Re: [Freesurfer] PetSurfer - MG coregister

External Email - Use Caution Dear Rahul, I just used the wiki of the Freesurfer functions, the information is very complete. If you want to use Freesurfer, you can start by doing the cortical reconstruction process for each subject ( https://secure-web.cisco.com/1Lj_XzmtE_iAYreTtm

Re: [Freesurfer] PetSurfer - MG coregister

External Email - Use Caution Thank you so much. Now I at least get a direction from where to start. Regards: Rahul Sharma Research Scholar NIT Silchar Assam 9827834360 *"Manners Maketh Man"* On Wed, Jan 18, 2023 at 5:36 PM Marina Fernández < marina.fdez.alva...@gmail.com> wro

[Freesurfer] ROI Analysis

External Email - Use Caution Hello FreeSurfer Community! I previously asked a question about volume quantification using an external atlas (in fact, there are 20 brain masks corresponding to the regions of interest). I managed to perform the quantification with the following comma

[Freesurfer] Two basic questions: brainmask file versions and qcache

External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all well. I have two relatively basic questions that I am hoping to get some help with. My basic planned processing pipeline is: Run initial recon-all with gcut and ws flags Edit white matter/pial v

[Freesurfer] TRACULA trac-all error

External Email - Use Caution Hey, I'm trying to run "trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial" but keep getting this error : /shared/centos7/freesurfer/7.3.2/bin/free/sources.csh: No such file or directory. My colleague ran this step on the same data

[Freesurfer] Dijk.m - Freesurfer Dijkstra MATLAB function

External Email - Use Caution Hi there, I'm looking to use the *Dijkstra matlab code* provided by freesurfer, titled 'dijk.m'. It calculates the *shortest path* from node 's' to node 't'. I want to use this to calculate the distance from 1 vertex to another on an inflated cortical

Re: [Freesurfer] TRACULA trac-all error

Hi Nita, What is your FREESURFER_HOME points to? It should be set to your Freesurfer 7.3.2 install directory. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Nita Akoh Sent: Wednesday, January 18, 2023 5:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer]

Re: [Freesurfer] dicom reading errors

External Email - Use Caution The output shows the command running on Ubuntu 18 linux and getting an error from the shell for a bad file descriptor (fd),Linux holowach 5.3.0-53-generic #47~18.04.1-ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x85_64 x86_64 GNU/Linuxsh: 1: Syntax

[Freesurfer] Skull stripping with external brainmask

External Email - Use Caution Dear FreeSurfer experts, I dealing with some issues regarding skull stripping in FreeSurfer (v7.1.1). It seems like the conventional approaches (e.g., adjusting -wsthresh) doesn’t seem to help. As well, applying these preprocessing steps to the raw T

Re: [Freesurfer] mri_label2vol error

External Email - Use Caution Hi Doug, That solved the problem like a charm. By the way, the volume came from brain.mgz. Thank you! Regards, Sean On Sat, Jan 14, 2023 at 12:28 AM Douglas N. Greve wrote: > What volume did the TF.label come from? Whatever it is, try adding > --tk