Re: [Freesurfer] Extracting stats from palm results (.mgz)
I have not really stressed the code with --pargs (it is a relatively new program), but if it produces the same output, then it should work On 2/19/19 5:01 PM, Daniel Leopold wrote: > > External Email - Use Caution > > Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to > take advantage of NPC and exchangeability blocks because I've got > twins and singletons in the sample. Does --pargs allow for all palm > functionality, including things like TFCE, eb's, and npc? Per another > thread, I looked through the fspalm code and my next approach is to > try mri_surfcluster or mri_volcluster with the .mgz palm results I've > already got. > > > Thanks, > Dan > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extracting stats from palm results (.mgz)
External Email - Use Caution Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to take advantage of NPC and exchangeability blocks because I've got twins and singletons in the sample. Does --pargs allow for all palm functionality, including things like TFCE, eb's, and npc? Per another thread, I looked through the fspalm code and my next approach is to try mri_surfcluster or mri_volcluster with the .mgz palm results I've already got. Thanks, Dan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extracting stats from palm results (.mgz)
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
>
> / 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
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extracting stats from palm results (.mgz)
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
/___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
