Re: [Freesurfer] -bigventricles

External Email - Use Caution Yes, you can still pass the "-bigventrical" argument to recon-all in version 7.2.0 and in version 6.0. Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Taylor, Lisa Sent: Monday, September

Re: [Freesurfer] SynthSeg volume labels

External Email - Use Caution Thanks for sharing the CSV Akila. Could you also share what command you used to generate this CSV and the corresponding terminal output please? I was not able to recreate this error on my end. From:

Re: [Freesurfer] [External] Re: Question about sclimbic

Hi Victor, I have not been able to recreate this error. Would you be able to share some sample image that I can use to recreate this error? Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Victor (BIDMC - Keshavan - Psychiatry)

Re: [Freesurfer] lh.pial lh.pialT1n same file?

If you want your links to also be copied over in Linux/Mac you can use the --a argument with the cp command: cp --a From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Thursday, December 22, 2022 11:59 AM To: Huang, Yujing ; Renew

Re: [Freesurfer] 7.3.2-patch issues - thalamic segmentation

Hi Katie, Thank you for pointing this out! Yes, please make changes to the core.py script in your '$FREESURFER/python/packages/freesurfer/subregions/' folder. I will update the patch instructions to reflect this as well. Best, Avnish From:

Re: [Freesurfer] mri_sclimbic_seg patch issue?

Hi Randy and Yann, For this fix you will have to update the surfa package that ships with Freesurfer. You can do this by: fspython -m pip install --upgrade surfa Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yann Quidé Sent: Tuesday,

Re: [Freesurfer] Recon-all output in MNI305, patient space, or other?

Hi Andrew, 1. The recon-all output is in the subject's native space. 2. So, registration of the volume (MNI) and surfaces (fsaverage) happens as part of the recon-all process, but they're not resampled automatically i.e. kept in the subject's native space. You can use mri_vol2vol command

Re: [Freesurfer] Freeview error

Hi, This error suggests that your cluster instance is not able to find the swrast drivers: libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast swrast is a software renderer. It is provided by libgl1-mesa-dri library. If the library is not installed, you

Re: [Freesurfer] What's the difference between pc1 and spc (glmfit)

Hi Ken, * Avg: average cortical thickness between time-points * Rate: rate of change of cortical thickness * pc1: rate of change wrt. the first time point * spc: rate of change wrt. average thickness You can find more info about these in this Longitudinal Tutorial:

Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

Temple University ____ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Kumar, Avnish Sent: Thursday, December 8, 2022 10:19 AM To: Freesurfer support list Subject: [External] Re: [Freesurfer] 7.3.2-patch issues - thalamic segmentation Hi Katie, Than

Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

rd recon-all call or is this meant for a special flag. Also I was also wondering what issue did it solve? Thank you. On Wed, Feb 22, 2023 at 11:52 PM Kumar, Avnish mailto:avnish.ku...@mgh.harvard.edu>> wrote: Hi Katie, The core.py file has been updated now. Please try downloading it a

Re: [Freesurfer] Error Sourcing Freesurfer

External Email - Use Caution Could you post the ouitput of these two commands: pwd ls /usr/local/freesurfer Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Turco, Isabella Sent: Tuesday, May 2, 2023 10:55 AM To:

Re: [Freesurfer] SynthSeg terminates with 'std::bad_alloc' error when using --threads option (>1)

External Email - Use Caution Seems like you're running out of memory when using more than 1 threads. Can you allocate more memory to the VM? You can also try running Synthseg without the --robust flag? From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Error Sourcing Freesurfer

External Email - Use Caution You could also try directly sourcing the FS-711 like this: if using bash: source /usr/local/freesurfer/nmr-stable711-env-bash if using csh: source /usr/local/freesurfer/nmr-stable711-env From:

Re: [Freesurfer] error with synthsr in Mac M1

This is because of a change in the C API starting in numpy 1.20.0. You likely have a numpy version <1.20.0 installed in your python environment. Can you upgrade your numpy installation and try synthsr

Re: [Freesurfer] FS FAST

Can you post the outputs of these three commands: which python which python3 brew info python Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Justin Oh Sent: Tuesday, February 7, 2023 11:18 AM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] MRI image quality metrics

You could also use these: 1. For CNR you can use the mri_cnr tool: mri_cnr [options]  For example: mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz 1. For SNR, you'll have to calculate them as: * Run the recon-all pipeline to process your MRI data. * Use

Re: [Freesurfer] change labels name

Hi John, You can edit the label names in the accompanying metadata file of your Atlas - maybe a .txt or .lut file? You can edit that in a simple text editor. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of John Anderson Sent: Thursday, February 9,

Re: [Freesurfer] ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage

Hi Lizanne, A possible solution would be to create a symbolic link to change your fsaverage symbolic links when you source a different Freesurfer version: Source 7.2.0 Go into $SUBJECTS_DIR rm fsaverage ln -s $FREESURFER/subjects/fsaverage Best, Avnish From:

Re: [Freesurfer] ScLimbic: error: could not allocate memory for slice 1 out of 256error: mri_convert --conform failed!

Are you running this on a shared computer where other jobs might be using a lot of the available memory? You can use the following command to check the amount of available RAM on your system: free -h Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] FS FAST

brew: command not found Justins-MacBook-Air:~ justinoh$ I've posted the outputs. Thank you for your assistance! Best, Justin Oh On Thu, Feb 9, 2023 at 9:53 AM Kumar, Avnish mailto:avnish.ku...@mgh.harvard.edu>> wrote: Can you post the outputs of these three commands: which python which p

Re: [Freesurfer] SynthSR Freesurfer Development Version Apple M1/2 Chip Compatability

External Email - Use Caution Can you share what version of numpy you are using? Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sorby-Adams, Annabel Sent: Wednesday, June 14, 2023 8:09 PM To: fsbuild ;