Hi Doug & Gaurav,

There are some instructions for running recon-all on skull stripped brains in the FAQ’s on the wiki

https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F

pasted below for reference.

Best wishes,

Henry

Q. I have already skull-stripped data. Can I submit it to recon-all?

A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently.

First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s <subjid>

Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s <subjid>

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Date: Wednesday, 26 June 2024 at 23:36
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRI watershed error

⚠ Caution: External sender

not sure, it might work

On 6/26/2024 2:21 PM, Gaurav Ambwani wrote:

External Email - Use Caution

Dear Freesurfer team,

In short I just wanted to know if it would be possible for me to put a skull stripped MRI into freesurfer for recon-all?

Thank you,

Best Wishes,

Gaurav Ambwani.

From: Gaurav Ambwani <ga62@st-andrews.ac.uk>
Sent: Wednesday, June 26, 2024 2:12 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRI watershed error
Dear Freesurfer team,

The issue with that is that on fsl I would need to skull strip the image that I want to input for the registration. The reference image doesn't have to be skull stripped, but the input image has to be skull stripped.

When I take the skull stripped image as my reference image and input the T1 MNI image, the registration isn't successful, i.e. the image seems warped.

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: Tuesday, June 25, 2024 9:51 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRI watershed error
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:
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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