
- caption: This panel shows a mosaic of the brain. This mosaic is the most suitable to
- screen head-motion intensity inhomogeneities, global/local noise, signal leakage
- (for example, from the eyeballs and across the phase-encoding axis), etc.
- subtitle: Voxel-wise average of BOLD time-series, zoomed-in covering just the brain
- bids: {datatype: figures, desc: stdev}
subtitle: Standard deviation of signal through time
caption: The voxel-wise standard deviation of the signal (variability along time).
@@ -45,43 +41,12 @@ sections:
subtitle: Carpetplot and nuisance signals
caption: The so-called «carpetplot» may assist in assessing head-motion
derived artifacts and respiation effects.
-- name: Extended visual report
+- name: Extended reports shared across echos
reportlets:
- - bids: {datatype: figures, desc: background}
- caption: This panel shows a mosaic enhancing the background around the head.
- Artifacts usually unveil themselves in the air surrounding the head, where no signal
- sources are present.
- subtitle: View of the background of the voxel-wise average of the BOLD timeseries
- - bids: {datatype: figures, desc: mean}
- subtitle: Average signal through time
- caption: The average signal calculated across the last axis (time).
- - bids: {datatype: figures, desc: airmask}
- caption: The hat-mask calculated internally by MRIQC. Some metrics will use this
- mask, for instance, to find out artifacts and estimate the spread of gaussian noise
- added to the signal. This mask leaves out the air around the face to avoid measuring
- noise sourcing from the eyeballs and their movement.
- subtitle: '«Hat»-mask'
- - bids: {datatype: figures, desc: noisefit}
- caption: The noise fit internally estimated by MRIQC to calculate the QI1 index
- proposed by Mortamet et al. (2009).
- subtitle: Distribution of the noise within the hat mask
- style:
- max-width: 450px
- - bids: {datatype: figures, desc: artifacts}
- caption: Mask of artifactual intensities identified within the hat-mask.
- subtitle: Artifactual intensities on the background
- bids: {datatype: figures, desc: brainmask}
caption: Brain mask as internally extracted by MRIQC. Defects on the brainmask could
indicate problematic aspects of the image quality-wise.
subtitle: Brain extraction performance
- - bids: {datatype: figures, desc: head}
- caption: A mask of the head calculated internally by MRIQC.
- subtitle: Head mask
- - bids: {datatype: figures, desc: segmentation}
- caption: Brain tissue segmentation, as internally extracted by MRIQC.
- Defects on this segmentation, as well as noisy tissue labels could
- indicate problematic aspects of the image quality-wise.
- subtitle: Brain tissue segmentation
- bids: {datatype: figures, desc: norm}
caption: This panel shows a quick-and-dirty nonlinear registration into
the MNI152NLin2009cAsym template accessed with
@@ -89,6 +54,22 @@ sections:
subtitle: Spatial normalization of the anatomical image
static: false
+- name: Extended echo-wise reports
+ ordering: echo
+ reportlets:
+ - bids: {datatype: figures, desc: background}
+ caption: This panel shows a mosaic enhancing the background around the head.
+ Artifacts usually unveil themselves in the air surrounding the head, where no signal
+ sources are present.
+ subtitle: View of the background of the voxel-wise average of the BOLD timeseries
+ - bids: {datatype: figures, desc: mean}
+ subtitle: Average signal through time
+ caption: The average signal calculated across the last axis (time).
+ - bids: {datatype: figures, desc: zoomed}
+ caption: This panel shows a mosaic of the brain. This mosaic is the most suitable to
+ screen head-motion intensity inhomogeneities, global/local noise, signal leakage
+ (for example, from the eyeballs and across the phase-encoding axis), etc.
+ subtitle: Voxel-wise average of BOLD time-series, zoomed-in covering just the brain
- name: About
nested: true
diff --git a/mriqc/data/testdata/group_bold.tsv b/mriqc/data/testdata/group_bold.tsv
index 779bba82a..7506e9995 100644
--- a/mriqc/data/testdata/group_bold.tsv
+++ b/mriqc/data/testdata/group_bold.tsv
@@ -1,10 +1,10 @@
bids_name aor aqi dummy_trs dvars_nstd dvars_std dvars_vstd efc fber fd_mean fd_num fd_perc fwhm_avg fwhm_x fwhm_y fwhm_z gcor gsr_x gsr_y size_t size_x size_y size_z snr spacing_tr spacing_x spacing_y spacing_z summary_bg_k summary_bg_mad summary_bg_mean summary_bg_median summary_bg_n summary_bg_p05 summary_bg_p95 summary_bg_stdv summary_fg_k summary_fg_mad summary_fg_mean summary_fg_median summary_fg_n summary_fg_p05 summary_fg_p95 summary_fg_stdv tsnr
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-sub-ds205s03_task-view_run-01_bold 0.0038563043478260866 0.010398965217391304 0 21.001368679560443 1.0080583680219781 0.9704656724175822 0.555268631792101 955.6907958984375 0.16520736608810047 18 19.565217391304348 1.9890683333333332 1.86912 2.1692175 1.9288675 0.0188429 -0.008540591225028038 0.04196126013994217 92 53 53 27 4.8924206716943655 2.200000047683716 4.0 4.0 4.0 24.78328036616209 7.284480140006654 48.01004600493635 25.337934494018555 55115.0 13.708492279052734 173.4195098876953 63.24374935408871 0.6193718723673731 135.63136294470496 785.625103328459 783.30322265625 20728.0 509.40557861328125 1057.23828125 160.10158982252509 56.46196937561035
-sub-ds205s03_task-view_run-02_bold 0.000538804347826087 0.00718998347826087 0 23.167324632417582 0.9661779338461531 0.9044185629670329 0.5566515976243607 906.2960815429688 0.22854716046970905 44 47.82608695652174 2.0270425000000003 1.898665 2.1941825 1.98828 0.350186 -0.008191297762095928 0.045305926352739334 92 53 53 27 4.819771892578718 2.200000047683716 4.0 4.0 4.0 24.552996566765586 7.135003381683008 48.0985481401069 25.58615016937256 55126.0 16.843839645385742 171.75970458984375 61.92351887941012 0.654934961442704 137.18513622307717 774.2342621452095 770.2647094726562 20717.0 498.0149230957031 1046.4920654296875 159.8096624186355 44.19522476196289
-sub-ds205s07_task-functionallocalizer_run-01_bold 0.005997083333333333 0.0056276609722222225 0 21.73490091760564 1.1161214411267604 1.0305108769014089 0.5398076828636086 979.1392822265625 0.1550487344317312 15 20.833333333333332 1.7913891666666668 1.7012025 1.8870975 1.7858675 0.0356344 -0.006339103449136019 0.029900137335062027 72 53 53 27 5.051380236662852 2.200000047683716 4.0 4.0 4.0 23.998434132266535 6.359841724478726 40.97200099097582 22.96632194519043 56199.0 13.510886192321777 148.19041442871094 54.7943334817377 0.42502710232227514 134.22454681982717 722.5941279030118 718.6438293457031 19644.0 477.47076416015625 953.461181640625 142.26320406635728 68.8161506652832
-sub-ds205s07_task-view_run-01_bold 0.0037941304347826085 0.009004425434782607 0 21.771277794505497 1.0383257392307694 0.9654323329670328 0.5374363883770776 996.05810546875 0.1520993052375479 15 16.304347826086957 1.8006975 1.698995 1.8907725 1.812325 0.0408048 -0.005473143886774778 0.029460299760103226 92 53 53 27 5.072217446804501 2.200000047683716 4.0 4.0 4.0 27.23682449098333 6.229042844827164 39.84597218066951 22.68582057952881 56266.0 13.13893985748291 139.88406372070312 53.19358553170623 0.3440927682297894 134.06510192792 720.2195639126317 715.9733276367188 19577.0 476.44183349609375 949.2680053710938 141.1522768548468 57.291603088378906
-sub-ds205s07_task-view_run-02_bold 0.001657826086956522 0.008996689347826086 0 21.519903371868143 1.03221585 0.9588135309890113 0.5394046827226318 978.5082397460938 0.15451170465747024 18 19.565217391304348 1.8057741666666667 1.7069875 1.8966275 1.8137075 0.0433865 -0.006386041175574064 0.03140100836753845 92 53 53 27 5.056518385567245 2.200000047683716 4.0 4.0 4.0 29.670872739050793 6.462488049835068 40.8786782498388 22.991168975830078 56204.0 13.375846862792969 145.70977783203125 55.307788548732276 0.4335730121828525 135.24980824168193 723.5399965684157 719.189453125 19639.0 481.1661376953125 953.2984008789062 142.22654558293314 59.76730728149414
-sub-ds205s09_task-view_acq-LR_run-01_bold 0.002976986301369863 0.013025251780821916 0 21.405761824861116 1.0611945656944441 0.9949810694444441 0.513063203363028 1207.71533203125 0.3258302280827085 45 61.64383561643836 1.7912675 1.6990475 1.91971 1.755045 0.0362147 -0.005499124526977539 0.01900400035083294 73 53 53 27 5.854353348400624 2.200000047683716 4.0 4.0 4.0 25.199608221336092 5.712747254148226 39.895556611046395 23.25909996032715 58097.0 15.119007110595703 139.44947814941406 56.095377999258176 1.178096485114681 117.15050549333893 796.3205729290771 808.3048706054688 17746.0 526.5880737304688 995.4718627929688 138.0651368134319 58.34690284729004
-sub-ds205s09_task-view_acq-LR_run-02_bold 0.005996575342465754 0.015215327260273973 0 34.39419094722222 1.6192232063888892 1.6501877419444442 0.5136460861041277 1192.3255615234375 0.3345943377548133 47 64.38356164383562 1.7920308333333335 1.6996125 1.920615 1.755865 0.0313875 -0.005142268259078264 0.018914325162768364 73 53 53 27 5.851459215059082 2.200000047683716 4.0 4.0 4.0 25.07199243533304 5.957362424448292 40.199861866481136 23.448966026306152 58096.0 15.263423919677734 139.87855529785156 56.15791257667716 1.1742077271466247 117.28293886411426 797.5247600734042 809.6943969726562 17747.0 526.8685302734375 997.0792846679688 138.3708840384822 51.352577209472656
-sub-ds205s09_task-view_acq-RL_run-01_bold 0.02578232876712329 0.02322782465753425 0 30.880940159027773 1.2222362369444444 1.0929697275 0.5115397239733915 1229.69287109375 0.5699059645824405 53 72.6027397260274 1.8186083333333334 1.72236 1.9520325 1.7814325 0.0447734 -0.003605152480304241 0.017525115981698036 73 53 53 27 5.840571587502318 2.200000047683716 4.0 4.0 4.0 28.28470212917516 5.378516442052904 39.71076207043191 23.19632911682129 58165.0 17.226463317871094 134.9324951171875 56.23862202860845 1.1305372215596474 117.89153513001754 800.2769560314895 813.4251403808594 17678.0 528.4014892578125 1001.2677612304688 139.26755646464403 45.58633995056152
+sub-ds205s03_task-functionallocalizer_run-01_bold 0.0038873170731707324 0.007676269512195123 0 23.556566426419753 1.111688350987654 1.037835274938272 0.5480388108408939 946.6738891601562 0.26118389619646404 32 39.02439024390244 2.460305 2.3309525 2.749775 2.3001875 0.0680646 -0.009326859377324581 0.05734974890947342 82 53 53 27 4.452167473312103 2.200000047683716 4.0 4.0 4.0 32.7759659672557 7.720380258975168 49.68507569151857 24.975608825683594 55688.0 2.341463327407837 179.5365753173828 79.87659545341923 1.3897322764135298 138.87641036027622 767.1765602872674 768.451171875 20155.0 461.5243835449219 1042.731689453125 172.5973051795346 60.897049377672374
+sub-ds205s03_task-view_run-01_bold 0.004324782608695651 0.008262664456521738 0 21.120018382857136 1.0831709981318685 1.0370256236263742 0.5459090166346154 1002.2031860351562 0.16520736608810047 18 19.565217391304348 2.342805 2.234215 2.613075 2.181125 0.0235103 -0.0050179013051092625 0.04793250188231468 92 53 53 27 4.4829699247170405 2.200000047683716 4.0 4.0 4.0 29.71988008857921 7.139052847581331 46.66574967004908 24.7608699798584 55362.0 0.032608695328235626 164.9891357421875 71.66784333938988 1.596677545134333 133.64368600192023 779.8773281882851 783.8695678710938 20481.0 457.5434875488281 1054.61962890625 174.85070038268285 62.58223795099184
+sub-ds205s03_task-view_run-02_bold 0.0012682608695652171 0.007114478586956522 0 33.47404192791209 1.3371308202197805 0.9764774098901093 0.5494999624875053 955.73681640625 0.22854716046970905 44 47.82608695652174 2.4598116666666665 2.3444425 2.7437 2.2912925 0.359354 -0.009432817809283733 0.052887145429849625 92 53 53 27 4.419438774661141 2.200000047683716 4.0 4.0 4.0 29.03249120482654 7.7192010499810335 49.54353785439428 24.934783935546875 55415.0 0.20652174949645996 181.78260803222656 80.45599936028407 1.4009872052560288 139.07454009400536 768.1427012059421 770.8587036132812 20428.0 459.5326232910156 1046.8260498046875 174.42029972293017 45.2559957196936
+sub-ds205s07_task-functionallocalizer_run-01_bold 0.006487361111111111 0.006664996805555556 0 26.95528650943662 1.4143280252112678 1.3278985984507037 0.5345065899755163 1009.7532348632812 0.1550487344317312 15 20.833333333333332 2.2598908333333334 2.16087 2.40925 2.2095525 0.0386767 -0.005986093543469906 0.03482493385672569 72 53 53 27 4.598492679701605 2.200000047683716 4.0 4.0 4.0 35.90517987432788 6.32165175453679 43.5521938439157 22.56944465637207 56450.0 0.0 157.3333282470703 77.35003442698779 1.656221989802022 134.60795658544046 716.0395720200634 717.1805419921875 19393.0 440.0694580078125 951.6666870117188 155.95589707318132 73.35539675597101
+sub-ds205s07_task-view_run-01_bold 0.005007608695652174 0.010561140108695653 0 26.932940011208803 1.2896941338461543 1.168551503516483 0.5321868933927048 1023.4715576171875 0.1520993052375479 15 16.304347826086957 2.266245 2.184035 2.4189475 2.1957525 0.0478984 -0.006112692411988974 0.03277275711297989 92 53 53 27 4.595802249004055 2.200000047683716 4.0 4.0 4.0 33.63529478261993 6.2365988314754315 42.79862974194479 22.380435943603516 56588.0 0.3804347813129425 153.56521606445312 75.85331035278197 1.585165284213823 135.14239559316104 713.6245609062549 715.9891357421875 19255.0 437.3913269042969 947.5869750976562 155.78793525432897 63.332828449318185
+sub-ds205s07_task-view_run-02_bold 0.0027991304347826083 0.008415782065217392 0 27.396022419560428 1.345632817142857 1.2136871409890106 0.5333849667366366 1016.1077880859375 0.15451170465747024 18 19.565217391304348 2.271710833333333 2.1726275 2.433375 2.20913 0.0505144 -0.005830460228025913 0.03532366082072258 92 53 53 27 4.598664236595992 2.200000047683716 4.0 4.0 4.0 36.078683930448996 6.575017673595487 43.39332640278381 22.565217971801758 56589.0 1.22826087474823 155.56521606445312 75.49560044499137 1.6540993322199018 136.17376514793506 717.751513360383 719.2989501953125 19254.0 443.8260803222656 952.5978393554688 156.41069531029106 64.89047080953605
+sub-ds205s09_task-view_acq-LR_run-01_bold 0.003159041095890411 0.010028379999999998 0 20.396152721388898 1.090989740416667 1.0059027894444443 0.5048353890125871 1243.320556640625 0.3258302280827085 45 61.64383561643836 2.0852608333333333 2.0588275 2.2995125 1.8974425 0.0461463 -0.0019858605228364468 0.021903924643993378 73 53 53 27 5.292682271102816 2.200000047683716 4.0 4.0 4.0 33.98009379704732 5.949264906571304 39.07313696894552 22.956466674804688 58369.0 1.0936830043792725 132.37034606933594 62.99641049623399 2.7398312528413937 115.58686871143783 791.6591133225957 809.4622802734375 17474.0 483.6707458496094 994.6715698242188 152.93552051211557 66.51667785644531
+sub-ds205s09_task-view_acq-LR_run-02_bold 0.005322328767123288 0.012026137260273973 0 33.41256753611111 1.7174510266666663 1.7695175424999998 0.5052536160578726 1231.6690673828125 0.3345943377548133 47 64.38356164383562 2.0866866666666666 2.0591175 2.3078075 1.893135 0.0393612 -0.0014911222970113158 0.021568207070231438 73 53 53 27 5.293464753553317 2.200000047683716 4.0 4.0 4.0 33.28261057706237 6.199152583273201 39.20170865624716 23.102066040039062 58361.0 1.1750245094299316 131.959716796875 62.4980652302799 2.7186948010130694 115.65690863557867 792.8781950379683 810.7703247070312 17482.0 484.3922119140625 996.912109375 153.16001398016576 59.753475189208984
+sub-ds205s09_task-view_acq-RL_run-01_bold 0.015073150684931508 0.015836369041095893 0 34.205267455972226 1.4370176472222222 1.2820233763888884 0.5044353080190683 1274.420654296875 0.5699059645824405 53 72.6027397260274 2.08056 2.068795 2.288455 1.88443 0.0560156 -0.0013055995805189013 0.018262900412082672 73 53 53 27 5.229556365898414 2.200000047683716 4.0 4.0 4.0 31.57766555712935 5.840893620522815 38.89056185642749 22.814455032348633 58350.0 3.888171911239624 132.03933715820312 61.89358205002823 2.599912401497959 117.24294190485038 794.526159305144 814.4539184570312 17493.0 471.96441650390625 999.9562377929688 155.73608576273267 52.76657485961914
diff --git a/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.json b/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.json
new file mode 100644
index 000000000..3a93d7ce1
--- /dev/null
+++ b/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.json
@@ -0,0 +1,3 @@
+{
+ "EchoTime": 0.030
+}
\ No newline at end of file
diff --git a/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.json b/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.json
new file mode 120000
index 000000000..22bc9c6f2
--- /dev/null
+++ b/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.json
@@ -0,0 +1 @@
+sub-01_task-mixedgamblestask_run-01_bold.json
\ No newline at end of file
diff --git a/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.json b/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.json
new file mode 120000
index 000000000..22bc9c6f2
--- /dev/null
+++ b/mriqc/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.json
@@ -0,0 +1 @@
+sub-01_task-mixedgamblestask_run-01_bold.json
\ No newline at end of file
diff --git a/mriqc/interfaces/bids.py b/mriqc/interfaces/bids.py
index eb48122ae..d4ae9de42 100644
--- a/mriqc/interfaces/bids.py
+++ b/mriqc/interfaces/bids.py
@@ -49,6 +49,7 @@ class IQMFileSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
rec_id = traits.Either(None, Str, usedefault=True)
run_id = traits.Either(None, traits.Int, usedefault=True)
dataset = Str(desc="dataset identifier")
+ dismiss_entities = traits.List(["part"], usedefault=True)
metadata = traits.Dict()
provenance = traits.Dict()
@@ -111,6 +112,17 @@ def _gen_outfile(self):
break
in_file = str(path.relative_to(bids_root))
+ if (
+ isdefined(self.inputs.dismiss_entities)
+ and (dismiss := self.inputs.dismiss_entities)
+ ):
+ for entity in dismiss:
+ bids_chunks = [
+ chunk for chunk in path.name.split("_")
+ if not chunk.startswith(f"{entity}-")
+ ]
+ path = path.parent / "_".join(bids_chunks)
+
# Build path and ensure directory exists
bids_path = out_dir / in_file.replace("".join(Path(in_file).suffixes), ".json")
bids_path.parent.mkdir(parents=True, exist_ok=True)
diff --git a/mriqc/interfaces/functional.py b/mriqc/interfaces/functional.py
index 38670745a..dd72af0f6 100644
--- a/mriqc/interfaces/functional.py
+++ b/mriqc/interfaces/functional.py
@@ -20,6 +20,7 @@
#
# https://www.nipreps.org/community/licensing/
#
+from __future__ import annotations
from os import path as op
import nibabel as nb
@@ -30,9 +31,12 @@
from nipype.interfaces.base import (
BaseInterfaceInputSpec,
File,
+ InputMultiObject,
+ isdefined,
SimpleInterface,
TraitedSpec,
traits,
+ Undefined,
)
@@ -267,6 +271,44 @@ def _run_interface(self, runtime):
return runtime
+class _SelectEchoInputSpec(BaseInterfaceInputSpec):
+ in_files = InputMultiObject(File(exists=True), mandatory=True, desc="input EPI file(s)")
+ metadata = InputMultiObject(traits.Dict(), desc="sidecar JSON files corresponding to in_files")
+ te_reference = traits.Float(0.030, usedefault=True, desc="reference SE-EPI echo time")
+
+
+class _SelectEchoOutputSpec(TraitedSpec):
+ out_file = File(desc="selected echo")
+ echo_index = traits.Int(desc="index of the selected echo")
+ is_multiecho = traits.Bool(desc="whether it is a multiecho dataset")
+
+
+class SelectEcho(SimpleInterface):
+ """
+ Computes anatomical :abbr:`QC (Quality Control)` measures on the
+ structural image given as input
+
+ """
+
+ input_spec = _SelectEchoInputSpec
+ output_spec = _SelectEchoOutputSpec
+
+ def _run_interface(self, runtime):
+ (
+ self._results["out_file"],
+ self._results["echo_index"],
+ ) = select_echo(
+ self.inputs.in_files,
+ te_echos=(
+ _get_echotime(self.inputs.metadata) if isdefined(self.inputs.metadata)
+ else None
+ ),
+ te_reference=self.inputs.te_reference,
+ )
+ self._results["is_multiecho"] = self._results["echo_index"] != -1
+ return runtime
+
+
def find_peaks(data):
t_z = [data[:, :, i, :].mean(axis=0).mean(axis=0) for i in range(data.shape[2])]
return t_z
@@ -292,3 +334,95 @@ def find_spikes(data, spike_thresh):
def _robust_zscore(data):
return (data - np.atleast_2d(np.median(data, axis=1)).T) / np.atleast_2d(data.std(axis=1)).T
+
+
+def select_echo(
+ in_files: str | list[str],
+ te_echos: list[float | Undefined | None] | None = None,
+ te_reference: float = 0.030,
+) -> str:
+ """
+ Select the echo file with the closest echo time to the reference echo time.
+
+ Used to grab the echo file when processing multi-echo data through workflows
+ that only accept a single file.
+
+ Parameters
+ ----------
+ in_files : :obj:`str` or :obj:`list`
+ A single filename or a list of filenames.
+ te_echos : :obj:`list` of :obj:`float`
+ List of echo times corresponding to each file.
+ If not a number (typically, a :obj:`~nipype.interfaces.base.Undefined`),
+ the function selects the second echo.
+ te_reference : float, optional
+ Reference echo time used to find the closest echo time.
+
+ Returns
+ -------
+ str
+ The selected echo file.
+
+ Examples
+ --------
+ >>> select_echo("single-echo.nii.gz")
+ ('single-echo.nii.gz', -1)
+
+ >>> select_echo(["single-echo.nii.gz"])
+ ('single-echo.nii.gz', -1)
+
+ >>> select_echo(
+ ... [f"echo{n}.nii.gz" for n in range(1,7)],
+ ... )
+ ('echo2.nii.gz', 1)
+
+ >>> select_echo(
+ ... [f"echo{n}.nii.gz" for n in range(1,7)],
+ ... te_echos=[12.5, 28.5, 34.2, 45.0, 56.1, 68.4],
+ ... te_reference=33.1,
+ ... )
+ ('echo3.nii.gz', 2)
+
+ >>> select_echo(
+ ... [f"echo{n}.nii.gz" for n in range(1,7)],
+ ... te_echos=[12.5, 28.5, 34.2, 45.0, 56.1],
+ ... te_reference=33.1,
+ ... )
+ ('echo2.nii.gz', 1)
+
+ >>> select_echo(
+ ... [f"echo{n}.nii.gz" for n in range(1,7)],
+ ... te_echos=[12.5, 28.5, 34.2, 45.0, 56.1, None],
+ ... te_reference=33.1,
+ ... )
+ ('echo2.nii.gz', 1)
+
+ """
+ if not isinstance(in_files, (list, tuple)):
+ return in_files, -1
+
+ if len(in_files) == 1:
+ return in_files[0], -1
+
+ import numpy as np
+
+ n_echos = len(in_files)
+ if te_echos is not None and len(te_echos) == n_echos:
+ try:
+ index = np.argmin(np.abs(np.array(te_echos) - te_reference))
+ return in_files[index], index
+ except TypeError:
+ pass
+
+ return in_files[1], 1
+
+
+def _get_echotime(inlist):
+ if isinstance(inlist, list):
+ retval = [_get_echotime(el) for el in inlist]
+ return retval[0] if len(retval) == 1 else retval
+
+ echo_time = inlist.get("EchoTime", None) if inlist else None
+
+ if echo_time:
+ return float(echo_time)
diff --git a/mriqc/reports/individual.py b/mriqc/reports/individual.py
index 1e2350dde..8619f1ec2 100644
--- a/mriqc/reports/individual.py
+++ b/mriqc/reports/individual.py
@@ -47,11 +47,13 @@ def _single_report(in_file):
from mriqc import config
# Ensure it's a Path
- in_file = Path(in_file)
+ in_file = Path(in_file if not isinstance(in_file, list) else in_file[0])
# Extract BIDS entities
entities = config.execution.layout.get_file(in_file).get_entities()
entities.pop("extension", None)
+ entities.pop("echo", None)
+ entities.pop("part", None)
report_type = entities.pop("datatype", None)
# Read output file:
diff --git a/mriqc/utils/bids.py b/mriqc/utils/bids.py
index 4ab142655..40bbfed8d 100644
--- a/mriqc/utils/bids.py
+++ b/mriqc/utils/bids.py
@@ -21,6 +21,8 @@
# https://www.nipreps.org/community/licensing/
#
"""PyBIDS tooling."""
+from __future__ import annotations
+
import json
import os
from pathlib import Path
@@ -90,3 +92,99 @@ def write_derivative_description(bids_dir, deriv_dir):
desc["License"] = orig_desc["License"]
Path.write_text(deriv_dir / "dataset_description.json", json.dumps(desc, indent=4))
+
+
+def derive_bids_fname(
+ orig_path: str | Path,
+ entity: str | None = None,
+ newsuffix: str | None = None,
+ newpath: str | Path | None = None,
+ newext: str | None = None,
+ position: int = -1,
+ absolute: bool = True,
+) -> Path | str:
+ """
+ Derive a new file name from a BIDS-formatted path.
+
+ Parameters
+ ----------
+ orig_path : :obj:`str` or :obj:`os.pathlike`
+ A filename (may or may not include path).
+ entity : :obj:`str`, optional
+ A new BIDS-like key-value pair.
+ newsuffix : :obj:`str`, optional
+ Replace the BIDS suffix.
+ newpath : :obj:`str` or :obj:`os.pathlike`, optional
+ Path to replace the path of the input orig_path.
+ newext : :obj:`str`, optional
+ Replace the extension of the file.
+ position : :obj:`int`, optional
+ Position to insert the entity in the filename.
+ absolute : :obj:`bool`, optional
+ If True (default), returns the absolute path of the modified filename.
+
+ Returns
+ -------
+ Absolute path of the modified filename
+
+ Examples
+ --------
+ >>> derive_bids_fname(
+ ... 'sub-001/ses-01/anat/sub-001_ses-01_T1w.nii.gz',
+ ... entity='desc-preproc',
+ ... absolute=False,
+ ... )
+ PosixPath('sub-001/ses-01/anat/sub-001_ses-01_desc-preproc_T1w.nii.gz')
+
+ >>> derive_bids_fname(
+ ... 'sub-001/ses-01/anat/sub-001_ses-01_T1w.nii.gz',
+ ... entity='desc-brain',
+ ... newsuffix='mask',
+ ... newext=".nii",
+ ... absolute=False,
+ ... ) # doctest: +ELLIPSIS
+ PosixPath('sub-001/ses-01/anat/sub-001_ses-01_desc-brain_mask.nii')
+
+ >>> derive_bids_fname(
+ ... 'sub-001/ses-01/anat/sub-001_ses-01_T1w.nii.gz',
+ ... entity='desc-brain',
+ ... newsuffix='mask',
+ ... newext=".nii",
+ ... newpath="/output/node",
+ ... absolute=True,
+ ... ) # doctest: +ELLIPSIS
+ PosixPath('/output/node/sub-001_ses-01_desc-brain_mask.nii')
+
+ >>> derive_bids_fname(
+ ... 'sub-001/ses-01/anat/sub-001_ses-01_T1w.nii.gz',
+ ... entity='desc-brain',
+ ... newsuffix='mask',
+ ... newext=".nii",
+ ... newpath=".",
+ ... absolute=False,
+ ... ) # doctest: +ELLIPSIS
+ PosixPath('sub-001_ses-01_desc-brain_mask.nii')
+
+ """
+
+ orig_path = Path(orig_path)
+ newpath = orig_path.parent if newpath is None else Path(newpath)
+
+ ext = "".join(orig_path.suffixes)
+ newext = newext if newext is not None else ext
+ orig_stem = orig_path.name.replace(ext, "")
+
+ suffix = orig_stem.rsplit("_", maxsplit=1)[-1].strip("_")
+ newsuffix = newsuffix.strip("_") if newsuffix is not None else suffix
+
+ orig_stem = orig_stem.replace(suffix, "").strip("_")
+ bidts = [bit for bit in orig_stem.split("_") if bit]
+ if entity:
+ if position == -1:
+ bidts.append(entity)
+ else:
+ bidts.insert(position, entity.strip("_"))
+
+ retval = (newpath / f"{'_'.join(bidts)}_{newsuffix}.{newext.strip('.')}")
+
+ return retval.absolute() if absolute else retval
diff --git a/mriqc/workflows/anatomical/base.py b/mriqc/workflows/anatomical/base.py
index 400dee068..0751ee327 100644
--- a/mriqc/workflows/anatomical/base.py
+++ b/mriqc/workflows/anatomical/base.py
@@ -86,6 +86,7 @@ def anat_qc_workflow(name="anatMRIQC"):
wf = anat_qc_workflow()
"""
+ from mriqc.workflows.shared import synthstrip_wf
dataset = config.workflow.inputs.get("t1w", []) + config.workflow.inputs.get("t2w", [])
@@ -682,101 +683,6 @@ def airmsk_wf(name="AirMaskWorkflow"):
return workflow
-def synthstrip_wf(name="synthstrip_wf", omp_nthreads=None):
- """Create a brain-extraction workflow using SynthStrip."""
- from nipype.interfaces.ants import N4BiasFieldCorrection
- from niworkflows.interfaces.nibabel import IntensityClip, ApplyMask
- from mriqc.interfaces.synthstrip import SynthStrip
-
- inputnode = pe.Node(niu.IdentityInterface(fields=["in_files"]), name="inputnode")
- outputnode = pe.Node(
- niu.IdentityInterface(fields=["out_corrected", "out_brain", "bias_image", "out_mask"]),
- name="outputnode",
- )
-
- # truncate target intensity for N4 correction
- pre_clip = pe.Node(IntensityClip(p_min=10, p_max=99.9), name="pre_clip")
-
- pre_n4 = pe.Node(
- N4BiasFieldCorrection(
- dimension=3,
- num_threads=omp_nthreads,
- rescale_intensities=True,
- copy_header=True,
- ),
- name="pre_n4",
- )
-
- post_n4 = pe.Node(
- N4BiasFieldCorrection(
- dimension=3,
- save_bias=True,
- num_threads=omp_nthreads,
- n_iterations=[50] * 4,
- copy_header=True,
- ),
- name="post_n4",
- )
-
- synthstrip = pe.Node(
- SynthStrip(num_threads=omp_nthreads),
- name="synthstrip",
- num_threads=omp_nthreads,
- )
-
- final_masked = pe.Node(ApplyMask(), name="final_masked")
- final_inu = pe.Node(niu.Function(function=_apply_bias_correction), name="final_inu")
-
- workflow = pe.Workflow(name=name)
- # fmt: off
- workflow.connect([
- (inputnode, final_inu, [("in_files", "in_file")]),
- (inputnode, pre_clip, [("in_files", "in_file")]),
- (pre_clip, pre_n4, [("out_file", "input_image")]),
- (pre_n4, synthstrip, [("output_image", "in_file")]),
- (synthstrip, post_n4, [("out_mask", "weight_image")]),
- (synthstrip, final_masked, [("out_mask", "in_mask")]),
- (pre_clip, post_n4, [("out_file", "input_image")]),
- (post_n4, final_inu, [("bias_image", "bias_image")]),
- (post_n4, final_masked, [("output_image", "in_file")]),
- (final_masked, outputnode, [("out_file", "out_brain")]),
- (post_n4, outputnode, [("bias_image", "bias_image")]),
- (synthstrip, outputnode, [("out_mask", "out_mask")]),
- (post_n4, outputnode, [("output_image", "out_corrected")]),
- ])
- # fmt: on
- return workflow
-
-
-def _apply_bias_correction(in_file, bias_image, out_file=None):
- import os.path as op
-
- import numpy as np
- import nibabel as nb
-
- img = nb.load(in_file)
- data = np.clip(
- img.get_fdata() * nb.load(bias_image).get_fdata(),
- a_min=0,
- a_max=None,
- )
- out_img = img.__class__(
- data.astype(img.get_data_dtype()),
- img.affine,
- img.header,
- )
-
- if out_file is None:
- fname, ext = op.splitext(op.basename(in_file))
- if ext == ".gz":
- fname, ext2 = op.splitext(fname)
- ext = ext2 + ext
- out_file = op.abspath(f"{fname}_inu{ext}")
-
- out_img.to_filename(out_file)
- return out_file
-
-
def _binarize(in_file, threshold=0.5, out_file=None):
import os.path as op
diff --git a/mriqc/workflows/diffusion/base.py b/mriqc/workflows/diffusion/base.py
index 470f02fa7..a81d08520 100644
--- a/mriqc/workflows/diffusion/base.py
+++ b/mriqc/workflows/diffusion/base.py
@@ -76,6 +76,7 @@ def dmri_qc_workflow(name="dwiMRIQC"):
ReadDWIMetadata,
WeightedStat,
)
+ from mriqc.workflows.shared import synthstrip_wf as dmri_bmsk_workflow
from mriqc.messages import BUILDING_WORKFLOW
workflow = pe.Workflow(name=name)
@@ -349,70 +350,6 @@ def compute_iqms(name="ComputeIQMs"):
return workflow
-def dmri_bmsk_workflow(name="dmri_brainmask", omp_nthreads=None):
- """
- Compute a brain mask for the input :abbr:`dMRI (diffusion MRI)` dataset.
-
- .. workflow::
-
- from mriqc.workflows.diffusion.base import dmri_bmsk_workflow
- from mriqc.testing import mock_config
- with mock_config():
- wf = dmri_bmsk_workflow()
-
-
- """
-
- from nipype.interfaces.ants import N4BiasFieldCorrection
- from niworkflows.interfaces.nibabel import ApplyMask
- from mriqc.interfaces.synthstrip import SynthStrip
- from mriqc.workflows.anatomical.base import _apply_bias_correction
-
- inputnode = pe.Node(niu.IdentityInterface(fields=["in_file"]), name="inputnode")
- outputnode = pe.Node(
- niu.IdentityInterface(fields=["out_corrected", "out_brain", "bias_image", "out_mask"]),
- name="outputnode",
- )
-
- post_n4 = pe.Node(
- N4BiasFieldCorrection(
- dimension=3,
- save_bias=True,
- num_threads=omp_nthreads,
- n_iterations=[50] * 4,
- copy_header=True,
- ),
- name="post_n4",
- )
-
- synthstrip = pe.Node(
- SynthStrip(num_threads=omp_nthreads),
- name="synthstrip",
- num_threads=omp_nthreads,
- )
-
- final_masked = pe.Node(ApplyMask(), name="final_masked")
- final_inu = pe.Node(niu.Function(function=_apply_bias_correction), name="final_inu")
-
- workflow = pe.Workflow(name=name)
- # fmt: off
- workflow.connect([
- (inputnode, final_inu, [("in_file", "in_file")]),
- (inputnode, synthstrip, [("in_file", "in_file")]),
- (inputnode, post_n4, [("in_file", "input_image")]),
- (synthstrip, post_n4, [("out_mask", "weight_image")]),
- (synthstrip, final_masked, [("out_mask", "in_mask")]),
- (post_n4, final_inu, [("bias_image", "bias_image")]),
- (post_n4, final_masked, [("output_image", "in_file")]),
- (final_masked, outputnode, [("out_file", "out_brain")]),
- (post_n4, outputnode, [("bias_image", "bias_image")]),
- (synthstrip, outputnode, [("out_mask", "out_mask")]),
- (post_n4, outputnode, [("output_image", "out_corrected")]),
- ])
- # fmt: on
- return workflow
-
-
def init_dmriref_wf(
in_file=None,
name="init_dmriref_wf",
diff --git a/mriqc/workflows/functional/base.py b/mriqc/workflows/functional/base.py
index 1ede04f61..3db1cb224 100644
--- a/mriqc/workflows/functional/base.py
+++ b/mriqc/workflows/functional/base.py
@@ -45,6 +45,8 @@
from mriqc import config
from nipype.interfaces import utility as niu
from nipype.pipeline import engine as pe
+from niworkflows.utils.connections import pop_file as _pop
+
from mriqc.interfaces.datalad import DataladIdentityInterface
from mriqc.workflows.functional.output import init_func_report_wf
@@ -64,8 +66,10 @@ def fmri_qc_workflow(name="funcMRIQC"):
"""
from nipype.algorithms.confounds import TSNR, NonSteadyStateDetector
from nipype.interfaces.afni import TStat
+ from niworkflows.interfaces.bids import ReadSidecarJSON
from niworkflows.interfaces.header import SanitizeImage
from mriqc.messages import BUILDING_WORKFLOW
+ from mriqc.interfaces.functional import SelectEcho
workflow = pe.Workflow(name=name)
@@ -76,7 +80,7 @@ def fmri_qc_workflow(name="funcMRIQC"):
message = BUILDING_WORKFLOW.format(
modality="functional",
detail=(
- f"for {len(dataset)} NIfTI files."
+ f"for {len(dataset)} BOLD runs."
if len(dataset) > 2
else f"({' and '.join(('<%s>' % v for v in dataset))})."
),
@@ -88,9 +92,10 @@ def fmri_qc_workflow(name="funcMRIQC"):
inputnode = pe.Node(niu.IdentityInterface(fields=["in_file"]), name="inputnode")
inputnode.iterables = [("in_file", dataset)]
- datalad_get = pe.Node(
+ datalad_get = pe.MapNode(
DataladIdentityInterface(fields=["in_file"], dataset_path=config.execution.bids_dir),
name="datalad_get",
+ iterfield=["in_file"],
)
outputnode = pe.Node(
@@ -98,32 +103,49 @@ def fmri_qc_workflow(name="funcMRIQC"):
name="outputnode",
)
+ # Get metadata
+ meta = pe.MapNode(ReadSidecarJSON(
+ index_db=config.execution.bids_database_dir
+ ), name="metadata", iterfield=["in_file"])
+
+ pick_echo = pe.Node(SelectEcho(), name="pick_echo")
+
non_steady_state_detector = pe.Node(NonSteadyStateDetector(), name="non_steady_state_detector")
- sanitize = pe.Node(SanitizeImage(), name="sanitize", mem_gb=mem_gb * 4.0)
- sanitize.inputs.max_32bit = config.execution.float32
+ sanitize = pe.MapNode(
+ SanitizeImage(max_32bit=config.execution.float32),
+ name="sanitize",
+ mem_gb=mem_gb * 4.0,
+ iterfield=["in_file"],
+ )
# Workflow --------------------------------------------------------
# 1. HMC: head motion correct
- hmcwf = hmc()
+ hmcwf = hmc(omp_nthreads=config.nipype.omp_nthreads)
# Set HMC settings
hmcwf.inputs.inputnode.fd_radius = config.workflow.fd_radius
# 2. Compute mean fmri
- mean = pe.Node(
+ mean = pe.MapNode(
TStat(options="-mean", outputtype="NIFTI_GZ"),
name="mean",
mem_gb=mem_gb * 1.5,
+ iterfield=["in_file"],
+ )
+
+ # Compute TSNR using nipype implementation
+ tsnr = pe.MapNode(
+ TSNR(),
+ name="compute_tsnr",
+ mem_gb=mem_gb * 2.5,
+ iterfield=["in_file"],
)
# EPI to MNI registration
ema = epi_mni_align()
- # Compute TSNR using nipype implementation
- tsnr = pe.Node(TSNR(), name="compute_tsnr", mem_gb=mem_gb * 2.5)
-
# 7. Compute IQMs
iqmswf = compute_iqms()
# Reports
@@ -133,22 +155,35 @@ def fmri_qc_workflow(name="funcMRIQC"):
workflow.connect([
(inputnode, datalad_get, [("in_file", "in_file")]),
- (inputnode, func_report_wf, [
- ("in_file", "inputnode.name_source"),
- ]),
- (datalad_get, iqmswf, [("in_file", "inputnode.in_file")]),
+ (datalad_get, meta, [("in_file", "in_file")]),
+ (datalad_get, pick_echo, [("in_file", "in_files")]),
(datalad_get, sanitize, [("in_file", "in_file")]),
- (datalad_get, non_steady_state_detector, [("in_file", "in_file")]),
+ (meta, pick_echo, [("out_dict", "metadata")]),
+ (pick_echo, non_steady_state_detector, [("out_file", "in_file")]),
(non_steady_state_detector, sanitize, [("n_volumes_to_discard", "n_volumes_to_discard")]),
(sanitize, hmcwf, [("out_file", "inputnode.in_file")]),
(hmcwf, mean, [("outputnode.out_file", "in_file")]),
(hmcwf, tsnr, [("outputnode.out_file", "in_file")]),
- (mean, ema, [("out_file", "inputnode.epi_mean")]),
+ (mean, ema, [(("out_file", _pop), "inputnode.epi_mean")]),
+ # Feed IQMs computation
+ (meta, iqmswf, [("out_dict", "inputnode.metadata"),
+ ("subject", "inputnode.subject"),
+ ("session", "inputnode.session"),
+ ("task", "inputnode.task"),
+ ("acquisition", "inputnode.acquisition"),
+ ("reconstruction", "inputnode.reconstruction"),
+ ("run", "inputnode.run")]),
+ (datalad_get, iqmswf, [("in_file", "inputnode.in_file")]),
(sanitize, iqmswf, [("out_file", "inputnode.in_ras")]),
(mean, iqmswf, [("out_file", "inputnode.epi_mean")]),
(hmcwf, iqmswf, [("outputnode.out_file", "inputnode.hmc_epi"),
("outputnode.out_fd", "inputnode.hmc_fd")]),
(tsnr, iqmswf, [("tsnr_file", "inputnode.in_tsnr")]),
+ (non_steady_state_detector, iqmswf, [("n_volumes_to_discard", "inputnode.exclude_index")]),
+ # Feed reportlet generation
+ (inputnode, func_report_wf, [
+ ("in_file", "inputnode.name_source"),
+ ]),
(sanitize, func_report_wf, [("out_file", "inputnode.in_ras")]),
(mean, func_report_wf, [("out_file", "inputnode.epi_mean")]),
(tsnr, func_report_wf, [("stddev_file", "inputnode.in_stddev")]),
@@ -160,13 +195,12 @@ def fmri_qc_workflow(name="funcMRIQC"):
("outputnode.epi_parc", "inputnode.epi_parc"),
("outputnode.report", "inputnode.mni_report"),
]),
- (non_steady_state_detector, iqmswf, [("n_volumes_to_discard", "inputnode.exclude_index")]),
(iqmswf, func_report_wf, [
("outputnode.out_file", "inputnode.in_iqms"),
("outputnode.out_dvars", "inputnode.in_dvars"),
("outputnode.outliers", "inputnode.outliers"),
- ("outputnode.meta_sidecar", "inputnode.meta_sidecar"),
]),
+ (meta, func_report_wf, [("out_dict", "inputnode.meta_sidecar")]),
(hmcwf, outputnode, [("outputnode.out_fd", "out_fd")]),
])
# fmt: on
@@ -183,13 +217,15 @@ def fmri_qc_workflow(name="funcMRIQC"):
# population specific changes to brain masking
if config.workflow.species == "human":
- skullstrip_epi = fmri_bmsk_workflow()
+ from mriqc.workflows.shared import synthstrip_wf as fmri_bmsk_workflow
+
+ skullstrip_epi = fmri_bmsk_workflow(omp_nthreads=config.nipype.omp_nthreads)
# fmt: off
workflow.connect([
- (mean, skullstrip_epi, [("out_file", "inputnode.in_file")]),
- (skullstrip_epi, ema, [("outputnode.out_file", "inputnode.epi_mask")]),
- (skullstrip_epi, iqmswf, [("outputnode.out_file", "inputnode.brainmask")]),
- (skullstrip_epi, func_report_wf, [("outputnode.out_file", "inputnode.brainmask")]),
+ (mean, skullstrip_epi, [(("out_file", _pop), "inputnode.in_files")]),
+ (skullstrip_epi, ema, [("outputnode.out_mask", "inputnode.epi_mask")]),
+ (skullstrip_epi, iqmswf, [("outputnode.out_mask", "inputnode.brainmask")]),
+ (skullstrip_epi, func_report_wf, [("outputnode.out_mask", "inputnode.brainmask")]),
])
# fmt: on
else:
@@ -216,11 +252,11 @@ def fmri_qc_workflow(name="funcMRIQC"):
if not config.execution.no_sub:
from mriqc.interfaces.webapi import UploadIQMs
- upldwf = pe.Node(UploadIQMs(
+ upldwf = pe.MapNode(UploadIQMs(
endpoint=config.execution.webapi_url,
auth_token=config.execution.webapi_token,
strict=config.execution.upload_strict,
- ), name="UploadMetrics")
+ ), name="UploadMetrics", iterfield=["in_iqms"])
# fmt: off
workflow.connect([
@@ -245,7 +281,6 @@ def compute_iqms(name="ComputeIQMs"):
"""
from nipype.algorithms.confounds import ComputeDVARS
from nipype.interfaces.afni import OutlierCount, QualityIndex
- from niworkflows.interfaces.bids import ReadSidecarJSON
from mriqc.interfaces import FunctionalQC, IQMFileSink
from mriqc.interfaces.reports import AddProvenance
@@ -268,6 +303,12 @@ def compute_iqms(name="ComputeIQMs"):
"in_tsnr",
"metadata",
"exclude_index",
+ "subject",
+ "session",
+ "task",
+ "acquisition",
+ "reconstruction",
+ "run",
]
),
name="inputnode",
@@ -280,7 +321,6 @@ def compute_iqms(name="ComputeIQMs"):
"outliers",
"out_spikes",
"out_fft",
- "meta_sidecar",
]
),
name="outputnode",
@@ -290,32 +330,40 @@ def compute_iqms(name="ComputeIQMs"):
inputnode.inputs.fd_thres = config.workflow.fd_thres
# Compute DVARS
- dvnode = pe.Node(
+ dvnode = pe.MapNode(
ComputeDVARS(save_plot=False, save_all=True),
name="ComputeDVARS",
mem_gb=mem_gb * 3,
+ iterfield=["in_file"],
)
# AFNI quality measures
- fwhm_interface = get_fwhmx()
- fwhm = pe.Node(fwhm_interface, name="smoothness")
- # fwhm.inputs.acf = True # add when AFNI >= 16
- outliers = pe.Node(
+ fwhm = pe.MapNode(get_fwhmx(), name="smoothness", iterfield=["in_file"])
+ fwhm.inputs.acf = True # Only AFNI >= 16
+
+ outliers = pe.MapNode(
OutlierCount(fraction=True, out_file="outliers.out"),
name="outliers",
mem_gb=mem_gb * 2.5,
+ iterfield=["in_file"],
)
- quality = pe.Node(
+ quality = pe.MapNode(
QualityIndex(automask=True),
out_file="quality.out",
name="quality",
mem_gb=mem_gb * 3,
+ iterfield=["in_file"],
)
- gcor = pe.Node(GCOR(), name="gcor", mem_gb=mem_gb * 2)
+ gcor = pe.MapNode(GCOR(), name="gcor", mem_gb=mem_gb * 2, iterfield=["in_file"])
- measures = pe.Node(FunctionalQC(), name="measures", mem_gb=mem_gb * 3)
+ measures = pe.MapNode(
+ FunctionalQC(),
+ name="measures",
+ mem_gb=mem_gb * 3,
+ iterfield=["in_epi", "in_hmc", "in_tsnr", "in_dvars", "in_fwhm"],
+ )
# fmt: off
workflow.connect([
@@ -341,19 +389,15 @@ def compute_iqms(name="ComputeIQMs"):
])
# fmt: on
- # Add metadata
- meta = pe.Node(ReadSidecarJSON(
- index_db=config.execution.bids_database_dir
- ), name="metadata")
-
- addprov = pe.Node(
+ addprov = pe.MapNode(
AddProvenance(modality="bold"),
name="provenance",
run_without_submitting=True,
+ iterfield=["in_file"],
)
# Save to JSON file
- datasink = pe.Node(
+ datasink = pe.MapNode(
IQMFileSink(
modality="bold",
out_dir=str(config.execution.output_dir),
@@ -361,28 +405,27 @@ def compute_iqms(name="ComputeIQMs"):
),
name="datasink",
run_without_submitting=True,
+ iterfield=["in_file", "root", "metadata", "provenance"],
)
# fmt: off
workflow.connect([
- (inputnode, datasink, [("in_file", "in_file"),
- ("exclude_index", "dummy_trs")]),
- (inputnode, meta, [("in_file", "in_file")]),
(inputnode, addprov, [("in_file", "in_file")]),
- (meta, datasink, [("subject", "subject_id"),
- ("session", "session_id"),
- ("task", "task_id"),
- ("acquisition", "acq_id"),
- ("reconstruction", "rec_id"),
- ("run", "run_id"),
- ("out_dict", "metadata")]),
+ (inputnode, datasink, [("in_file", "in_file"),
+ ("exclude_index", "dummy_trs"),
+ (("subject", _pop), "subject_id"),
+ (("session", _pop), "session_id"),
+ (("task", _pop), "task_id"),
+ (("acquisition", _pop), "acq_id"),
+ (("reconstruction", _pop), "rec_id"),
+ (("run", _pop), "run_id"),
+ ("metadata", "metadata")]),
(addprov, datasink, [("out_prov", "provenance")]),
(outliers, datasink, [(("out_file", _parse_tout), "aor")]),
(gcor, datasink, [(("out", _tofloat), "gcor")]),
(quality, datasink, [(("out_file", _parse_tqual), "aqi")]),
(measures, datasink, [("out_qc", "root")]),
(datasink, outputnode, [("out_file", "out_file")]),
- (meta, outputnode, [("out_dict", "meta_sidecar")]),
])
# fmt: on
@@ -390,13 +433,14 @@ def compute_iqms(name="ComputeIQMs"):
if config.workflow.fft_spikes_detector:
from mriqc.workflows.utils import slice_wise_fft
- spikes_fft = pe.Node(
+ spikes_fft = pe.MapNode(
niu.Function(
input_names=["in_file"],
output_names=["n_spikes", "out_spikes", "out_fft"],
function=slice_wise_fft,
),
name="SpikesFinderFFT",
+ iterfield=["in_file"],
)
# fmt: off
@@ -441,7 +485,7 @@ def fmri_bmsk_workflow(name="fMRIBrainMask"):
return workflow
-def hmc(name="fMRI_HMC"):
+def hmc(name="fMRI_HMC", omp_nthreads=None):
"""
Create a :abbr:`HMC (head motion correction)` workflow for fMRI.
@@ -468,9 +512,9 @@ def hmc(name="fMRI_HMC"):
outputnode = pe.Node(niu.IdentityInterface(fields=["out_file", "out_fd"]), name="outputnode")
# calculate hmc parameters
- hmc = pe.Node(
+ estimate_hm = pe.Node(
Volreg(args="-Fourier -twopass", zpad=4, outputtype="NIFTI_GZ"),
- name="motion_correct",
+ name="estimate_hm",
mem_gb=mem_gb * 2.5,
)
@@ -480,49 +524,73 @@ def hmc(name="fMRI_HMC"):
name="ComputeFD",
)
+ # Apply transforms to other echos
+ apply_hmc = pe.MapNode(
+ niu.Function(function=_apply_transforms, input_names=["in_file", "in_xfm"]),
+ name="apply_hmc",
+ iterfield=["in_file"],
+ # NiTransforms is a memory hog, so ensure only one process is running at a time
+ num_threads=config.environment.cpu_count,
+ )
+
# fmt: off
workflow.connect([
(inputnode, fdnode, [("fd_radius", "radius")]),
- (hmc, outputnode, [("out_file", "out_file")]),
- (hmc, fdnode, [("oned_file", "in_file")]),
+ (estimate_hm, apply_hmc, [("oned_matrix_save", "in_xfm")]),
+ (apply_hmc, outputnode, [("out", "out_file")]),
+ (estimate_hm, fdnode, [("oned_file", "in_file")]),
(fdnode, outputnode, [("out_file", "out_fd")]),
])
# fmt: on
- # despiking, and deoblique
-
- deoblique_node = pe.Node(Refit(deoblique=True), name="deoblique")
-
- despike_node = pe.Node(Despike(outputtype="NIFTI_GZ"), name="despike")
+ if not (config.workflow.despike or config.workflow.deoblique):
+ # fmt: off
+ workflow.connect([
+ (inputnode, estimate_hm, [(("in_file", _pop), "in_file")]),
+ (inputnode, apply_hmc, [("in_file", "in_file")]),
+ ])
+ # fmt: on
+ return workflow
+ # despiking, and deoblique
+ deoblique_node = pe.MapNode(
+ Refit(deoblique=True),
+ name="deoblique",
+ iterfield=["in_file"],
+ )
+ despike_node = pe.MapNode(
+ Despike(outputtype="NIFTI_GZ"),
+ name="despike",
+ iterfield=["in_file"],
+ )
if config.workflow.despike and config.workflow.deoblique:
# fmt: off
workflow.connect([
(inputnode, despike_node, [("in_file", "in_file")]),
(despike_node, deoblique_node, [("out_file", "in_file")]),
- (deoblique_node, hmc, [("out_file", "in_file")]),
+ (deoblique_node, estimate_hm, [(("out_file", _pop), "in_file")]),
+ (deoblique_node, apply_hmc, [("out_file", "in_file")]),
])
# fmt: on
elif config.workflow.despike:
# fmt: off
workflow.connect([
(inputnode, despike_node, [("in_file", "in_file")]),
- (despike_node, hmc, [("out_file", "in_file")]),
+ (despike_node, estimate_hm, [(("out_file", _pop), "in_file")]),
+ (despike_node, apply_hmc, [("out_file", "in_file")]),
])
# fmt: on
elif config.workflow.deoblique:
# fmt: off
workflow.connect([
(inputnode, deoblique_node, [("in_file", "in_file")]),
- (deoblique_node, hmc, [("out_file", "in_file")]),
+ (deoblique_node, estimate_hm, [(("out_file", _pop), "in_file")]),
+ (deoblique_node, apply_hmc, [("out_file", "in_file")]),
])
# fmt: on
else:
- # fmt: off
- workflow.connect([
- (inputnode, hmc, [("in_file", "in_file")]),
- ])
- # fmt: on
+ raise NotImplementedError
+
return workflow
@@ -665,13 +733,13 @@ def epi_mni_align(name="SpatialNormalization"):
return workflow
-def _mean(inlist):
- import numpy as np
-
- return np.mean(inlist)
-
-
def _parse_tqual(in_file):
+ if isinstance(in_file, (list, tuple)):
+ return (
+ [_parse_tqual(f) for f in in_file] if len(in_file) > 1
+ else _parse_tqual(in_file[0])
+ )
+
import numpy as np
with open(in_file, "r") as fin:
@@ -680,7 +748,30 @@ def _parse_tqual(in_file):
def _parse_tout(in_file):
+ if isinstance(in_file, (list, tuple)):
+ return (
+ [_parse_tout(f) for f in in_file] if len(in_file) > 1
+ else _parse_tout(in_file[0])
+ )
+
import numpy as np
data = np.loadtxt(in_file) # pylint: disable=no-member
return data.mean()
+
+
+def _apply_transforms(in_file, in_xfm):
+ from pathlib import Path
+ from nitransforms.linear import load
+ from mriqc.utils.bids import derive_bids_fname
+
+ realigned = load(in_xfm, fmt="afni", reference=in_file, moving=in_file).apply(in_file)
+ out_file = derive_bids_fname(
+ in_file,
+ entity="desc-realigned",
+ newpath=Path.cwd(),
+ absolute=True,
+ )
+
+ realigned.to_filename(out_file)
+ return str(out_file)
diff --git a/mriqc/workflows/functional/output.py b/mriqc/workflows/functional/output.py
index fc6a421ce..f620cb2a1 100644
--- a/mriqc/workflows/functional/output.py
+++ b/mriqc/workflows/functional/output.py
@@ -81,7 +81,7 @@ def init_func_report_wf(name="func_report_wf"):
# Set FD threshold
inputnode.inputs.fd_thres = config.workflow.fd_thres
- spmask = pe.Node(
+ spmask = pe.MapNode(
niu.Function(
input_names=["in_file", "in_mask"],
output_names=["out_file", "out_plot"],
@@ -89,12 +89,14 @@ def init_func_report_wf(name="func_report_wf"):
),
name="SpikesMask",
mem_gb=mem_gb * 3.5,
+ iterfield=["in_file"],
)
- spikes_bg = pe.Node(
+ spikes_bg = pe.MapNode(
Spikes(no_zscore=True, detrend=False),
name="SpikesFinderBgMask",
mem_gb=mem_gb * 2.5,
+ iterfield=["in_file", "in_mask"],
)
# Generate crown mask
@@ -103,7 +105,12 @@ def init_func_report_wf(name="func_report_wf"):
subtract_mask = pe.Node(BinarySubtraction(), name="subtract_mask")
parcels = pe.Node(niu.Function(function=_carpet_parcellation), name="parcels")
- bigplot = pe.Node(FMRISummary(), name="BigPlot", mem_gb=mem_gb * 3.5)
+ bigplot = pe.MapNode(
+ FMRISummary(),
+ name="BigPlot",
+ mem_gb=mem_gb * 3.5,
+ iterfield=["in_func", "dvars", "outliers", "in_spikes_bg"],
+ )
# fmt: off
workflow.connect([
@@ -118,58 +125,66 @@ def init_func_report_wf(name="func_report_wf"):
(inputnode, parcels, [("epi_parc", "segmentation")]),
(inputnode, dilated_mask, [("brainmask", "in_mask")]),
(inputnode, subtract_mask, [("brainmask", "in_subtract")]),
+ (spmask, spikes_bg, [("out_file", "in_mask")]),
(dilated_mask, subtract_mask, [("out_mask", "in_base")]),
(subtract_mask, parcels, [("out_mask", "crown_mask")]),
(parcels, bigplot, [("out", "in_segm")]),
(spikes_bg, bigplot, [("out_tsz", "in_spikes_bg")]),
- (spmask, spikes_bg, [("out_file", "in_mask")]),
])
# fmt: on
- mosaic_mean = pe.Node(
+ mosaic_mean = pe.MapNode(
PlotMosaic(
out_file="plot_func_mean_mosaic1.svg",
cmap="Greys_r",
),
name="PlotMosaicMean",
+ iterfield=["in_file"],
)
- mosaic_stddev = pe.Node(
+ mosaic_stddev = pe.MapNode(
PlotMosaic(
out_file="plot_func_stddev_mosaic2_stddev.svg",
cmap="viridis",
),
name="PlotMosaicSD",
+ iterfield=["in_file"],
)
- ds_report_mean = pe.Node(
+ ds_report_mean = pe.MapNode(
DerivativesDataSink(
base_directory=reportlets_dir,
desc="mean",
datatype="figures",
+ dismiss_entities=("part",)
),
name="ds_report_mean",
run_without_submitting=True,
+ iterfield=["in_file", "source_file"],
)
- ds_report_stdev = pe.Node(
+ ds_report_stdev = pe.MapNode(
DerivativesDataSink(
base_directory=reportlets_dir,
desc="stdev",
datatype="figures",
+ dismiss_entities=("part",)
),
name="ds_report_stdev",
run_without_submitting=True,
+ iterfield=["in_file", "source_file"],
)
- ds_report_carpet = pe.Node(
+ ds_report_carpet = pe.MapNode(
DerivativesDataSink(
base_directory=reportlets_dir,
desc="carpet",
datatype="figures",
+ dismiss_entities=("part",)
),
name="ds_report_carpet",
run_without_submitting=True,
+ iterfield=["in_file", "source_file"],
)
# fmt: off
@@ -201,6 +216,7 @@ def init_func_report_wf(name="func_report_wf"):
base_directory=reportlets_dir,
desc="spikes",
datatype="figures",
+ dismiss_entities=("part",)
),
name="ds_report_spikes",
run_without_submitting=True,
@@ -220,21 +236,24 @@ def init_func_report_wf(name="func_report_wf"):
return workflow
# Verbose-reporting goes here
+ from niworkflows.utils.connections import pop_file as _pop
from nireports.interfaces import PlotContours
- mosaic_zoom = pe.Node(
+ mosaic_zoom = pe.MapNode(
PlotMosaic(
cmap="Greys_r",
),
name="PlotMosaicZoomed",
+ iterfield=["in_file"],
)
- mosaic_noise = pe.Node(
+ mosaic_noise = pe.MapNode(
PlotMosaic(
only_noise=True,
cmap="viridis_r",
),
name="PlotMosaicNoise",
+ iterfield=["in_file"]
)
if config.workflow.species.lower() in ("rat", "mouse"):
@@ -254,24 +273,28 @@ def init_func_report_wf(name="func_report_wf"):
name="PlotBrainmask",
)
- ds_report_zoomed = pe.Node(
+ ds_report_zoomed = pe.MapNode(
DerivativesDataSink(
base_directory=reportlets_dir,
desc="zoomed",
datatype="figures",
+ dismiss_entities=("part",)
),
name="ds_report_zoomed",
run_without_submitting=True,
+ iterfield=["in_file", "source_file"],
)
- ds_report_background = pe.Node(
+ ds_report_background = pe.MapNode(
DerivativesDataSink(
base_directory=reportlets_dir,
desc="background",
datatype="figures",
+ dismiss_entities=("part",)
),
name="ds_report_background",
run_without_submitting=True,
+ iterfield=["in_file", "source_file"],
)
ds_report_bmask = pe.Node(
@@ -279,6 +302,7 @@ def init_func_report_wf(name="func_report_wf"):
base_directory=reportlets_dir,
desc="brainmask",
datatype="figures",
+ dismiss_entities=("part", "echo"),
),
name="ds_report_bmask",
run_without_submitting=True,
@@ -289,6 +313,7 @@ def init_func_report_wf(name="func_report_wf"):
base_directory=reportlets_dir,
desc="norm",
datatype="figures",
+ dismiss_entities=("part", "echo"),
),
name="ds_report_norm",
run_without_submitting=True,
@@ -298,7 +323,7 @@ def init_func_report_wf(name="func_report_wf"):
workflow.connect([
(inputnode, ds_report_norm, [("mni_report", "in_file"),
("name_source", "source_file")]),
- (inputnode, plot_bmask, [("epi_mean", "in_file"),
+ (inputnode, plot_bmask, [(("epi_mean", _pop), "in_file"),
("brainmask", "in_contours")]),
(inputnode, mosaic_zoom, [("epi_mean", "in_file"),
("brainmask", "bbox_mask_file")]),
@@ -308,7 +333,7 @@ def init_func_report_wf(name="func_report_wf"):
(inputnode, ds_report_bmask, [("name_source", "source_file")]),
(mosaic_zoom, ds_report_zoomed, [("out_file", "in_file")]),
(mosaic_noise, ds_report_background, [("out_file", "in_file")]),
- (plot_bmask, ds_report_bmask, [("out_file", "in_file")]),
+ (plot_bmask, ds_report_bmask, [(("out_file", _pop), "in_file")]),
])
# fmt: on
@@ -398,4 +423,7 @@ def _carpet_parcellation(segmentation, crown_mask):
def _get_tr(meta_dict):
+ if isinstance(meta_dict, (list, tuple)):
+ meta_dict = meta_dict[0]
+
return meta_dict.get("RepetitionTime", None)
diff --git a/mriqc/workflows/shared.py b/mriqc/workflows/shared.py
new file mode 100644
index 000000000..c2c778a07
--- /dev/null
+++ b/mriqc/workflows/shared.py
@@ -0,0 +1,88 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2023 The NiPreps Developers
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+# https://www.nipreps.org/community/licensing/
+#
+"""Shared workflows."""
+from nipype.interfaces import utility as niu
+from nipype.pipeline import engine as pe
+
+
+def synthstrip_wf(name="synthstrip_wf", omp_nthreads=None):
+ """Create a brain-extraction workflow using SynthStrip."""
+ from nipype.interfaces.ants import N4BiasFieldCorrection
+ from niworkflows.interfaces.nibabel import IntensityClip, ApplyMask
+ from mriqc.interfaces.synthstrip import SynthStrip
+
+ inputnode = pe.Node(niu.IdentityInterface(fields=["in_files"]), name="inputnode")
+ outputnode = pe.Node(
+ niu.IdentityInterface(fields=["out_corrected", "out_brain", "bias_image", "out_mask"]),
+ name="outputnode",
+ )
+
+ # truncate target intensity for N4 correction
+ pre_clip = pe.Node(IntensityClip(p_min=10, p_max=99.9), name="pre_clip")
+
+ pre_n4 = pe.Node(
+ N4BiasFieldCorrection(
+ dimension=3,
+ num_threads=omp_nthreads,
+ rescale_intensities=True,
+ copy_header=True,
+ ),
+ name="pre_n4",
+ )
+
+ post_n4 = pe.Node(
+ N4BiasFieldCorrection(
+ dimension=3,
+ save_bias=True,
+ num_threads=omp_nthreads,
+ n_iterations=[50] * 4,
+ copy_header=True,
+ ),
+ name="post_n4",
+ )
+
+ synthstrip = pe.Node(
+ SynthStrip(num_threads=omp_nthreads),
+ name="synthstrip",
+ num_threads=omp_nthreads,
+ )
+
+ final_masked = pe.Node(ApplyMask(), name="final_masked")
+
+ workflow = pe.Workflow(name=name)
+ # fmt: off
+ workflow.connect([
+ (inputnode, pre_clip, [("in_files", "in_file")]),
+ (pre_clip, pre_n4, [("out_file", "input_image")]),
+ (pre_n4, synthstrip, [("output_image", "in_file")]),
+ (synthstrip, post_n4, [("out_mask", "weight_image")]),
+ (synthstrip, final_masked, [("out_mask", "in_mask")]),
+ (pre_clip, post_n4, [("out_file", "input_image")]),
+ (post_n4, final_masked, [("output_image", "in_file")]),
+ (final_masked, outputnode, [("out_file", "out_brain")]),
+ (post_n4, outputnode, [("bias_image", "bias_image")]),
+ (synthstrip, outputnode, [("out_mask", "out_mask")]),
+ (post_n4, outputnode, [("output_image", "out_corrected")]),
+ ])
+ # fmt: on
+ return workflow
diff --git a/mriqc/workflows/utils.py b/mriqc/workflows/utils.py
index 690c88a67..10c30f100 100644
--- a/mriqc/workflows/utils.py
+++ b/mriqc/workflows/utils.py
@@ -25,9 +25,11 @@
def _tofloat(inlist):
if isinstance(inlist, (list, tuple)):
- return [float(el) for el in inlist]
- else:
- return float(inlist)
+ return (
+ [_tofloat(el) for el in inlist] if len(inlist) > 1
+ else _tofloat(inlist[0])
+ )
+ return float(inlist)
def fwhm_dict(fwhm):