[Freesurfer] DEFECT 57

Hi all, One of my subject exited with error after 5 days of processing. This is what it said, CORRECTING DEFECT 57 (vertices=101022, convex hull=10822) Excessive topologic defect encountered: could not allocate 536232126 edges for retessellation Cannot allocate memory Darwin chikkus-MacBook-Pro.l

[Freesurfer] Pial boundaries

Hello, I would like to ask if there are any commands or any manual edits I can use to fix the pial boundaries even if the white matter boundaries are fine. The white matter boundaries follow the white matter pretty good but there is some grey matter missing at some areas. Its not a massive problem

[Freesurfer] Generate mask from surface in diffusion space

Dear freesurfers I'm using bbregister and mri_surf2surf to transform intermediate cortical surfaces and mid surfaces normals to diffusion space. Next I'm trying to generate volumes from these surfaces (in the same diffusion space), however the generated volumes are much thicker then the generated

[Freesurfer] nb0 question

Hi list, I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 is the first volume: I put nb0=1. For some subjects I have 16 direction but b=0 is the last of volume in dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to position of b=0 in the bval

Re: [Freesurfer] Registration & segmentation with FSL - obtaining correlation matrix..

On Feb 20, 2013, at 3:02 PM, Sudhin A. Shah wrote: Hello I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat & aseg2feat) When I extract the values (as per the matlab code below), I see NaNs in certain regions. Of the 19 datasets that I have analyzed I have see NaN

Re: [Freesurfer] Pial boundaries

Can you send us an image? On Feb 21, 2013, at 7:24 AM, melinaki p-t wrote: > Hello, > > I would like to ask if there are any commands or any manual edits I can use > to fix the pial boundaries even if the white matter boundaries are fine. > The white matter boundaries follow the white matter

Re: [Freesurfer] DEFECT 57

Hi Chikku That is a giant defect - almost the size of an entire hemi. Something is badly wrong. Check the aseg and filled volumes to see what's going on, and the ?h.orig.nofix Bruce On Feb 21, 2013, at 5:35 AM, Varghese Chikku wrote: > Hi all, > One of my subject exited with error after 5

Re: [Freesurfer] Pial boundaries

I am afraid I can't... Can you give any advise without pictures? Thank you in advance. Melina 2013/2/21 Bruce Fischl > Can you send us an image? > > > > On Feb 21, 2013, at 7:24 AM, melinaki p-t wrote: > > > Hello, > > > > I would like to ask if there are any commands or any manual edits I can

[Freesurfer] longitudinal sulci depth change

Hello, I was wondering if I could get some clarification regarding the longitudinal measure of rate of change in sulci depth. In our study we have a patient population that participated in an intervention and a similar group of wait list controls. We have scans for pre and post intervention time

Re: [Freesurfer] nb0 question

Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter where in the table it is. From the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Step7.3: Specifying Number Of low-b Images The last step to set up if not using original DICOMs would be to specify the

Re: [Freesurfer] nb0 question

Hi Juan, The number of b0 images can be more than 1; it is specified when you acquire the image. Hth, Shantanu On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote: > Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter > where in the table it is. From the tutorial: >

Re: [Freesurfer] nb0 question

Of course! But, if I understood correctly, Stefano only has one, either at the beginning of the end of the gradient table, and in both cases nb0=1 Cheers, /Eugenio On Thu, February 21, 2013 12:20 pm, Shantanu Ghosh wrote: > Hi Juan, > The number of b0 images can be more than 1; it is specified wh

[Freesurfer] dual installation question

If I want to install the new Freesurfer version but retain the older Freesurfer install as well, what issues might I face? Is it simply sourcing the usual setup scripts? export FREESURFER_HOME=/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh - Josh __

Re: [Freesurfer] dual installation question

Hi Josh, you can modify the SetUpFreeSurfer.sh to source the correct version. Hth, Shantanu On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote: > If I want to install the new Freesurfer version but retain the older > Freesurfer install as well, what issues might I face? > Is it simply sourcing t

Re: [Freesurfer] dual installation question

Or you may have multiple freesurfer versions within the freesurfer director, something like /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc. and then export FREESURFER_HOME=/freesurfer/5.1 etc Hth, S. On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote: > Hi Josh, > y

[Freesurfer] Tkregister2 / Tksurfer / Tkmedit Won't Open

Hello freesurfers, I just ran registration of my functional images and am trying to visualize the registration for assessment. However, when I use the commands "tkregister-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold -funcstem f" or "tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID --surf

Re: [Freesurfer] Help with the error info: mghRead subject/surf/lh.inflated.H, could not open file

No one ever encountered this kind of full path problem? recon-all works fine, but recon-all -qcache stopped because of this kind of problem. Any hint would be appreciated. Xiaowei On Wed, Feb 20, 2013 at 5:07 PM, Xiaowei Song wrote: > Dear Bruce and freesurfer experts, > > I am trying to use m

[Freesurfer] mri_vol2vol call problem

Greetings lords of freesurfer! I am having a problem getting a combined cvs warp+bbregister to map an FA volume onto a template. mri_vol2vol --targ 816 --m3z combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff

[Freesurfer] tkregister2 window error: Remote login

Hello, I am remotely logged in to my Ubuntu system(from Mac). I have previously run tkregister2 but am now having trouble; Opening window subj Window type not found register: tkoinitwindow(name) failed. Is there a solution to this? Thanks, S ___ Fre

Re: [Freesurfer] Help with the error info: mghRead subject/surf/lh.inflated.H, could not open file

The weird problem is solved after I traced a day. The real problem is that my full path contains dot. After I removed the dot, everything works fine. Then I guess this maybe some kind of mri_read bug in mriio.c or FreeSurfer file name convention I don't know. Xiaowei On Thu, Feb 21, 2013 at 2:

Re: [Freesurfer] Tkregister2 / Tksurfer / Tkmedit Won't Open

Daniel, What operating system are you on? If your using MacOS, you must have XQuartz installed in order to use the the Tkregister2/Tksurfer/Tkmedit tools. Check the Application->Utilities folder to see if its already installed. If not, you can download it from here: http://xquartz.macosforge.org/

[Freesurfer] mri_vol2vol call

Hi I found my old notes ( re my message earlier) I think this is now correct for mapping subject 822 FA onto my template 816, I know the cvs technology is recent, so just asking to make sure there is now a newer/prefered way. mri_vol2vol --targ /study5/aa-scratch/TEENEMO/twins_freesurfer/816/

Re: [Freesurfer] dual installation question

Thanks. Best, - Josh On Thu, Feb 21, 2013 at 10:05 AM, Shantanu Ghosh < shant...@nmr.mgh.harvard.edu> wrote: > Or you may have multiple freesurfer versions within the freesurfer > director, something like > /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc. > and then > exp