I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly.
The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform.
Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal.
-Jeff Eriksen
Hi Jeff, see if this page answers your question http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug
On 1/10/13 6:24 PM, Jeff Eriksen wrote:
I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly.
The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform.
Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal.
-Jeff Eriksen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jeff, here was my response from a few days ago. Let me know if you need anything else. doug
On 1/10/13 11:56 PM, Douglas Greve wrote:
Hi Jeff, see if this page answers your question http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug
On 1/10/13 6:24 PM, Jeff Eriksen wrote:
I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly.
The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform.
Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal.
-Jeff Eriksen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jeff, This wiki page has info on resampling structural data to diffusion space (3.1.3) and masking (3.1.4).
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion
-Louis
On Mon, 14 Jan 2013, Douglas Greve wrote:
Hi Jeff, here was my response from a few days ago. Let me know if you need anything else. doug
On 1/10/13 11:56 PM, Douglas Greve wrote: Hi Jeff, see if this page answers your question http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug
On 1/10/13 6:24 PM, Jeff Eriksen wrote: I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly.The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform.
Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal.
-Jeff Eriksen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I am reposting this since I did not get any response. Can I clarify my problem/request in any way? Can anyone point me to some avenues for further exploration?
Thanks, -Jeff
From: Jeff Eriksen <eriksenj@ohsu.edumailto:eriksenj@ohsu.edu> Date: Thursday, January 10, 2013 3:24 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: reversing recon-all resampling
I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly.
The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform.
Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal.
-Jeff Eriksen
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Jeff Eriksen -
Louis Nicholas Vinke