Miscellaneous scripts
freesurfer2mpr_4dfp
transform freesurfer generated images back to atlas space
Usage: freesurfer2mpr_4dfp <(4dfp) mpr> <(4dfp) orig> [options]
Examples:
freesurfer2mpr_4dfp vc1234_654-3[.4dfp.img] vc1234_orig
freesurfer2mpr_4dfp vc1234_654-3 vc1234_orig -T711-2V -alh.ribbon.mgz -arh.ribbon apply
Options
-skew |
general affine orig->mpr registeration (default 6 parameter rigid body) |
-T<target> |
specify atlas representative target |
-a<segimg> |
add named (4dfp format) freesurfer segemntation result to “apply” list |
apply |
proceed directly to transform (4dfp format) segmentations |
force |
force atlas transformation of segmentation results even if it already exists |
setecho |
set echo |
N.B.: <(4dfp) orig> is the freesurfer-resampled 256x256x256 coronal mpr N.B.: the default “apply” list includes (4dfp format) images named *parc* and *aseg*
Tip
You must convert the freesurfer-created mgz (i.e. orig, aparc+aseg) images to 4dfp before running this script. For more details, see Creating a Freesurfer ROI Mask.
split_ROIs
split peak_4dfp ROI image into multiple mask images
Usage: split_ROIs <4dfp ROI file> [start_ROI_number] [end_ROI_number] [options]
Examples:
split_ROIs sum_condition_time_anova_ROI[.4dfp[.img]] 0 82
Options
[<start|end>_ROI_number] |
ROI numbers count from 0 (fidl convention) (defaults are 0, nROI-1) |
-x |
flip ROI to contralateral hemisphere |
-0 |
name output mask file by ROI number (default name as in ifh) |
-d<int> |
specify difference between ROI number and voxel value (default 2) |
N.B.: split_ROIs output files are put into the subdirectory ./single_ROIs
brec
parse rec file by procedure depth
Usage: brec <my_file[.rec]> [-depth_limit]