Hello Bruce,
Let me rephrase my question. When I pass a brain MRI to freesurfer, it transforms the image spatially before it does the segmentation. Now the segmented objects have different orientation from the original MRI. My question is how can I transform the segmentation back to original MRI?
Thanks Shahab
__________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Hi Shahab,
I think:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg_raw.mgz
should do it (-rl says to reslice like the rawavg.mgz file, and -rt says to used nearest nbr resampling)
Bruce
On Sat, 25 Mar 2006, Shahabuddin Ansari wrote:
Hello Bruce,
Let me rephrase my question. When I pass a brain MRI to freesurfer, it transforms the image spatially before it does the segmentation. Now the segmented objects have different orientation from the original MRI. My question is how can I transform the segmentation back to original MRI?
Thanks Shahab
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
p.s. from the subject's mri dir.
On Sat, 25 Mar 2006, Shahabuddin Ansari wrote:
Hello Bruce,
Let me rephrase my question. When I pass a brain MRI to freesurfer, it transforms the image spatially before it does the segmentation. Now the segmented objects have different orientation from the original MRI. My question is how can I transform the segmentation back to original MRI?
Thanks Shahab
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Your answer crossed my question in cyber space. I always knew the freesurfer people were superhuman!
Brian
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Sat, 25 Mar 2006 19:27:11 -0500 (EST) To: Shahabuddin Ansari ansari_shahab@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Transformation of segmenation
p.s. from the subject's mri dir.
On Sat, 25 Mar 2006, Shahabuddin Ansari wrote:
Hello Bruce,
Let me rephrase my question. When I pass a brain MRI to freesurfer, it transforms the image spatially before it does the segmentation. Now the segmented objects have different orientation from the original MRI. My question is how can I transform the segmentation back to original MRI?
Thanks Shahab
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Folks, I have a related issue. My problem could be easy to solve if I could maintain original resolution from AFNI to Freesurfer and then back to AFNI. For instance, I would like to force no reslicing/interpolation with mri_convert. My original resolution is .938 x .938 x 1. I thought that there was a way to do this with mri_convert, but I can't seem to get it to work. There are ways to get the aseg to align with the original anat if it's moved back to AFNI, but no change in resolution would make it easier.
Brian
From: Shahabuddin Ansari ansari_shahab@yahoo.com Date: Sat, 25 Mar 2006 16:07:24 -0800 (PST) To: fischl@nmr.mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Transformation of segmenation
Hello Bruce,
Let me rephrase my question. When I pass a brain MRI to freesurfer, it transforms the image spatially before it does the segmentation. Now the segmented objects have different orientation from the original MRI. My question is how can I transform the segmentation back to original MRI?
Thanks Shahab
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sorry Brian, but we don't process anisotropic data at the moment. You have to go to isotropic then back. Bruce
On Sat, 25 Mar 2006, Brian Schweinsburg, Ph.D. wrote:
Hi Folks, I have a related issue. My problem could be easy to solve if I could maintain original resolution from AFNI to Freesurfer and then back to AFNI. For instance, I would like to force no reslicing/interpolation with mri_convert. My original resolution is .938 x .938 x 1. I thought that there was a way to do this with mri_convert, but I can't seem to get it to work. There are ways to get the aseg to align with the original anat if it's moved back to AFNI, but no change in resolution would make it easier.
Brian
From: Shahabuddin Ansari ansari_shahab@yahoo.com Date: Sat, 25 Mar 2006 16:07:24 -0800 (PST) To: fischl@nmr.mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Transformation of segmenation
Hello Bruce,
Let me rephrase my question. When I pass a brain MRI to freesurfer, it transforms the image spatially before it does the segmentation. Now the segmented objects have different orientation from the original MRI. My question is how can I transform the segmentation back to original MRI?
Thanks Shahab
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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
-
Brian Schweinsburg, Ph.D. -
Bruce Fischl -
Shahabuddin Ansari