[Freesurfer] Segmentation failure

Dear all, we observe some segmentation faults in the temporal lobe in single patients. Gyri are within the brain mask but outside the pail boundaries. Editing brain mask.mgz or wm.mgz does not resolves the problem. Examples are attached. How can we add missing brain? we are using free surfer

Re: [Freesurfer] thresh labels

Are there any other groups of labels which are, by default, produced in comparable less vs more restrictive ways? Regards,   Don   snip On 14-09-08 12:39 PM, Anastasia Yendiki wrote: Hi David - On the difference between .thresh and not .thresh labels: The BA labels come from averaging

Re: [Freesurfer] Help with pial boundary

Dear Bruce, I've uploaded 2 subjects, both with the same problems, it'll be great if you can take a look. https://dl.dropboxusercontent.com/u/6070302/GUSTO_01_04002.tar.gz https://dl.dropboxusercontent.com/u/6070302/GUSTO_01_04011.tar.gz Yes, I've gone through the tutorials. I've added back wm

Re: [Freesurfer] Syntax Error: trac-all -bedp

Hi Anastasia and FS-community Thanks for your quick and helpful answer. I hope your server doesn’t treat me like SPAM already. ;-) Anyways I have some several other questions. Is there a way to run bedpostX for different subjects in a row? Or do I have to run it for each subject separately.

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Hi Michele - The anatomical segmentation does look good, but from the screenshot the DWI data seems to be noisy in the orbitofrontal area, which may be affecting the uncinate. It's hard to tell just from one slice. If you upload all the tracula output directories of this subject (dmri,

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

uploaded (and activated). Thanks! On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michele - The anatomical segmentation does look good, but from the screenshot the DWI data seems to be noisy in the orbitofrontal area, which may be affecting the

Re: [Freesurfer] problems with tracula pre-processing (bvecs)

Thanks, Michele. Hard to tell what's causing this, perhaps a bit of distortion orbitofrontally. You may be able to fix this type of thing by reinitializing the tract reconstruction: Add set reinit = 1 to your configuration file, set the pathlist to include only the left and right uncinate,

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

Hi Doug, Running it as you suggested didn't work either. I tried it as follows: 1) /homes/8/hhe0/Documents/mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 1 1.3 mcz1_1.3 --sim-sign abs --cwpvalthresh .05 It says: 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

Not sure what is wrong. Is it executable? Were you able to save the file from your email or did you cut and paste it into a file and save the file? On 09/10/2014 04:03 PM, Eryilmaz, Huseyin Hamdi wrote: Hi Doug, Running it as you suggested didn't work either. I tried it as follows: 1)

Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh

Yes I could save the file from my email into '/homes/8/hhe0/Documents'. Under 'Permissions' tab of this file, 'Allow executing file as program' option is checked. I can try cd'ing into that folder then run the command as : mri_glmfit-sim --glmdir ANALYSISPATH --sim mc-z 1 1.3

[Freesurfer] mri_cvs_register

Hey everyone, i have tried to run the mri_cvs_register command but it returned an error in the second step. It returned: VolumeMorph load - failed to open input stream I have entered: mri_cvs_register --mov sub1 --template sub2 What could i do to fix it? Thanks for your help Ben

Re: [Freesurfer] mri_cvs_register

Hi Ben, What version of freesurfer are you using? Lilla On Wed, 10 Sep 2014, bigben2...@web.de wrote: Hey everyone,   i have tried to run the mri_cvs_register command but it returned an error in the second step. It returned:   VolumeMorph load - failed to open input stream   I have

Re: [Freesurfer] mri_cvs_register

Could you also send the log file along? Thanks, Lilla On Wed, 10 Sep 2014, bigben2...@web.de wrote: I'm using the version stable v5.3.0. Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Compiling Freesurfer from source ends with error regarding libtool version mismatch

Hi, I'm trying to compile Freesurfer current dev version from read only cvs repo according to developers guide on my machine with Ubuntu 14.04, gcc 4.8.2, I proceed as follows in dev/ directory: 1- ./setup_configure: which finishes without error 2- ./configure with vxl and mni library

[Freesurfer] HCP Pipelines v3.4.0 Released

*News from the Human Connectome Project (HCP)* *September 10, 2014* *HCP Processing Pipelines Released * ​The WU-Minn HCP Consortium is pleased to announce the open source release of HCP data processing pipelines at https://github.com/Washington-University/Pipelines. To download, click