Hello FreeSurfer Developers and Community,
I am working with an axial T1-weighted post-contrast MRI, with an original voxel size of 1×1×5.5 mm. I resampled this MRI in 3D Slicer using B-Spline interpolation and then saved it as a mgz file. After running recon-all on this resampled file, I noticed that the right hemisphere’s segmentation and parcellation are flawed. Also, considering the age and health situation of this patient, i believe the WM hypointensities are overestimated in the left hemisphere.
I am using the following version of FreeSurfer: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460. The command line was: recon-all -s 12th_recon_output -i input.mgz -all -parallel -openmp 12
I’ve attached the recon-all log file, a screenshot from Freeview to illustrate the issue, and mri_info file. I would greatly appreciate any guidance, troubleshooting advice, or suggestions on what might have gone wrong and how to correct this issue.
Thank you in advance for your help!
Best regards, Nima
Try using recon-all-clinical.sh; it works a lot better on these thick slice data
On 1/28/2025 12:24 PM, Taghizadeh Mortezaei, Nima wrote:
Hello FreeSurfer Developers and Community,
I am working with an axial T1-weighted post-contrast MRI, with an original voxel size of 1×1×5.5 mm. I resampled this MRI in 3D Slicer using B-Spline interpolation and then saved it as a mgz file. After running recon-all on this resampled file, I noticed that the right hemisphere’s segmentation and parcellation are flawed. Also, considering the age and health situation of this patient, i believe the WM hypointensities are overestimated in the left hemisphere.
I am using the following version of FreeSurfer: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460. The command line was: recon-all -s 12th_recon_output -i input.mgz -all -parallel -openmp 12
I’ve attached the recon-all log file, a screenshot from Freeview to illustrate the issue, and mri_info file. I would greatly appreciate any guidance, troubleshooting advice, or suggestions on what might have gone wrong and how to correct this issue.
Thank you in advance for your help!
Best regards, Nima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for your guidance. I already tried recon-all-clinical.sh; however, I was wondering why did this happen? Could it be related to resampling process or the orientation?
Thanks, Nima ________________________________ 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, January 28, 2025 12:41 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation
Try using recon-all-clinical.sh; it works a lot better on these thick slice data
On 1/28/2025 12:24 PM, Taghizadeh Mortezaei, Nima wrote: Hello FreeSurfer Developers and Community,
I am working with an axial T1-weighted post-contrast MRI, with an original voxel size of 1×1×5.5 mm. I resampled this MRI in 3D Slicer using B-Spline interpolation and then saved it as a mgz file. After running recon-all on this resampled file, I noticed that the right hemisphere’s segmentation and parcellation are flawed. Also, considering the age and health situation of this patient, i believe the WM hypointensities are overestimated in the left hemisphere.
I am using the following version of FreeSurfer: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460. The command line was: recon-all -s 12th_recon_output -i input.mgz -all -parallel -openmp 12
I’ve attached the recon-all log file, a screenshot from Freeview to illustrate the issue, and mri_info file. I would greatly appreciate any guidance, troubleshooting advice, or suggestions on what might have gone wrong and how to correct this issue.
Thank you in advance for your help!
Best regards, Nima
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is likely due to the slice thickness. recon-all was build with the assumption that the data would be high res (~1mm). It becomes hard to resolve cortex at lower resolutions, so, while recon-all-clinical will finish and give you results, there is no way to get around the resolution limits.
On 1/28/2025 6:57 PM, Taghizadeh Mortezaei, Nima wrote:
Thanks for your guidance. I already tried recon-all-clinical.sh; however, I was wondering why did this happen? Could it be related to resampling process or the orientation?
Thanks, Nima
*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, January 28, 2025 12:41 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation Try using recon-all-clinical.sh; it works a lot better on these thick slice data
On 1/28/2025 12:24 PM, Taghizadeh Mortezaei, Nima wrote:
Hello FreeSurfer Developers and Community,
I am working with an axial T1-weighted post-contrast MRI, with an original voxel size of 1×1×5.5 mm. I resampled this MRI in 3D Slicer using B-Spline interpolation and then saved it as a mgz file. After running recon-all on this resampled file, I noticed that the right hemisphere’s segmentation and parcellation are flawed. Also, considering the age and health situation of this patient, i believe the WM hypointensities are overestimated in the left hemisphere.
I am using the following version of FreeSurfer: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460. The command line was: recon-all -s 12th_recon_output -i input.mgz -all -parallel -openmp 12
I’ve attached the recon-all log file, a screenshot from Freeview to illustrate the issue, and mri_info file. I would greatly appreciate any guidance, troubleshooting advice, or suggestions on what might have gone wrong and how to correct this issue.
Thank you in advance for your help!
Best regards, Nima
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
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Taghizadeh Mortezaei, Nima