External Email - Use Caution I found the .gcs files in a git repo: https://github.com/faskowit/multiAtlasTT
El mar., 14 jul. 2020 a las 11:58, Glasser, Matthew (<glass...@wustl.edu>) escribió: > External Email - Use Caution > > So how exactly did you make a .gcs without the individual subject > parcellations or the multi-modal features used for classifying cortical > areas? Note that we are working on a tool for folks to do this. > > > > Matt. > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Álvaro > Deleglise <alvarodelegl...@gmail.com> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Tuesday, July 14, 2020 at 9:49 AM > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for > stats > > > > * External Email - Use Caution * > > Hi Alina and Matthew, > > I think there is a simple solution to the problem. You can use the .gcs > files of the parcellation you are interested in! You have to run the > mris_ca_label command to apply the parcellation in individual subject space > and get de .annot files of each hemisphere. Then, you can use > mris_anatomical_stats to get the .stats files from these annot files. > Finally, you can use aparcstats2table to get the metrics of your > parcellation. > > > > Here's and example: > > mris_ca_label -l $SUBJECTS_DIR/<subject_name>/label/?h.cortex.label \ > <subject_name> lh $SUBJECTS_DIR/<subject_name>/surf/?h.sphere.reg \ > <gcs_file_dir>/?h.parcellation_X.gcs \ > $SUBJECTS_DIR/<subject_name>/label/?h.parcellation_X.annot > > > > mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f > stats/?h.parcellation_X.stats -b -a label/?h.parcellation_X.annot -c > label/aparc.parcellation_X.ctab <subjid> ?h > > > > If you want to, I can provide you the .gcs files of the HCP-MMP1-Atlas. > > > > > > El mar., 14 jul. 2020 a las 11:19, Glasser, Matthew (<glass...@wustl.edu>) > escribió: > > External Email - Use Caution > > I would find using something like ciftify ( > https://github.com/edickie/ciftify) potentially more straightforward (and > then you can just use wb_command -cifti-parcellate on > ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii). > It is possible to go the other direction too (e.g. using this link: > https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI > and then perhaps someone on the list can explain how to go from GIFTI on > fsaverage to .annot on the native meshes and extract the stats. > > Matt. > > On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Alina Rojas" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > alinacol...@gmail.com> wrote: > > * External Email - Caution * > > External Email - Use Caution > > Hello Freesurfer support list, > > I’m attempting to map the HCP-MMP1-Atlas to the individual brains of > my subjects to get the values of the parcellation, like aparc.stats but > aparc being HCP-MMP1. The aim ist to compare the cortical thickness of the > Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the > archive and didn’t find the solution. It would be so great if you could > help me! > > Thank you and regards, > > Alina Rojas > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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