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Hi all,
Do you have any suggestions on how I could extract stats (e.g., thickness,
area, LGI, etc.) from a cluster(s) identified via palm? I've tried
mri_label2label in order to turn the palm output .mgz into a paint .label
file, but mri_label2label cannot seem to read the .mgz, .mgz.nii (i.e.,
.mgz mri_converted to .nii), or .mgz.nii.gz files. My inputs to palm are 4D
.mgh files, hence the .mgz results, which are in a data-per-vertex format.
Here are the errors I get when trying convert/input .mgz and .mgz.nii files:
G??M{?Kӭ7?xK/i?Mb4Ե??(???.!?t:6>|???ѧ???+F??c\Ϟ??U}??m?/8q?~ي???\???C??n?h+???~?????}?w*jo???ʵS_??_??w?????????>ԏ??N?no+?8w
mri_label2label: could not scan # of lines from label file
ERROR reading
wordadhd_lgi_cft3.1/wordadhd_lgi_cft3.1_lh_tfce_tstat_cfwep_c4.mgz
/<??c9
mri_label2label: could not scan # of lines from label file
ERROR reading
wordadhd_lgi_cft3.1/wordadhd_lgi_cft3.1_lh_tfce_tstat_cfwep_c4.mgz.nii
As a follow-up to this question, is it possible to threshold the input
label/cluster map during the mri_label2label process? Given that my palm
.mgz results were saved as logp files, I'd like to threshold the maps at
1.301. My assumption is that I'd instead have to do the following:
1) mri_binarize --i ${map} --o ${map}_bin --min 1.301
2) mri_label2label --s fsaverage --srclabel ${map}_bin --trglabel
$subjects/${map}_bin.label --regmethod surface --hemi ${hemi}
3) mri_anatomical_stats -l ${map}_bin.label -f label_stats $subjects $hemi
4) aparcstats2table etc.
Thank you for your attention and help!
With gratitude,
Dan
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