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added optional argument 'subjects_dir' to project_volume_data #304

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added optional argument 'subjects_dir' to project_volume_data #304

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8 changes: 7 additions & 1 deletion surfer/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ def read_stc(filepath):
def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
projmeth="frac", projsum="avg", projarg=[0, 1, .1],
surf="white", smooth_fwhm=3, mask_label=None,
target_subject=None, verbose=None):
target_subject=None, subjects_dir=None, verbose=None):
"""Sample MRI volume onto cortical manifold.

Note: this requires Freesurfer to be installed with correct
Expand Down Expand Up @@ -168,6 +168,10 @@ def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
Path to label file to constrain projection; otherwise uses cortex
target_subject : string
Subject to warp data to in surface space after projection
subjects_dir : string | None
If not None, this directory will be used as the subjects directory
instead of the value set using the SUBJECTS_DIR environment
variable.
verbose : bool, str, int, or None
If not None, override default verbose level (see surfer.verbose).
"""
Expand Down Expand Up @@ -225,6 +229,8 @@ def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
cmd_list.extend(["--mask", mask_label])
if target_subject is not None:
cmd_list.extend(["--trgsubject", target_subject])
if subjects_dir is not None:
cmd_list.extend(["--sd", subjects_dir])

# Execute the command
out_file = mktemp(prefix="pysurfer-v2s", suffix='.mgz')
Expand Down