Re: [Freesurfer] Question about hippocampal sub-volume extraction

Hi Wei, I think the easiest is to run quantifyHAsubregions.sh twice and manually concatenate the 2 output text files. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On May 7, 2021, at 20:17, Wei Shao mailto:ws...@res

Re: [Freesurfer] Question about hippocampal sub-volume extraction

External Email - Use Caution Hello, there I just want to follow up on this question, is there any command that I can use to extract the T2 sub-volume from two different groups of subjects(AVP and BAY) of the hippocampus from Freesurfer? Best, Wei On Mon, May 3, 2021 at 8:13 PM W

Re: [Freesurfer] How white matter voxel is represented on the surface ?

Hi John, It depends on how you sample from the volume to the surface, but yes, in general voxels in the white matter (and deep gray matter and csf and bone, etc….) won’t show up on the surface Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of John Gelburg Sent: Friday, M

[Freesurfer] How white matter voxel is represented on the surface ?

External Email - Use Caution Dear list, I am sorry for a newbie question: Suppose I analyze the fMRI data in a volumetric way using SPM. I have a voxel that appears in a white matter. Does this mean that this voxel will not appear on the surface? In other words, there would be no

Re: [Freesurfer] mri_label2vol error

Hi Melissa, If the command runs fine in the terminal but not from python, it’s most likely because python is messing with aspects of your env before running commands in a subshell. The easiest solution is to upgrade to FS v7, where this problem no longer exists, but if you’re stuck at v6, you s

Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

Yes, it might be a normalization issue. You could try using the `-no-ants-n4` recon-all flag to fallback to the v6 normalization method. As for the wm edits, you don’t really need to load the surfaces, just the norm.mgz and wm.mgz, but if you wanted to visualize the initial smooth tessellation

Re: [Freesurfer] Error in SAMSEG preprocessing

If the output directory is missing seg.mgz, then samseg failed. You’ll have to send us the log or some sort of information about the error for us to debug this. Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alberto Del Cerro Leon Date: Friday, May 7, 2021 at 6:49 AM

[Freesurfer] mri_label2vol error

External Email - Use Caution Hi, I get the following error message when I run mri_label2vol (freesurfer v 6.0) in a jupyter notebook(6.1.4) with python (v3.8.5): dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfe

Re: [Freesurfer] Multiple Freesurfer(s)

Hi Giulio, I’ll follow up off-list. Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Giulio Degano Date: Friday, May 7, 2021 at 3:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Multiple Freesurfer(s) External Email - Use Caution Hi all, I am trying to

[Freesurfer] Job ad: MRI physicist, University of Delaware

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, and MRI-compatible

[Freesurfer] Error in SAMSEG preprocessing

External Email - Use Caution Hello, I am trying to use SAMSEG to segment white matter lesions, I ran the following command: run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii' '/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate --lesion --lesi

Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology

External Email - Use Caution Hi Andrew, thank you for looking at the data! I did check out that tutorial first, and the first thing it tells you to do is load various surfaces into Freeview, which was what brought me here. In this subject's `surf` directory there are no ?h.wh

[Freesurfer] Multiple Freesurfer(s)

External Email - Use Caution Hi all, I am trying to install multiple Freesurfer versions on a Linux server (academic purposes, Linux Ubuntu 20.04). I was able to install 7.1 and 5.3 (I used two different folders) and I also got the licenses. While 7.1 runs with no problem, for 5