Re: [Freesurfer] Annotation file's LUT

yes, that is all of them On Thu, 25 Feb 2016, Faeze Vedaei wrote: > Hi Freesurfer experts, > I want to have all the label files extracted from the annotation file base > on Destrieux atlas. I used the command mri_annotaion2label to do this. The > result is just 75 labels. Are these all the regions

Re: [Freesurfer] Fwd: View several Annot files in Tksurfer

Hi Faezeh the annotations label every vertex. How would you view more than one at the same time? cheers Bruce On Wed, 24 Feb 2016, Faeze Vedaei wrote: Hi Freesurfer Experts, In order to view specific annot files by tksurfer in Freesurfer, I used mris_label2annot command to create annot files

[Freesurfer] Annotation file's LUT

Hi Freesurfer experts, I want to have all the label files extracted from the annotation file base on Destrieux atlas. I used the command mri_annotaion2label to do this. The result is just 75 labels. Are these all the regions included in annotation file? Can you let me know how I can access to all

Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

Hi Bruce, I'll have a look at mri_ca_train. Thanks again! Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: donderdag 25 februari 2016 20:58 Aa

[Freesurfer] Map label from lh to rh

Hi, I want to map a label from one hemi to the other (all on fsaverage). I tried mri_label2label: mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel lh.a.label --trglabel rh.flipped_lh.a.label --regmethod surface but I think I need to specify a reg file to go between hemispheres

Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

Hi Jelmer no, that won't work as the gca contains more information than that. YOu will need to use mri_ca_train to create a new gca, which should be relatively straightforward cheers Bruce On Thu, 25 Feb 2016, Kok, JG (neuro) wrote: > Hi Bruce, > > Thanks for your quick reply. I do not have

Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

Hi Bruce, Thanks for your quick reply. I do not have manually split asegs, I wish to create them all automatically. I'm hoping it is possible to read RB_all_2008-03-26.gca (preferably in MATLAB, using fread), and adjust all putamen values posterior from the coronal plane through the anterior co

Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

Hi Jelmer if you have manually split asegs you can use them as input to mri_ca_train to create a new gca that has the separated putamen. You'll need to add a couple of entries to FreeSurferColorLUT.txt to specify how to display and name the new entries as well cheers Bruce On Thu, 25 Feb 2016

Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points

Hi Ed if you run the skull stripping the autorecon2 and autorecon3 it should detect and preserve your manual interventions cheers Bruce On Thu, 25 Feb 2016, Gronenschild Ed (NP) wrote: > Hi, > > I have made some manual skullstrip adjustments and added a > number of control points in the white

Re: [Freesurfer] Permission denied error with mri_surfcluster command

Hi Douglas, Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the C

Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points

Hi Ed, I'm not sure if this'll help you, but I read your question right after I posted mine, and thought to let you know the solution I used in cases where I had to add control points: " Or Make Life Easier recon-all -make all -s subjid " is copied from one of the Freesurfer Powerpoint slides

[Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

Hi, I wish to split the putamen in an anterior part and a posterior part in >60 subjects which have been analyzed by the recon-all stream (FS version 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the coronal plane through the anterior commissure) and apply this "new" atlas t

[Freesurfer] How to invoke skullstrip adjustments and wm control points

Hi, I have made some manual skullstrip adjustments and added a number of control points in the white matter. How should I proceed with recon-all to incorporate both adjustments? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http

[Freesurfer] Problem with brainstem substructures segmentation

Dear Freesurfer users, We have downloaded the Freesurfer 6.0 version since we are really interested in the brainstem segmentation. We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM. We installed freesurfer6.0 on a virtual machine Linux (CentOs 6.7) enabling 4vcpu 11Gb of RAM. Dis