External Email - Use Caution        

Dear Freesurfer team, 

Sorry for sending the emails in a such a patchy format. 

I took the T1 MNI image and registered that to the patient MRI. I did this without skull stripping in FSL. It seems to have worked pretty well. 

I ran the T1 MNI registered but not skull stripped through recon-all and seems to have given me an aseg.mgz file that is registered to my patient MRI. 

However, since FSL mentions that it is necessary to skull strip before registration I am not certain that it would work each time. I will probably send an email to FSL regarding this too. 

If you have a workaround based on my previous emails please do let me know. 

Thank you,
Best Wishes, 
Gaurav Ambwani. 
From: Gaurav Ambwani <ga62@st-andrews.ac.uk>
Sent: Tuesday, June 25, 2024 5:30 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRI watershed error
 
Dear Freesurfer team, 

I also wanted to point out that I do the skull stripping in Slicer using the "HD brain extraction tool", after which I save the file as a .nii file then put it into FSL for FLIRT linear registration with the patient MRI. Since I am trying to register the T1 MNI image to the patient MRI. 

Could I do the skull stripping and registration and then individually run the autorecon2, autorecon2-cp, autorecon-wm etc. steps subsequently in order. Do you think that this would be feasible. 

Thank you, 
Best Wishes, 
Gaurav Ambwani.  
From: Gaurav Ambwani <ga62@st-andrews.ac.uk>
Sent: Tuesday, June 25, 2024 12:31 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRI watershed error
 
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:

        External Email - Use Caution        

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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