Re: [Freesurfer] extracting cortical parcellation
Hi Atena the vertex indices are stored in the first column. You should be able to use them to look up into any overlay you want cheers Bruce On Wed, 6 Mar 2019, Atena Rezaei wrote: 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, 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
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
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
Re: [Freesurfer] extracting cortical parcellation
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
