[Freesurfer] tkmedit_error

Dear FreeSurfer experts, I have a problem running any command in the terminal (Ubuntu 12.04). For example when I run the following command tkmedit bert orig.mgz I get the following error ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has

Re: [Freesurfer] tracula: bvec-error

Hi Anastasia,I’m using this version of tracula.trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki ExpI’ve attached the log-file you requested. Robby De Pauw, dra.Ghent UniversityDepartment of Physiotherapy and Rehabilitation Sciences3B3De Pintelaan 185B-9000 Ghentrobby.dep...@ugent.be trac-all.log

[Freesurfer] trac-all bvec (nifti many subjects)

Dear Freesurfers, I am trying to run trac-all with many subjects through a configuration file. The first subject gets processed without error, but after that I keep getting errors, that the dwi_orig_flip.mghdti.bvecs file cannot be found. This is my command with the output (below configuration

Re: [Freesurfer] matrix is ill-conditioned or badly scaled

Hi Doug Thanks a lot for your answer Cheers Jürgen --- - Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97

[Freesurfer] Fwd: Re: success and failure of wm surfaces in (almost) identical structural image

Thanks to Eugenio, for the tip! We did look at (orig,nu,T1,brainmask,norm,nu,noneck, aseg, wm, filled).mgz. The only one showing a difference where our white matter error occurs is filled.mgz. In some of the other previous images are minor differences around that area, but not overlapping the

Re: [Freesurfer] asymmetry analyses

thank you! Angela You can use --paired-diff-norm instead of --paired-diff, this will compute (L-R)/((L+R)/2) You can then divide the output by 2, eg, fscalc output.mgh div 2 -o output.div2.mgh doug On 8/24/14 9:52 AM, angela.fav...@unipd.it wrote: Hi all, I have a question about

Re: [Freesurfer] problemi with mri_glmfit-sim

thank you! that solved my problem! I think this has something to do with the unix LOCALE because it is interpreting the 2.0 as 2,0 using the comma , instead of the . I actually don't know how to fix this. If you run echo $LANG does it return en_US.UTF-8 if not, as a test, try setenv

[Freesurfer] ERROR: cannot find AFNI command 3dvolreg.afni

Dear FreeSurferAs I am trying to preprocess my fMRI data through FsFast, I came across this error:ERROR: cannot find AFNI command 3dvolreg.afniI’m using a mac and bash-shell. I’ve also attached the log-file.This is the command I used:preproc-sess -s GEZ_004_HACO/ -surface fsaverage -mni305 -fwhm 5

Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image

Dear Sebastian, Attached is the *.orig for both recon (green being the one with wm error and red being the one with error). Unfortunately they are not identical; a section of the dura is misclassified as wm in the red delineation. As mentionned before, both orig.mgz are numerically identical

Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image

Hi Vincent, On Aug 26, 2014, at 16:45 , Vincent Beliveau vincent.beliv...@nru.dk wrote: Dear Sebastian, Attached is the *.orig for both recon (green being the one with wm error and red being the one with error). I see, what about the *.orig.nofix? I just noticed that the *.orig

Re: [Freesurfer] labelled tissue segmentation mask back to native

thank you Bruce and Douglas for your reply! Alejandra 2014-08-20 13:07 GMT+02:00 Alejandra Machado amachf...@gmail.com: Hello, I was wondering if FS has an output mask (labelled volume) for each tissue types (gm+wm+venctricular_csf) that I can then turn into each subject's native space.

Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image

how about the ?h.orig.nofix On 08/26/2014 10:45 AM, Vincent Beliveau wrote: Dear Sebastian, Attached is the *.orig for both recon (green being the one with wm error and red being the one with error). Unfortunately they are not identical; a section of the dura is misclassified as wm in

[Freesurfer] freesurfer version vs cvs version

Hello, I have 80 subjects' MRIs that were segmented in 2009 with a version of freesurfer that included this (cvs_version $Id: mri_segstats.c,v 1.11.2.5 2006/04/13 18:57:07 nicks Exp $) in the aseg.stats output. The other 19 of my subjects segmented in 2013 display this (cvs_version $Id:

Re: [Freesurfer] ERROR: cannot find AFNI command 3dvolreg.afni

Hello Robby, You can download the 3dvolreg.afni file using the following link: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/5.3.0-patch/lion/ Please download it and copy it to your /Applications/freesurfer/bin directory. -Zeke On 08/26/2014 10:42 AM, Robby De Pauw wrote: Dear

[Freesurfer] Color scale in tksurfer

Dear all, I've got a question: is the color that I get for significant clusters in tksurfer depending on the contrast vector specified? For example: when I get a red cluster and my question of interest would be: is there a difference between Males and Females regressing out the effect of age and

[Freesurfer] watershed surface to volume rendering

Freesurfer, We have scans that have recon-all completed. Following recon-all, we completed watershed (under the MNE toolbox) to extract skull and scalp from the T1 scans. The outputs of this algorithm are outer brain, inner skull, outer skull and outer scalp surfaces. We are

Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image

And is that area outside of the brain not present in the wm.mgz or filled.mgz on the good output? The orig.nofix should hug the boundary of the wm.mgz doug On 08/26/2014 04:53 PM, Vincent Beliveau wrote: I've attached ?h.orig.nofix for both recon with and without wm error. They are

Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image

That area outside the brain is not present in both wm.mgz and filled.mgz for the failed output but for the good output, it is present in wm.mgz but not in filled.mgz (see attached figures). Again, given the similarity of the inputs it is surprising that the wm.mgz and filled.mgz end up being

[Freesurfer] White Matter and Pial Edit Question

Dear Freesurfer Experts, I'm working on a younger population (around age 8), and I seem to have an issue with the pial and wm surfaces grabbing dura on the images. I've run gcut, -wsthresh at about 15, and even used the talairach_with_skull_2.lta registration file to no avail, and I'd rather not

Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image

In the bad output of the fill, is it hanging onto the mask by a small thread, one that does not exist in the good wm/fill? When the wm is analyzed to get the fill, it removes islands. I think that extracerebral stuff is an island in the good (and so removed) and still connected in the bad. It

Re: [Freesurfer] Individual commands in preproc-sess

Hi Reza, if you look in preproc-sess you will see each of the commands that gets run. You can adapt the command lines from that doug On 08/24/2014 07:52 PM, Reza Rajimehr wrote: Hi, I want to use FreeSurfer v5.3 and its FS-FAST for the functional analysis of monkey data. To have a better

Re: [Freesurfer] freesurfer version vs cvs version

Joel, The 'recon-all.log' file in the 'scripts' directory of the subject should have the version of freesurfer used. Also, the file 'build-stamp.txt' in that same directory will show the version used. N, On Tue, 2014-08-26 at 18:31 +, Joel R Pieper wrote: Hello, I have 80 subjects'

[Freesurfer] Cortical gray matter surface area

Hi all, I am a little unclear as to how to find the cortical grey matter volume in the stats output files. The ?.aparc.stats file shows: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 What about grey? Thanks, Will ___ Freesurfer

[Freesurfer] Change in the location/path and the name of subject

Hi, I have got anatomicals of a subject from someone else. The anatomicals have been processed, and the surfaces have been reconstructed. The path to these files in my machine is obviously different from the path where data have been analyzed. I also want to change the name of the subject and

Re: [Freesurfer] Change in the location/path and the name of subject

no, that should not affect anything. Once you do the fMRI analysis, changing the subject name then means having to re-register (or change the name in the registration files). doug On 8/27/14 12:05 AM, Reza Rajimehr wrote: Hi, I have got anatomicals of a subject from someone else. The

Re: [Freesurfer] Cortical gray matter surface area

The volume for each structure is given as the 4th column. If you want total GM volume, look in aseg.stats doug On 8/26/14 8:43 PM, will brown wrote: Hi all, I am a little unclear as to how to find the cortical grey matter volume in the stats output files. The ?.aparc.stats file shows: