you can compute the registration with the skull-stripped image, and then apply the registration to the whole head image
On 6/25/2024 12:31 PM, Gaurav Ambwani wrote:
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Dear Freesurfer team,
I can't put the whole head into FSL for registration, I have to put the skull stripped version into FSL. I have to put in the skull stripped head because the MNI_freesurfer_T1.nii.gz is registered to the stroke patient's T1 weighted image.
Using the I want the aseg, aparc, etc. files to be derived from the MNI_freesurfer_T1.nii.gz image. And for some reason it isn't working. I hope that this clarifies what I was trying to do.
Thank you, Best Wishes, Gaurav Ambwani.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU *Sent:* Monday, June 24, 2024 9:50 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] MRI watershed error Sorry, I'm not sure what the problem is that you are describing. I see from the recon-all file that MNI_freesurfer_T1.nii.gz is your input. What is that? Is that after skull stripping? Why not just give it the full head? On 6/20/2024 3:52 PM, Gaurav Ambwani wrote:
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Dear Freesurfer developers,
I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain extraction tool in 3D slicer, and then I registered it in fsl to a skull stripped version of a T1 weighted image of a Stroke patient (which I got from Openneuro).
The purpose of doing this is to, get the aseg.mgz file and overlay that onto the MRI of the stroke patient.
Previously I have taken the T1 1mm MNI image and received an aseg.mgz file which I have overlayed onto my MNI registered T1 weighted stroke MRI and that worked perfectly. However, This time I have taken the T1 1mm MNI image registered that to my stroke T1 MRI, and the registered image hasn't gone through freesurfer.
I have attached the recon-all.log file in this email.
Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Distributor ID: Ubuntu Description: Ubuntu 22.04.4 LTS Release: 22.04 Codename: jammy
I am using a WSL in windows 11 (64 bit)
Thank you, Best Wishes, Gaurav Ambwani.
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