Re: [Freesurfer] Matlab R2014b exits while executing segmentThalamicNuclei.sh in FS v7.1.1 under OS Big Sur

External Email - Use Caution Andrew, many thanks for reply. The issue has been fixed by downgrading the OSX. Best Joe > On May 25, 2021, at 4:57 PM, Hoopes, Andrew wrote: > > > Hi Joe, > > Is this the full command output from start to finish? There is usually some > helpful

[Freesurfer] preproc-sess fmri image to self surface

External Email - Use Caution Dear freesurfer expert: My name is Mingyang. I want to preprocess fmri image and map the timepoints to its corresponding T1 surface. However, when I use preproc-sess command, it seems that the output image has the wrong dimensions. Could you give me

Re: [Freesurfer] Multiple Versions Installed

External Email - Use Caution Awesome, thanks for providing more details! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department

Re: [Freesurfer] Multiple Versions Installed

External Email - Use Caution If on the Mac you use the *.pkg file  (or on linux the *.rpm) installers, then different versions of freesurfer will be installed automatically under a directory with the appropriate version number, e.g., on the Mac /Applications/freesurfer/{7.0.0, 7

Re: [Freesurfer] Multiple Versions Installed

External Email - Use Caution Thanks for the quick reply Andrew! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physi

Re: [Freesurfer] Multiple Versions Installed

Hi Nárlon, There’s no harm in installing multiple versions of freesurfer on one filesystem. The FS distribution is confined to the directory it’s installed to, so we suggest organizing a FREESURFER_HOME directory structure like: /Applications/freesurfer/5.3 /Applications/freesurfer/6.0 /Applica

Re: [Freesurfer] Recon-all running on a loop

Hi Diana, Can you send the recon-all.cmd file? Have you tried running without parallel processing enabled? Best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of DIANA ORTEGA CRUZ <100315...@alumnos.uc3m.es> Date: Friday, May 21, 2021 at 11:00 AM To: freesurfer@nmr.mgh.harvar

Re: [Freesurfer] Matlab R2014b exits while executing segmentThalamicNuclei.sh in FS v7.1.1 under OS Big Sur

Hi Joe, Is this the full command output from start to finish? There is usually some helpful information preceding the “Segmentation violation detected” error. Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Xin Qiao Date: Thursday, May 20, 2021 at 12:44 AM To: freesurf

Re: [Freesurfer] Recon-all error

External Email - Use Caution Hello, please ignore my message below: the problem was in the name of the folder "Group 0". Please do excuse me for bothering you, best, GT > Il 24/05/2021 17:57 g.ton...@libero.it ha scritto: > > > Hello FreeSurfer Developers, > >

[Freesurfer] Multiple Versions Installed

External Email - Use Caution Dear FreeSurfer experts, I was wondering if there are any problems in having installed two different versions of FreeSurfer on the same MacOS computer? We have 5.3 installed and wanted to install 7.1.1, but keep the older version in case older data

[Freesurfer] CSF file

External Email - Use Caution Hi Freesurfer experts: I used recon-all all to in my MPRAGE image and I would like to know which file is the corresponding to the CSF (cerebral spinal fluid). Also, which is the correct file to choose for the brain extracted image, because I see 2 fi

Re: [Freesurfer] Processing MRI help

Hi Arunan That is a giant defect and means something large (but possibly easily fixable) went wrong. Have you looked at the subject? We have a tutorial on our website for fixing topological defects, but in this case it will be something very large (like a lot of the skull attached, or the 2 hem

Re: [Freesurfer] How to extract the GM and WM

External Email - Use Caution Hi Bruce, I was wondering if there is way to continue the process to recon-all once I have done the recon-all with the option -autorecon1. Thanks a lot, Aldo From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf

[Freesurfer] FreeSurfer (v 6.0) skull stripping problems

External Email - Use Caution Hi everyone, I am processing the NIFD dataset (visit 1) and the FS (v 6.0) segmentation consistently includes dura mater in the pial boundary in most subjects (I could not attach example snapshots to this email, but they are available if required).

Re: [Freesurfer] Problem with talairach check in Freesurfer 7

External Email - Use Caution I've some subjects where talairach transform by FS7 was not optimal and thus eTIV was inaccurate. Because I'm interested in eTIV corrected volumes I need to correct it somehow. In my previous email I described my problems with correcting talairach trans