External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@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 <g...@st-andrews.ac.uk><mailto:g...@st-andrews.ac.uk> Sent: Wednesday, June 26, 2024 2:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Tuesday, June 25, 2024 9:51 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto: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: External Email - Use Caution 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Monday, June 24, 2024 9:50 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto: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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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