Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask
Dear Freesurfer experts,
We are about to do a mass reprocessing in our lab to update our FS 5.0 data to the FS 5.1 and would like to do the following all in one run:
1) Preserve the wm and pial edits made in the 5.0 data in 5.1 From our understanding, using the command -------------------------------------------- recon-all -all -s subjid -------------------------------------------- will preserve our (wm and pial) edits when rerunning recon-all as long as we do not use any -clear command. We've tested this command and it works. However, we would also like to (go to #2)
2) Recreate the cerebellum in brainmask while preserving our edits. We recently learned that the cerebellum should not be edited in brainmask.mgz as this would affect the volumetric measurements of this region. Since we are interested in this measurement, we want to recreate brainmask.mgz when rerunning recon-all. I came across a post that suggested adding the option -clean-bm and using brain.finalsurfs.manedit.mgz when rerunning reconall. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20406.html). The documentation on brain.finalsurfs.manedit.mgz suggests that this image determines the final surfaces, regardless of what brainmask.mgz looks like, which is why we could still use -cleanbm to recreate brainmask AND preserve our edits.
However, when we ran the command -------------------------------------------- recon-all -all -clean-bm -s subjid (with brain.finalsurfs.manedit.mgz containing our edits in 5.0) -------------------------------------------- the edits were only preserved in one subject that we tested. The edits did not appear to be preserved at all in the other subjects. Does anyone have any explanations for why edits were preserved in this subject but not the other test subjects? Since running reconall takes a long time, we will really appreciate it if there is a way to carry over the edits we made but also recreate brainmask to get the cerebellum in one run. (Alternatively, we can add voxels back to the cerebellum, but this method would be more time consuming.) If brain.finalsurfs.manedit.mgz is indeed used to determine the final surface, would be possible to make all edits in brain.finalsurfs.manedit.mgz instead of brainmask.mgz? It seems more efficient and intuitive to make edits in one place.
We would like to move forward with our reprocessing and are looking forward to your responses.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edumailto:Vy_dinh@rush.edu
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edumailto:Vy_dinh@rush.edu
Hi Vy, I'm not sure why that only seems to be working sometimes. Can you send me a case it did work on and a case it didn't work on? Allison
On Thu, 12 Jan 2012, Vy Dinh wrote:
Dear Freesurfer experts, We are about to do a mass reprocessing in our lab to update our FS 5.0 data to the FS 5.1 and would like to do the following all in one run:
- Preserve the wm and pial edits made in the 5.0 data in 5.1
From our understanding, using the command -------------------------------------------- recon-all -all -s subjid -------------------------------------------- will preserve our (wm and pial) edits when rerunning recon-all as long as we do not use any -clear command. We've tested this command and it works. However, we would also like to (go to #2)
- Recreate the cerebellum in brainmask while preserving our edits.
We recently learned that the cerebellum should not be edited in brainmask.mgz as this would affect the volumetric measurements of this region. Since we are interested in this measurement, we want to recreate brainmask.mgz when rerunning recon-all. I came across a post that suggested adding the option -clean-bm and using brain.finalsurfs.manedit.mgz when rerunning reconall.(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20406.html). The documentation on brain.finalsurfs.manedit.mgz suggests that this image determines the final surfaces, regardless of what brainmask.mgz looks like, which is why we could still use -cleanbm to recreate brainmask AND preserve our edits.
However, when we ran the command -------------------------------------------- recon-all -all -clean-bm -s subjid (with brain.finalsurfs.manedit.mgz containing our edits in 5.0) -------------------------------------------- the edits were only preserved in one subject that we tested. The edits did not appear to be preserved at all in the other subjects. Does anyone have any explanations for why edits were preserved in this subject but not the other test subjects? Since running reconall takes a long time, we will really appreciate it if there is a way to carry over the edits we made but also recreate brainmask to get the cerebellum in one run. (Alternatively, we can add voxels back to the cerebellum, but this method would be more time consuming.) If brain.finalsurfs.manedit.mgz is indeed used to determine the final surface, would be possible to make all edits in brain.finalsurfs.manedit.mgz instead of brainmask.mgz? It seems more efficient and intuitive to make edits in one place.
We would like to move forward with our reprocessing and are looking forward to your responses.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
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Hi Allison,
Upon a closer look, it appears that there were still some corrections to be made for the subject whose 5.0 corrections "were preserved," just not as many edits for this subject as the others. (The difference in the amount of edits we need to make were significant, however.)
For one subject, I ran [recon-all -all -s subjid] in 5.1, the edits carried over in 5.1. But then I took this subject again and ran [recon-all -all -clean-bm -subjid] with brain.finalsurfs.manedit.mgz in the subj/mri/ directory and when I checked this subject in tkmedit the next morning, I had the same issues with the edits not being preserved. Have you observed these results with running -clean-bm in your lab?
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
________________________________________ From: Allison Player [astevens@nmr.mgh.harvard.edu] Sent: Thursday, January 12, 2012 3:18 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.goldman@gmail.com Subject: Re: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask
Hi Vy, I'm not sure why that only seems to be working sometimes. Can you send me a case it did work on and a case it didn't work on? Allison
On Thu, 12 Jan 2012, Vy Dinh wrote:
Dear Freesurfer experts, We are about to do a mass reprocessing in our lab to update our FS 5.0 data to the FS 5.1 and would like to do the following all in one run:
- Preserve the wm and pial edits made in the 5.0 data in 5.1 From our understanding, using the command
recon-all -all -s subjid
will preserve our (wm and pial) edits when rerunning recon-all as longas we do not use any -clear command. We've tested this command and it works. However, we would also like to (go to #2)
- Recreate the cerebellum in brainmask while preserving our edits. We recently learned that the cerebellum should not be edited in
brainmask.mgz as this would affect the volumetric measurements of this region. Since we are interested in this measurement, we want to recreate brainmask.mgz when rerunning recon-all. I came across a post that suggested adding the option -clean-bm and using brain.finalsurfs.manedit.mgz when rerunning reconall.(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20406.html). The documentation on brain.finalsurfs.manedit.mgz suggests that this image determines the final surfaces, regardless of what brainmask.mgz looks like, which is why we could still use -cleanbm to recreate brainmask AND preserve our edits.
However, when we ran the command
recon-all -all -clean-bm -s subjid (withbrain.finalsurfs.manedit.mgz containing our edits in 5.0)
the edits were only preserved in one subject that we tested. The edits did not appear to be preserved at all in the other subjects. Does anyone have any explanations for why edits were preserved in this subject but not the other test subjects? Since running reconall takes a long time, we will really appreciate it if there is a way to carry over the edits we made but also recreate brainmask to get the cerebellum in one run. (Alternatively, we can add voxels back to the cerebellum, but this method would be more time consuming.) If brain.finalsurfs.manedit.mgz is indeed used to determine the final surface, would be possible to make all edits in brain.finalsurfs.manedit.mgz instead of brainmask.mgz? It seems more efficient and intuitive to make edits in one place.
We would like to move forward with our reprocessing and are looking forward to your responses.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
Haven't noticed it but maybe we missed something. I'd like to look at your case if I can to try to figure it out. If you'd rather not send the case, I'll try some testing on this end to see if I can replicate it.
On Fri, 13 Jan 2012, Vy Dinh wrote:
Hi Allison,
Upon a closer look, it appears that there were still some corrections to be made for the subject whose 5.0 corrections "were preserved," just not as many edits for this subject as the others. (The difference in the amount of edits we need to make were significant, however.)
For one subject, I ran [recon-all -all -s subjid] in 5.1, the edits carried over in 5.1. But then I took this subject again and ran [recon-all -all -clean-bm -subjid] with brain.finalsurfs.manedit.mgz in the subj/mri/ directory and when I checked this subject in tkmedit the next morning, I had the same issues with the edits not being preserved. Have you observed these results with running -clean-bm in your lab?
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
From: Allison Player [astevens@nmr.mgh.harvard.edu] Sent: Thursday, January 12, 2012 3:18 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.goldman@gmail.com Subject: Re: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask
Hi Vy, I'm not sure why that only seems to be working sometimes. Can you send me a case it did work on and a case it didn't work on? Allison
On Thu, 12 Jan 2012, Vy Dinh wrote:
Dear Freesurfer experts, We are about to do a mass reprocessing in our lab to update our FS 5.0 data to the FS 5.1 and would like to do the following all in one run:
- Preserve the wm and pial edits made in the 5.0 data in 5.1 From our understanding, using the command
recon-all -all -s subjid
will preserve our (wm and pial) edits when rerunning recon-all as longas we do not use any -clear command. We've tested this command and it works. However, we would also like to (go to #2)
- Recreate the cerebellum in brainmask while preserving our edits. We recently learned that the cerebellum should not be edited in
brainmask.mgz as this would affect the volumetric measurements of this region. Since we are interested in this measurement, we want to recreate brainmask.mgz when rerunning recon-all. I came across a post that suggested adding the option -clean-bm and using brain.finalsurfs.manedit.mgz when rerunning reconall.(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20406.html). The documentation on brain.finalsurfs.manedit.mgz suggests that this image determines the final surfaces, regardless of what brainmask.mgz looks like, which is why we could still use -cleanbm to recreate brainmask AND preserve our edits.
However, when we ran the command
recon-all -all -clean-bm -s subjid (withbrain.finalsurfs.manedit.mgz containing our edits in 5.0)
the edits were only preserved in one subject that we tested. The edits did not appear to be preserved at all in the other subjects. Does anyone have any explanations for why edits were preserved in this subject but not the other test subjects? Since running reconall takes a long time, we will really appreciate it if there is a way to carry over the edits we made but also recreate brainmask to get the cerebellum in one run. (Alternatively, we can add voxels back to the cerebellum, but this method would be more time consuming.) If brain.finalsurfs.manedit.mgz is indeed used to determine the final surface, would be possible to make all edits in brain.finalsurfs.manedit.mgz instead of brainmask.mgz? It seems more efficient and intuitive to make edits in one place.
We would like to move forward with our reprocessing and are looking forward to your responses.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
Can you please test [recon-all -all -clean-bm -s subjid] with one of your subjects in 5.1 (with brain.finalsurfs.manedit.mgz in your subject's mri directory)? If it does work, then at least we can rule out that version 5.1 does not have a bug and I can troubleshoot on my end. If that does not work, then I will send you the files (will save us all some time).
Many thanks in advance,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
________________________________________ From: Allison Player [astevens@nmr.mgh.harvard.edu] Sent: Friday, January 13, 2012 3:55 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.goldman@gmail.com Subject: RE: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask
Haven't noticed it but maybe we missed something. I'd like to look at your case if I can to try to figure it out. If you'd rather not send the case, I'll try some testing on this end to see if I can replicate it.
On Fri, 13 Jan 2012, Vy Dinh wrote:
Hi Allison,
Upon a closer look, it appears that there were still some corrections to be made for the subject whose 5.0 corrections "were preserved," just not as many edits for this subject as the others. (The difference in the amount of edits we need to make were significant, however.)
For one subject, I ran [recon-all -all -s subjid] in 5.1, the edits carried over in 5.1. But then I took this subject again and ran [recon-all -all -clean-bm -subjid] with brain.finalsurfs.manedit.mgz in the subj/mri/ directory and when I checked this subject in tkmedit the next morning, I had the same issues with the edits not being preserved. Have you observed these results with running -clean-bm in your lab?
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
From: Allison Player [astevens@nmr.mgh.harvard.edu] Sent: Thursday, January 12, 2012 3:18 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.goldman@gmail.com Subject: Re: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask
Hi Vy, I'm not sure why that only seems to be working sometimes. Can you send me a case it did work on and a case it didn't work on? Allison
On Thu, 12 Jan 2012, Vy Dinh wrote:
Dear Freesurfer experts, We are about to do a mass reprocessing in our lab to update our FS 5.0 data to the FS 5.1 and would like to do the following all in one run:
- Preserve the wm and pial edits made in the 5.0 data in 5.1 From our understanding, using the command
recon-all -all -s subjid
will preserve our (wm and pial) edits when rerunning recon-all as longas we do not use any -clear command. We've tested this command and it works. However, we would also like to (go to #2)
- Recreate the cerebellum in brainmask while preserving our edits. We recently learned that the cerebellum should not be edited in
brainmask.mgz as this would affect the volumetric measurements of this region. Since we are interested in this measurement, we want to recreate brainmask.mgz when rerunning recon-all. I came across a post that suggested adding the option -clean-bm and using brain.finalsurfs.manedit.mgz when rerunning reconall.(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20406.html). The documentation on brain.finalsurfs.manedit.mgz suggests that this image determines the final surfaces, regardless of what brainmask.mgz looks like, which is why we could still use -cleanbm to recreate brainmask AND preserve our edits.
However, when we ran the command
recon-all -all -clean-bm -s subjid (withbrain.finalsurfs.manedit.mgz containing our edits in 5.0)
the edits were only preserved in one subject that we tested. The edits did not appear to be preserved at all in the other subjects. Does anyone have any explanations for why edits were preserved in this subject but not the other test subjects? Since running reconall takes a long time, we will really appreciate it if there is a way to carry over the edits we made but also recreate brainmask to get the cerebellum in one run. (Alternatively, we can add voxels back to the cerebellum, but this method would be more time consuming.) If brain.finalsurfs.manedit.mgz is indeed used to determine the final surface, would be possible to make all edits in brain.finalsurfs.manedit.mgz instead of brainmask.mgz? It seems more efficient and intuitive to make edits in one place.
We would like to move forward with our reprocessing and are looking forward to your responses.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
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