Dear Developers,
I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized.
We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem:
recon-all -autorecon2-pial -autorecon3 -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) or recon-all -autorecon3-pial -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
*Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces? * * * *What solutions would you suggest in resolving this problem?* * * Thank you,
Vy Dinh Research Associate Department of Neurological Sciences Rush University Medical Center
BTW, we are using Freesurfer 5.1: freesurfer-i686-apple-darwin9.8.0-stable5-20110525
On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh vy_dinh@rush.edu wrote:
Dear Developers,
I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized.
We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem:
recon-all -autorecon2-pial -autorecon3 -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) or recon-all -autorecon3-pial -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
*Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces? *
*What solutions would you suggest in resolving this problem?*
Thank you,
Vy Dinh Research Associate Department of Neurological Sciences Rush University Medical Center
Was wondering if anyone from the Freesurfer team is looking into this issue yet.
On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh vy_dinh@rush.edu wrote:
BTW, we are using Freesurfer 5.1: freesurfer-i686-apple-darwin9.8.0-stable5-20110525
On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh vy_dinh@rush.edu wrote:
Dear Developers,
I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized.
We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem:
recon-all -autorecon2-pial -autorecon3 -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) or recon-all -autorecon3-pial -long tpN tp_base ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
*Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces? *
*What solutions would you suggest in resolving this problem?*
Thank you,
Vy Dinh Research Associate Department of Neurological Sciences Rush University Medical Center
Hi Vy,
not sure what it going on in your data. Surfaces are copied from the base and if they are not accurate there you need to fix it there. It seems you did that and you worked the edits in the right order.
What exactly happened? You fixed cross and base and everything look fine. When you run long it looks fine, but when you edit long and run it again it messes up?
Did you edit only the brain.finalsurfs or also other things at the same time? Also, if you edited long, these edits will be kept and not replaced with new edits from base or cross. So if cross or base get edited it may be good to rename or remove the edit file in the long and run long without edits again. This way the cross and base edits get transferred to long automatically. Only if that is not sufficient you need to do edits in the long.
Sorry I cannot say more right now without knowing what you did.
Best, Martin
On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh <vy_dinh@rush.edu mailto:vy_dinh@rush.edu> wrote:
BTW, we are using Freesurfer 5.1: freesurfer-i686-apple-darwin9.8.0-stable5-20110525 On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh <vy_dinh@rush.edu <mailto:vy_dinh@rush.edu>> wrote: Dear Developers, I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized. We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem: recon-all -autorecon2-pial -autorecon3 -long tpN tp_base (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) or recon-all -autorecon3-pial -long tpN tp_base (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) *Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces? * * * *What solutions would you suggest in resolving this problem?* * * Thank you, Vy Dinh Research Associate Department of Neurological Sciences Rush University Medical Center
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Also: brain.finalsurfs.manedit is mainly for correcting situations where the pial surface extends into the cerebellum. Did that happen in your case without editing? For other edits (e.g. pial including dura) you should fix the brainmask.mgz .
Best, Martin
On 04/01/2013 04:39 PM, Martin Reuter wrote:
Hi Vy,
not sure what it going on in your data. Surfaces are copied from the base and if they are not accurate there you need to fix it there. It seems you did that and you worked the edits in the right order.
What exactly happened? You fixed cross and base and everything look fine. When you run long it looks fine, but when you edit long and run it again it messes up?
Did you edit only the brain.finalsurfs or also other things at the same time? Also, if you edited long, these edits will be kept and not replaced with new edits from base or cross. So if cross or base get edited it may be good to rename or remove the edit file in the long and run long without edits again. This way the cross and base edits get transferred to long automatically. Only if that is not sufficient you need to do edits in the long.
Sorry I cannot say more right now without knowing what you did.
Best, Martin
On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh <vy_dinh@rush.edu mailto:vy_dinh@rush.edu> wrote:
BTW, we are using Freesurfer 5.1: freesurfer-i686-apple-darwin9.8.0-stable5-20110525 On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh <vy_dinh@rush.edu <mailto:vy_dinh@rush.edu>> wrote: Dear Developers, I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized. We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem: recon-all -autorecon2-pial -autorecon3 -long tpN tp_base (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) or recon-all -autorecon3-pial -long tpN tp_base (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) *Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces? * * * *What solutions would you suggest in resolving this problem?* * * Thank you, Vy Dinh Research Associate Department of Neurological Sciences Rush University Medical Center
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web :http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Vy and Martin
there was a bug in mri_mask that I just fixed that caused the brain.finalsurfs.mgz to be empty when the brain.finalsurfs.manedit.mgz existed. Vy: if you tell us what hardware/software platform you are using we can get you an updated version. Not sure if this will fix your problem, but it might. I also modified mris_make_surfaces in a way that could help and you can try a new version of that if mri_mask doesn't fix things for you
cheers Bruce On Mon, 1 Apr 2013, Martin Reuter wrote:
Also: brain.finalsurfs.manedit is mainly for correcting situations where the pial surface extends into the cerebellum. Did that happen in your case without editing? For other edits (e.g. pial including dura) you should fix the brainmask.mgz .
Best, Martin
On 04/01/2013 04:39 PM, Martin Reuter wrote: Hi Vy,
not sure what it going on in your data. Surfaces are copied from the base and if they are not accurate there you need to fix it there. It seems you did that and you worked the edits in the right order. What exactly happened? You fixed cross and base and everything look fine. When you run long it looks fine, but when you edit long and run it again it messes up? Did you edit only the brain.finalsurfs or also other things at the same time? Also, if you edited long, these edits will be kept and not replaced with new edits from base or cross. So if cross or base get edited it may be good to rename or remove the edit file in the long and run long without edits again. This way the cross and base edits get transferred to long automatically. Only if that is not sufficient you need to do edits in the long. Sorry I cannot say more right now without knowing what you did. Best, Martin On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh <vy_dinh@rush.edu> wrote: BTW, we are using Freesurfer 5.1: freesurfer-i686-apple-darwin9.8.0-stable5-20110525 On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh <vy_dinh@rush.edu> wrote: Dear Developers,I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized.
We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem:
recon-all -autorecon2-pial -autorecon3 -long tpN tp_base (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) or recon-all -autorecon3-pial -long tpN tp_base (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces?
What solutions would you suggest in resolving this problem?
Thank you,
Vy Dinh Research Associate Department of Neurological Sciences Rush University Medical Center
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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Bruce Fischl -
Martin Reuter -
Vy Dinh