see this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 2/16/19 6:48 PM, Daniel Leopold wrote:
>
> External Email - Use Caution
>
> 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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