Re: [Freesurfer] extracting cortical parcellation
External Email - Use Caution Hi Bruce, I am going to extract the cortical parcellation file with its color table from freesurfer then import that in the other interface to detect and visualize the somatosensory (3b broadmann ) area. Therefore, I need the fifth column with some values for vertices. BR, Atena On Wed, Mar 6, 2019 at 5:47 PM Bruce Fischl wrote: > Hi Atena > > what were you hoping would be in the fifth column? What are you hoping to > create your own annotation files from? Can you give us a bigger picture of > what you are trying to achieve? > > cheers > Bruce > > > On Wed, 6 Mar 2019, Atena Rezaei > wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > Thanks for your comment! > > I used mri_annotation2label to existed lh.aparc.annot file in label > folder > > and got the labels. but the labels' text file contain 0 in fifth column. > > I need to create atlas from my own data including surface parcellation. > how > > can I do that? I found commands; > > mris_ca_train and mris_ca_label, > > how can I make the annotation files from my own data? > > > > BR, > > Atena > > > > On Wed, Mar 6, 2019 at 1:10 AM Bruce Fischl > > wrote: > > Hi Atena > > > > yes, mri_annotation2label should work, although it really > > depends on what > > you want to do next > > > > cheers > > Bruce > > On Wed, 6 Mar 2019, Atena Rezaei wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello, > > > > > > I am trying to extract the cortical parcellation(atlas) file > > from freesurfer with all the labels. I found > > > the lh.aparc.annot file in label folder. Should I use > > mri_annotation2label to create labels? or how can I > > > extract the whole file? > > > Thanks for ur help! > > > > > > BR, > > > Atena > > > > > > > > >___ > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] extracting cortical parcellation
External Email - Use Caution Hi Bruce, Thanks for your comment! I used mri_annotation2label to existed lh.aparc.annot file in label folder and got the labels. but the labels' text file contain 0 in fifth column. I need to create atlas from my own data including surface parcellation. how can I do that? I found commands; mris_ca_train and mris_ca_label, how can I make the annotation files from my own data? BR, Atena On Wed, Mar 6, 2019 at 1:10 AM Bruce Fischl wrote: > Hi Atena > > yes, mri_annotation2label should work, although it really depends on what > you want to do next > > cheers > Bruce > On Wed, 6 Mar 2019, Atena Rezaei wrote: > > > > > External Email - Use Caution > > > > Hello, > > > > I am trying to extract the cortical parcellation(atlas) file from > freesurfer with all the labels. I found > > the lh.aparc.annot file in label folder. Should I use > mri_annotation2label to create labels? or how can I > > extract the whole file? > > Thanks for ur help! > > > > BR, > > Atena > > > > > >___ > 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 cortical parcellation
External Email - Use Caution Hello, I am trying to extract the cortical parcellation(atlas) file from freesurfer with all the labels. I found the lh.aparc.annot file in label folder. Should I use mri_annotation2label to create labels? or how can I extract the whole file? Thanks for ur help! BR, Atena ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] extracting mesh file of layers in ascii format
External Email - Use Caution Hi, How can I extract the mesh file of gray matter, white matter, Cerebellum and Thalamus from freesurfer in Ascii format? Thanks in advance! BR, Atena ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
