External Email - Use Caution
Hello FreeSurfur Developers, A have completed the segmentation of T1 MRI image using recon all. I want to know how to get the segmentation of specific structures using mri and surf folders. For example, Thalamus, prefrontal lobe, grey matter and then save each one, so I can use them for machine learning later. Looking forward to hearing from you. Best regards,Ammar Shujaa Addin
do you mean you want a binary mask? If so you can run something like mri_binarize --i aseg.mgz --match 17 --o left.hippocampus.mgz where 17 is the index for left hippo as found in $FREESURFER_HOME/FreeSurferColorLUT.txt
On 8/3/2021 4:18 AM, Ammar Shujaa wrote:
External Email - Use Caution
Hello FreeSurfur Developers,
A have completed the segmentation of T1 MRI image using recon all.
I want to know how to get the segmentation of specific structures using mri and surf folders. For example, Thalamus, prefrontal lobe, grey matter and then save each one, so I can use them for machine learning later.
Looking forward to hearing from you.
Best regards, Ammar Shujaa Addin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ammar
In the mri dir there are segmented volumed called aseg.mgz and aparc+aseg.mgz where every voxel has an index into the FreeSurferColorLUT.txt lookup file
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ammar Shujaa Sent: Tuesday, August 3, 2021 4:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] How to extract individual structures after recon-all
External Email - Use Caution Hello FreeSurfur Developers,
A have completed the segmentation of T1 MRI image using recon all.
I want to know how to get the segmentation of specific structures using mri and surf folders. For example, Thalamus, prefrontal lobe, grey matter and then save each one, so I can use them for machine learning later.
Looking forward to hearing from you.
Best regards, Ammar Shujaa Addin
and you can use mri_binarize --i aseg.mgz --match index1 index2 --o yourmask.mgz
On 8/3/2021 10:07 AM, Fischl, Bruce wrote:
Hi Ammar
In the mri dir there are segmented volumed called aseg.mgz and aparc+aseg.mgz where every voxel has an index into the FreeSurferColorLUT.txt lookup file
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Ammar Shujaa *Sent:* Tuesday, August 3, 2021 4:19 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] How to extract individual structures after recon-all
* External Email - Use Caution *
Hello FreeSurfur Developers,
A have completed the segmentation of T1 MRI image using recon all.
I want to know how to get the segmentation of specific structures using mri and surf folders. For example, Thalamus, prefrontal lobe, grey matter and then save each one, so I can use them for machine learning later.
Looking forward to hearing from you.
Best regards,
Ammar Shujaa Addin
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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Ammar Shujaa -
Douglas N. Greve -
Fischl, Bruce