[Freesurfer] Thalamic sub-nuclei

Dear all, I am interested in analyzing thalamic sub-nuclei separately, instead of the whole thalamus. I've noticed that in the FreeSurferColorLUT.txt file there are some labels that correspond to thalamic sub-nuclei (Labels #No. 8001-8014). However, I do not find those labels in my

Re: [Freesurfer] Thalamic sub-nuclei

Hi Cristina sorry, while thalamic nuclei are of interest to us we haven't developed anything for labeling them yet. cheers Bruce On Mon, 31 Aug 2015, Lois Gomez, Cristina wrote: Dear all,   I am interested in analyzing thalamic sub-nuclei separately, instead of the whole thalamus. I've

[Freesurfer] converting ROI .label to MNI space for SPM8

Forgive me, but I'm re-posting my query below hoping someone will respond this time around. Thanks in advance! Dear Freesurfers, I'm hoping you can help me resolve an issue I'm having with regard to converting my ROI labels from freesurfer space (Taliarach) to MNI space in prep for using these

Re: [Freesurfer] mri_volsynth

some of this is answered if you run the command with --help On 8/31/15 3:33 PM, John Anderson wrote: Hi Freesurfers, I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10) I used the following command line to create the volume but I don't know how to

Re: [Freesurfer] converting ROI .label to MNI space for SPM8

I'm not sure what is going wrong, but I would use mri_label2vol directly instead of using the combination of mri_convert and tkregister. Instead of passing it a registration file, use --regheader brainmask.mgz On 8/31/15 5:26 PM, Emma Thompson wrote: Forgive me, but I'm re-posting my query

Re: [Freesurfer] Error running recon-all -localGI

Marie, Yes, I'm getting this error for all subjects. Unfortunately, I'm unable to send you any of our subjects to look at. You've helped in identifying that our ROIs are not getting saved, though. Do you have a guess as to why that might be? Otherwise, we'll have to figure out why they're

Re: [Freesurfer] mri_volsynth

Thank you for the quick response. I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13 is this command line correct: mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii   Bests,

[Freesurfer] Did not find any volume geometry information in the surface

Hi, I am running mri_glmfit followed by mri_glmfit-sim running the left hemisphere everything works perfect all the way to the visualization in freeview - then I just chift the command to rh instead - running exactly the same command and when I am opening my results in freeview everything gets

Re: [Freesurfer] Did not find any volume geometry information in the surface

Eric, It will be easier to help, if you provide a much more detailed description of what you did: the full command line, the version of freesurfer, and all terminal output (http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting this may help). hth D On Mon, Aug 31, 2015 at 3:27 PM, Erik Lindberg

Re: [Freesurfer] mri_volsynth

No, you will need to decide how big you want your voxels to be. If you use --volres 1 1 1 1 then that should work. It will put the center of the volume at that coordiate. If you want a single voxel, then use --dim 1 1 1 1 and --volres 6.25 6.25 7.5 1 On 8/31/15 7:52 PM, John Anderson wrote:

Re: [Freesurfer] mri_volsynth

Thank you! Actually when I run mri_volsynth --help I can't find --revol. is it the same flag --res? also what is the relationship between --dim and --volres?   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box

Re: [Freesurfer] mri_volsynth

sorry, --res (not --volres). res is the voxel size (volume resolution). dim is the number of voxels in each dimension On 8/31/15 10:16 PM, John Anderson wrote: Thank you! Actually when I run mri_volsynth --help I can't find --revol. is it the same flag --res? also what is the relationship

Re: [Freesurfer] mri_volsynth

Perfect! Thank you very much for your help. Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: Monday, August 31, 2015 at 4:30 PM

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

after several attempts with multiple subjects command -autorecon2-noaseg -subjid mysubject followed by command recon-all -aparc2aseg aseg.mgz edits, are Not reflected onto the aparc+aseg.mgz On Aug 25, 2015, at 2:05 PM, Douglas N Greve wrote: > yes > > On 08/25/2015 01:11 PM, fmri wrote:

[Freesurfer] mri_compute_volume_fractions not filling some sulci properly

Hello Freesurfers, I have been using mri_compute_volume_fractions for a while and I just noticed something weird. Some clearly csf pixels (sometime very large groups) are not filled in the *.csf.mgz image mri_compute_volume_fractions produces The first following figure shows a posterior

Re: [Freesurfer] MRITOTAL

Thanks Bruce, Could you please suggest something for me t sort out this issue for future projects. All PCs will have UBUNTU 14.04 and not of them was able to run the 8 subjects. If I install an older version of UBUNTU then Ii dont get and update and so can not install tcsh and csh. Today I am

[Freesurfer] license file not found

Hi All, This is my first time using the software. I have installed FreeSurfer on a Mac machine and everything installed fine. I obtained a license using the form and saved the four lines to a license.txt file in my FREESURFER_HOME directory (/Applications/freesurfer on my computer). Yet

Re: [Freesurfer] niiRead error

Hi Katarina it looks like that file might be corrupted. Where did you get it from? Can you view it in freeview? Maybe that partition was full when you copied it there or something similar? cheers Bruce On Mon, 31 Aug 2015, Katarina Trojacanec wrote: Dear experts, After running

Re: [Freesurfer] MRITOTAL

Hi Ali it's not that I know that the quality is fine. It might be (or not), but this seems to be a perl error that doesn't have to do with quality Bruce On Mon, 31 Aug 2015, Ali Radaideh wrote: Dear Bruce and ​Jürgen, Now I see something important which may help solving the problem. I

[Freesurfer] niiRead error

Dear experts, After running recon-all I got this output: --- Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp:

Re: [Freesurfer] license file not found

Yep, that did the trick. I found an archived post where someone had a similar issue. Thanks. Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter

Re: [Freesurfer] license file not found

Hi Michael does /Applications/freesurfer/.license exist? Do you have permission to read it? Don't name the file license.txt - rename it to .license cheers Bruce On Mon, 31 Aug 2015, Amlung, Michael wrote: Hi All, This is my first time using the software. I have installed FreeSurfer on a

Re: [Freesurfer] MRITOTAL

Dear Bruce and ​Jürgen, Now I see something important which may help solving the problem. I have 31 PCs in my lab and all of them are installed with UBUNTU 14.04. 30 PCs were able to process all 47 subjects successfully. But failed to process the remaining 8 subjects. Fortunately, one PC is

[Freesurfer] mri_volsynth

Hi Freesurfers, I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10) I used the following command line to create the volume but I don't know how to choose it is position in scanner space.   mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii     I