[Freesurfer] question abt mri_vol2surf....

Hello All, I have a simple question. I have functional data (3 mm cubic voxels) from 20 subjects that I am using mri_vol2surf to resample on the fsaverage surface. I want to run qdec or mri_glmfit on these data. In order to do grp stats with functional data, what surface do I need to specify in

[Freesurfer] recon-all -s $subject -make all

Hello FreeSurfers, recon-all -make is working now, but it's taking as long as it did the first time I ran it. I originally ran "recon-all -s cb -i CB_anat+org.BRIK -i CB_anat2+orig.BRIK -all" (for example) back in May and haven't messed with the results except for generating some label files with

Re: [Freesurfer] Longitudinal processing clarification

You can edit just the base if you will only be working with the longitudinal stream. Currently, running the cross-sectional stream is necessary only to get the 'norm.mgz' file, for input to the base subject. n. On Sun, 2010-02-14 at 14:06 -0800, Mehul Sampat wrote: > Hi Nick (and Martin) > > C

Re: [Freesurfer] Wmparc Destrieux atlas

To get the Destrieux atlas parcellations in the wmparc, first have a look at the -wmparc section of the recon-all table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable those last two commands would be modified like this: mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown --ribbo

Re: [Freesurfer] question abt mri_vol2surf....

the default surf is the 'white' surf, but this only means the coordinates in the output surface file will have the white surface coordinates. the vertices still remain one-to-one matched between the white-pial-and-inflated-(and-sphere), so the -surf arg is irrelevant for your group analysis. n.

Re: [Freesurfer] recon-all -s $subject -make all

recon-all -make all uses the unix 'make' utility, and the file $FREESURFER_HOME/bin/recon-all.makefile, to examine the 'build' dependencies between files. that is, looking at this table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable it can be seen that files are dependent on files

Re: [Freesurfer] question abt mri_vol2surf....

ok thats what i thought but just wanted to double check... Thx - Original Message - From: "Nick Schmansky" To: "Ritobrato Datta" Cc: "freesurfer" Sent: Tuesday, February 16, 2010 12:58:07 PM GMT -05:00 US/Canada Eastern Subject: Re: [Freesurfer] question abt mri_vol2surf the defau

[Freesurfer] mris_anatomical_stats error

Dear experts, i try to run the command mris_anatomical_stats to get GrayVol, ThickAvg, etc from the left cortex as following: mris_anatomical_stats -l lh.cortex.label -f nmr033_2/stats/lh.cortex.stats nmr033_2 lh so the output is like following and did not generate any stats file(lh.cortex.stats

Re: [Freesurfer] mris_anatomical_stats error

hmmm, sounds like a bug. If you tar and gzip the subject and drop it on our site we'll take a look. On Tue, 16 Feb 2010 yzha...@artsci.wustl.edu wrote: > Dear experts, > > i try to run the command mris_anatomical_stats to get GrayVol, ThickAvg, > etc from the left cortex as following: > > mris_a

[Freesurfer] Gyrification index for individual regions

I managed to obtain outputs from recon-all lGI ­ now I would like to obtain a mean gyrification index (not sure if the mean is meaningful?!) for all vertices within 3 ROIs as defined by Destrieux atlas - How should I do this? Can I treat lGI surfaces just as thockness maps ­ in which case can I us

[Freesurfer] tractography and freesurfer

I have a colleague who is interested in the DTI toolkit to coregister DTI results with FreeSurfer's segmentation. Is that available in any form yet? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Pre

Re: [Freesurfer] tractography and freesurfer

Hi Dana, sure, that stuff is available. You should be able to use bbregister to register the dti to the anatomicals cheers Bruce On Tue, 16 Feb 2010, Dana W. Moore wrote: > I have a colleague who is interested in the DTI toolkit to coregister > DTI results with FreeSurfer's segmentation. Is th

Re: [Freesurfer] ROI based on Talairach coordinate

Hello, Thanks Bruce, Super, it works well! I tried to make my rois in a script (to do it in many subjects), by using the commands: select_talairach_point x1 y1 z1 select_orig_vertex_coordinates mark_vertex path_new_path_from_marked_vertices but I did not manage to get the vertex number (index

Re: [Freesurfer] ROI based on Talairach coordinate

Hi Leila, it will set the global variable named "select" after the call to select_talairach_point x1 y1 z1. You can then use it (with $select) afterwards. cheers, Bruce On Wed, 17 Feb 2010, Ben Hamida Cammoun Leila Faiza wrote: Hello, Thanks Bruce, Super, it works well! I tried to make