Re: [Freesurfer] Freesurfer issue

External Email - Use Caution Please try the following, … open a new terminal and run the bash shell … I am cd’d to /tmp though it should not matter ... $ cd /tmp$ bash The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For

[Freesurfer] Freesurfer issue

External Email - Use Caution Dear Freesurfer team, Several members of our lab tried setting up Freesurfer (V.7.4.1) and about 5-6 people have encountered the same problem (all of the on macOS) of freeview crashing when we are trying to load the T1 from the folder bert>mri>T1. We

Re: [Freesurfer] ln: failed to create symbolic link 'file': Operation not supported error

External Email - Use Caution Hello Gizem, Are you by any chance running Ubuntu Linux through WSL or a VM on a Windows machine - AND/OR - trying to write your data from Ubuntu linux to a mounted NTFS file system on a Windows machine? The Windows file system does not support

[Freesurfer] T2 FLAIR images

External Email - Use Caution Good evening all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/

Re: [Freesurfer] Installation tensorflow: protobuf requires Python '>=3.7' but the running Python is 3.6.8

External Email - Use Caution Hello Joost, It looks like you are using an old 2020 development build prior to fspython being updated to version 3.8.X with a newer version of tensorflow installed. The latest 7.4.1 release from June 2023 should have a tensorflow version 2.12

[Freesurfer] Help running freesurfer for FEAT-preprocessed functional data?

External Email - Use Caution Hello! I am trying to run some freesurfer commands for a pipeline. However, I am coming in with functional data preprocessed by FEAT (EPI correction and general mcflirt, etc). For reference, I'm trying to run this following script: preproc-sess -s .

[Freesurfer] Installation tensorflow: protobuf requires Python '>=3.7' but the running Python is 3.6.8

External Email - Use Caution Hello FreeSurfer Developers, I would like to run samseg with the lesion module, hence samseg is asking to install Tensorflow using the following command: fspython -m pip install tensorflow==1.13.1 However, when execute the command, I get the

[Freesurfer] RA Position for Human Intracranial EEG Lab

External Email - Use Caution Dear all, The human intracranial EEG Laboratory at The Feinstein Institutes for Medical Research - Hofstra Northwell School of Medicine in New York is looking for a research assistant with earliest start date in October 2023. The successful

Re: [Freesurfer] Question about glmfit results and visualization by using Freeview

External Email - Use Caution On 8/9/2023 5:03 AM, inbal paran wrote: External Email - Use Caution Dear FreeSurfer developers, Thank you for your response to my previous questions, I have a few more (I'm inexperienced with both Freesurfer and Linux): 1. Can I

Re: [Freesurfer] Fundi of Sulci

External Email - Use Caution you can use mri_surf2vol also you can try mris_skeletonize to label the fundi run both with --help to get more info On 8/8/2023 11:34 AM, Bluye Demessie wrote: > External Email - Use Caution > > Dear FreeSurfers, > > I am hoping to do an

Re: [Freesurfer] mri_segstats --avgwf output question

External Email - Use Caution It is going to list the cluster=0 value as the first value. cluster=0 are all the voxels not in a cluster. If you want to exclude this, just add --excludeid 0 On 8/10/2023 7:58 PM, Lara Foland-Ross wrote: External Email - Use Caution Hi

[Freesurfer] Extracting Mean Cortical Thickness from Specific Region

External Email - Use Caution Dear FreeSurfer Experts, I am new to FreeSurfer and I need to extract the mean cortical thickness from a specific region for each subject in my dataset (then for my 2 groups). I have already identified a significant cluster from a group analysis,

Re: [Freesurfer] Freesurfer Virtual Machine Password Request

External Email - Use Caution Hello, Thanks for offering to help out. I need help in these two areas. 1. Password to open the downloaded zip file that contains the Ubuntu+ free surfer image. 2. Password to open the image in virtual box. As per the doc I am referring, our username

[Freesurfer] Freesurfer Virtual Machine Password Request

External Email - Use Caution Hi, I'm looking to get the virtual machine password as I have been trying to get freesurfer to run on my windows computer. Please let me know if you need more information from me before sending, I'd be happy to provide it. Thank you! Regards, Gabriel

[Freesurfer] Password Required for Freesurfer

External Email - Use Caution Respected Manager, I am Ameiy Acharya, an undergrad at VIT Chennai. I need to use the Freesurfer software for an academic project. I am using the Virtual Box Ubuntu implementation of Freesurfer on Windows. There is a password required to extract the