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 <g...@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 <g...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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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