Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Do not clean up FA for degenerate tensors within DTI node #1215

Closed
oesteban opened this issue Mar 22, 2024 · 2 comments · Fixed by #1131
Closed

Do not clean up FA for degenerate tensors within DTI node #1215

oesteban opened this issue Mar 22, 2024 · 2 comments · Fixed by #1131
Labels
bug

Comments

@oesteban
Copy link
Member

What happened?

We are immediately cleaning up the FA:

mriqc/mriqc/interfaces/diffusion.py

Lines 472 to 473 in 61b59e0

fa_data[np.isnan(fa_data)] = 0
fa_data = np.clip(fa_data, 0, 1)
and that precludes that we calculate the percentage of degenerate tensors as an IQM or plot them highlighted for visual QA/QC.

Methods that require a "massaged" FA (e.g., to calculate the CC mask) should take these two easy steps on their own.

/cc @arokem @teresamg

What command did you use?

-m dwi

What version of the software are you running?

master

How are you running this software?

Local installation ("bare-metal")

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response
@oesteban oesteban added the bug label Mar 22, 2024
oesteban added a commit to arokem/mriqc that referenced this issue Mar 22, 2024
@oesteban
wip: preparing new interfaces
6f32f34 
Here I will continue creating the diffusion QC Nipype interface and also
transfer the preprocessing that was in the QC module.

Resolves: nipreps#1215.
@oesteban oesteban linked a pull request Mar 22, 2024 that will close this issue
ENH: Adds diffusion-related IQMs. #1131
Merged
oesteban added a commit to arokem/mriqc that referenced this issue Mar 22, 2024
@oesteban
wip: preparing new interfaces
27d22f7 
Here I will continue creating the diffusion QC Nipype interface and also
transfer the preprocessing that was in the QC module.

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 22, 2024
@oesteban
wip: preparing new interfaces
b23e9bd 
Here I will continue creating the diffusion QC Nipype interface and also
transfer the preprocessing that was in the QC module.

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 22, 2024
@oesteban
wip: preparing new interfaces
9f127d5 
Here I will continue creating the diffusion QC Nipype interface and also
transfer the preprocessing that was in the QC module.

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 22, 2024
@oesteban
wip: preparing new interfaces
a7ec9b4 
Here I will continue creating the diffusion QC Nipype interface and also
transfer the preprocessing that was in the QC module.

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 22, 2024
@oesteban
wip: preparing new interfaces
bc5510d 
Here I will continue creating the diffusion QC Nipype interface and also
transfer the preprocessing that was in the QC module.

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 22, 2024
@oesteban
wip: preparing new interfaces
c33b99f 
Here I will continue creating the diffusion QC Nipype interface and also
transfer the preprocessing that was in the QC module.

Resolves: nipreps#1215.
@arokem
Copy link
Collaborator

arokem commented Mar 22, 2024

What's the point of the FA file? Where is it used subsequent to saving?

@oesteban
Copy link
Member Author

oesteban commented Mar 23, 2024 via email

oesteban added a commit to arokem/mriqc that referenced this issue Mar 25, 2024
@oesteban
wip: preparing new interfaces
af779bd 
Here I will continue creating the diffusion QC Nipype interface and also
transfer the preprocessing that was in the QC module.

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 25, 2024
@oesteban
wip: preparing new interfaces
00c4faa 
- [x] Start with interface for IQMs calculation.
- [x] Accommodate calculation of spikes masks, WM mask, etc.
- [x] Start with workflow connections

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 28, 2024
@oesteban
wip: preparing new interfaces
0355192 
- [x] Start with interface for IQMs calculation.
- [x] Accommodate calculation of spikes masks, WM mask, etc.
- [x] Start with workflow connections

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 29, 2024
@oesteban
wip: preparing new interfaces
098b18e 
- [x] Start with interface for IQMs calculation.
- [x] Accommodate calculation of spikes masks, WM mask, etc.
- [x] Start with workflow connections

Resolves: nipreps#1215.
oesteban added a commit to arokem/mriqc that referenced this issue Mar 31, 2024
@oesteban
enh: preparing new interfaces
3666d48 
- [x] Start with interface for IQMs calculation.
- [x] Accommodate calculation of spikes masks, WM mask, etc.
- [x] Start with workflow connections

Resolves: nipreps#1215.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

ENH: Adds diffusion-related IQMs. arokem/mriqc
2 participants
@arokem @oesteban