Re: [Freesurfer] Fwd: Fwd: monte-carlo error in longitudinal pipeline

something is wrong with the mask (the terminal output says that there are no voxels in the mask) On 1/30/18 11:51 AM, miracle ozzoude wrote: -- Forwarded message -- From: *miracle ozzoude* > Date: Fri, Jan 26, 2018 at 7:08

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

that usually means that something has gone wrong with the analysis. Do the maps look ok? In particular, look at the mask On 1/20/18 1:56 PM, miracle ozzoude wrote: Hello Doug, I tried using the MC tables that FS distributed. However, i got an error about " cannot find

Re: [Freesurfer] Issue with mri_convert on centOS 7

Hi Danielle can you post the full command line and screen output? cheers Bruce On Tue, 30 Jan 2018, Cooke,Danielle ( BIDMC - Neurology ) wrote: Hello,   I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The error

[Freesurfer] Issue with mri_convert on centOS 7

Hello, I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The error that results is: Segmentation fault (core dumped) I've tried on multiple machines with both operating systems to confirm the issue. I was wondering if

[Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

Hi, I’m trying to use the Yeo2011 annotations to create individual volume masks in subject space. I first use mri_surf2surf to map the annotations from fsaverage to individual subjects: mri_surf2surf --srcsubject fsaverage --trgsubject subject --hemi rh --sval-annot

Re: [Freesurfer] Strange Segmentation

Dear Arkadiy, I see sometimes these kind of errors. I think they are caused by local mis-segmentation due to WM hypointensities (enlarged perivascular spaces or other lesions, usually benign) located just under GM. Sometimes it is hard to discern where it is a hypointensity and where it is

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Does the file /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If so, can you run it with -debug as the first option and send the terminal output? On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote: Hello FreeSurfer experts, I am getting this strange error when running

[Freesurfer] A question about FS6 hippocampal subfield segmentation output file

Dear FreeSurfer experts, in the txt files [lr]h.hippoSfVolumes-T1.v10.txt we can see the volumes of individual hippocampal subfields - I was wondering what are the units in which volume is given? Millimeters cubic, voxels, or something else? Thanks in advance! Best, Darko

Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)

See tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula#Settingupaconfigurationfile From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Renew Andrade Sent: Tuesday,

Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)

What is the configuration file or where can I find it? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is

[Freesurfer] Fwd: Fwd: monte-carlo error in longitudinal pipeline

-- Forwarded message -- From: miracle ozzoude Date: Fri, Jan 26, 2018 at 7:08 PM Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline To: Freesurfer support list Hello Doug, Thanks for the patience.

[Freesurfer] Programmer/Research Tech position available at Washington University in St. Louis

RESEARCH TECHNICIAN POSITION IN NEUROIMAGING POSITION SUMMARY: Applications are invited for a research technician at Washington University in St. Louis. This well-established laboratory studies the structural and functional organization of the human brain using multi-modal imaging: including

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Kyung the thickness values are stored as "curvature" file format that you can load into matlab with read_curv.m. Alternatively, you can convert them to ascii with mris_convert and do what you want with them. For each index, you can look up its location on the white or pial (or whatever

[Freesurfer] Calculating cortex scalp distance of a region of interest

Dear Freesurfer experts, I would like to calculate the mean distance from cortex to the scalp in a region of interest (the area under the stimulator), to investigate the influence of this distance on tDCS effects. A similar question was asked in the archives, and the use of

[Freesurfer] fast_selxavg3.m error/analysis.info file

Hello FreeSurfer experts, I am getting this strange error when running selxavg3-sess. (in selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) When the system enters fast_selxavg3, it cannot read analysis.info, thus produces the following output: #@# Sess05