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.
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Monday, June 24, 2024 9:50 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Monday, June 24, 2024 9:50 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@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:
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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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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.Ihavealrea...
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.ukmailto:ga62@st-andrews.ac.uk Sent: Wednesday, June 26, 2024 2:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Tuesday, June 25, 2024 9:51 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Monday, June 24, 2024 9:50 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Gaurav Ambwani -
Tregidgo, Henry