Re: [Freesurfer] EasyReg Troubleshoot - Killed

External Email - Use Caution Hi, Would you be able to provide any more insight to this? I'd like to see if I could get it working on my dataset. Thanks! Nadia Nadia Kane Junior Imaging Specialist University Imaging Centers | University of Minnesota

Re: [Freesurfer] Cerebellum + Subcortical models extraction

External Email - Use Caution I don't know about recon-all-clinical, but you can get a decent cerebellum seg with mri_synthseg. I don't think anything will give you great GM/WM segmentation in cblum as that requires super high resolution. On 5/15/2023 2:11 PM, Nathan Santana

Re: [Freesurfer] mri_synthmorph

External Email - Use Caution try fixing your qform first On 5/15/2023 3:28 PM, Nadia Kane wrote: External Email - Use Caution Hi, I tried using mri_synthmorph in FreeSurfer on synthetic mouse brain data, but my output moved image is just black pixels. Thanks, Nadia

Re: [Freesurfer] Approach for LR asymmetry analysis using ROIs?

External Email - Use Caution Does this help

Re: [Freesurfer] mri_robust_register for mouse brain?

External Email - Use Caution Did you see the part where it says: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented You probably need to set the qform or the sform On 5/15/2023 11:35 AM, Nadia Kane wrote:

Re: [Freesurfer] recon-all error: cannot find or read colortable_BARe: recon-all error: cannot find or read colortable_BA_thresh.txt_thresh.txt

External Email - Use Caution We should have an update for this installed there soon. - R. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] Approach for LR asymmetry analysis using ROIs?

External Email - Use Caution Hello FS Community, I'm working on a study about left-right asymmetry and one of the experiments I'd like to do is to directly compare the average percent change between sides for each ROI when processed using a volumetric registration and when

[Freesurfer] mri_synthmorph

External Email - Use Caution Hi, I tried using mri_synthmorph in FreeSurfer on synthetic mouse brain data, but my output moved image is just black pixels. Thanks, Nadia Nadia Kane Junior Imaging Specialist University Imaging Centers | University of Minnesota

Re: [Freesurfer] Cerebellum + Subcortical models extraction

External Email - Use Caution Sorry, I mistakenly sent the message without completing it, so, how I was saying: (I won't use these for clinical purposes, there can't be any concrete conclusions based on this kind of data). From:

[Freesurfer] Cerebellum + Subcortical models extraction

External Email - Use Caution Hi, I would like to know about the acquisitions of the cerebellum and subcortical areas. I ask if you, Freesurfer developers, could recommend any software script that allows me to extract the cerebellum in a high enough quality? Does Freesurfer

Re: [Freesurfer] Issue with running recon-all

External Email - Use Caution Hi Hengameh By far the most common reason for this is running out of disk space. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of hmarz...@student.ubc.ca Sent: Monday, May 15, 2023 1:02 PM To: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Issue with running recon-all

External Email - Use Caution Dear developers, I am writing to report an issue I encountered while running recon-all on some subjects. Specifically, I received an error message stating "error: freadFloat: fread failed" for several of the subjects. Starting surface-based

Re: [Freesurfer] mri_robust_register for mouse brain?

External Email - Use Caution This is the output I get from using mri_robust_register. It appears to have failed. mri_robust_register --mov lab2im/brains/brain_05.nii.gz --dst atlas/atlas.nii.gz --lta affine_brain_05.lta --satit --affine $Id: mri_robust_register.cpp,v 1.52.2.3

Re: [Freesurfer] mri_robust_register for mouse brain?

External Email - Use Caution I don't see why not. I think the only reason it might fail is if it makes some assumptions about the voxels size. You can also try mri_coreg; I wrote this so I'm pretty sure there are no such assumptions (but robust reg might work as well) On

Re: [Freesurfer] [FreeSurfer] Process terminated when talairach was running

External Email - Use Caution That means that the FS enviroment on the HCP is not set up correctly On 5/14/2023 10:36 PM, Krystal Xiwing Yau wrote: External Email - Use Caution Dear Douglas, It's on the HPC. Regards, Krystal

Re: [Freesurfer] Individualized subcortex atals generation with freesurfer derivatives

External Email - Use Caution That is a lot of non-FreeSurfer code. We only support FreeSurfer code. If this is a question about FS code, then please distill it down to that. On 5/15/2023 8:25 AM, bong516612 wrote: External Email - Use Caution Greetings esteemed

[Freesurfer] Individualized subcortex atals generation with freesurfer derivatives

External Email - Use CautionGreetings esteemed experts and professors,I am currently conducting a study to validate my own hypothesis, utilizing recently acquired UKB neuroimaging data.The core structure of my project is designed to replicate the work of He and Tong, generating an