Dear FreeSurfer team,
For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message): CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849) XL defect detected... It is stuck here since a whole day now, so I'm not expecting it to advance... Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors. Do you have any ideas what the problem might be or what I can do to work around it?
Thanks, Martin
Hi Martin
a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9
cheers Bruce
On Mon, 11 Dec 2017, Loeffler, Martin wrote:
Dear FreeSurfer team,
For a case report I’m running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I’m not expecting it to advance…
Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around it?
Thanks,
Martin
Dear Bruce,
thanks for the quick reply! You are right, of course. I do find errors in lh.inflated.nofix. I have attached a screenshot of the biggest errors I found.. Can you maybe guide me a little how to fix the issue? Do I just cancel the running recon-all process, and set control points and run again? Investing some time in manual editing would be fine as it's a case study...
Thanks for your help, Martin
________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Dezember 2017 22:47 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9
cheers Bruce
On Mon, 11 Dec 2017, Loeffler, Martin wrote:
Dear FreeSurfer team,
For a case report I’m running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I’m not expecting it to advance…
Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around it?
Thanks,
Martin
Hi Martin
we are happy to take a look, but can't really tell much from a screenshot. Feel free to upload the subject to our ftp site if you want us to help
cheers Bruce
On Tue, 12 Dec 2017, Loeffler, Martin wrote:
Dear Bruce,
thanks for the quick reply! You are right, of course. I do find errors in lh.inflated.nofix. I have attached a screenshot of the biggest errors I found.. Can you maybe guide me a little how to fix the issue? Do I just cancel the running recon-all process, and set control points and run again? Investing some time in manual editing would be fine as it's a case study...
Thanks for your help, Martin
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Dezember 2017 22:47 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9
cheers Bruce
On Mon, 11 Dec 2017, Loeffler, Martin wrote:
Dear FreeSurfer team,
For a case report I’m running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I’m not expecting it to advance…
Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around it?
Thanks,
Martin
Dear Bruce, I have uploaded the respective files. If there is something missing let me know. Cheers, Martin
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Dezember 2017 16:35 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
we are happy to take a look, but can't really tell much from a screenshot. Feel free to upload the subject to our ftp site if you want us to help
cheers Bruce
On Tue, 12 Dec 2017, Loeffler, Martin wrote:
Dear Bruce,
thanks for the quick reply! You are right, of course. I do find errors in lh.inflated.nofix. I have attached a screenshot of the biggest errors I found.. Can you maybe guide me a little how to fix the issue? Do I just cancel the running recon-all process, and set control points and run again? Investing some time in manual editing would be fine as it's a case study...
Thanks for your help, Martin
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Dezember 2017 22:47 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9
cheers Bruce
On Mon, 11 Dec 2017, Loeffler, Martin wrote:
Dear FreeSurfer team,
For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I'm not expecting it to advance.
Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around it?
Thanks,
Martin
Hi Martin,
We've taken a look at the scans you uploaded, and unfortunately it won't be possible to run the standard recon-all on your subject. Recon-all is not designed to work on scans with such large lesions. If you are interested, there may be a way to generate a reasonable model of the right hemisphere.
Best,
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loeffler, Martin martin.loeffler@zi-mannheim.de Sent: Tuesday, December 12, 2017 11:57:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Dear Bruce, I have uploaded the respective files. If there is something missing let me know. Cheers, Martin
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Dezember 2017 16:35 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
we are happy to take a look, but can't really tell much from a screenshot. Feel free to upload the subject to our ftp site if you want us to help
cheers Bruce
On Tue, 12 Dec 2017, Loeffler, Martin wrote:
Dear Bruce,
thanks for the quick reply! You are right, of course. I do find errors in lh.inflated.nofix. I have attached a screenshot of the biggest errors I found.. Can you maybe guide me a little how to fix the issue? Do I just cancel the running recon-all process, and set control points and run again? Investing some time in manual editing would be fine as it's a case study...
Thanks for your help, Martin
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Dezember 2017 22:47 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9
cheers Bruce
On Mon, 11 Dec 2017, Loeffler, Martin wrote:
Dear FreeSurfer team,
For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I'm not expecting it to advance.
Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around it?
Thanks,
Martin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce, Dear Bram,
Thanks a lot for having a look. Unfortunately the left hemisphere is equally important as the right one for our question of interest. With a lot of patience the recon-all has finished and the result looks surprisingly ok. I have additionally re-run it (recon-all -autorecon2-cp -autorecon3 -s Case) after setting control points to correct errors in the wm.mgz. Some errors were corrected, but not all. Next I would like to correct the surfaces. My questions:
- I know that recon-all is not designed for such a subject. But is there any argument against continuing the analysis now?
- What can I do for those errors where the wm.mgz is still false, despite control points? I have uploaded the respective files.
Best, Martin
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram Ryder Gesendet: Mittwoch, 13. Dezember 2017 23:23 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin,
We've taken a look at the scans you uploaded, and unfortunately it won't be possible to run the standard recon-all on your subject. Recon-all is not designed to work on scans with such large lesions. If you are interested, there may be a way to generate a reasonable model of the right hemisphere.
Best,
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Loeffler, Martin <martin.loeffler@zi-mannheim.demailto:martin.loeffler@zi-mannheim.de> Sent: Tuesday, December 12, 2017 11:57:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Dear Bruce, I have uploaded the respective files. If there is something missing let me know. Cheers, Martin
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Dezember 2017 16:35 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
we are happy to take a look, but can't really tell much from a screenshot. Feel free to upload the subject to our ftp site if you want us to help
cheers Bruce
On Tue, 12 Dec 2017, Loeffler, Martin wrote:
Dear Bruce,
thanks for the quick reply! You are right, of course. I do find errors in lh.inflated.nofix. I have attached a screenshot of the biggest errors I found.. Can you maybe guide me a little how to fix the issue? Do I just cancel the running recon-all process, and set control points and run again? Investing some time in manual editing would be fine as it's a case study...
Thanks for your help, Martin
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Dezember 2017 22:47 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9
cheers Bruce
On Mon, 11 Dec 2017, Loeffler, Martin wrote:
Dear FreeSurfer team,
For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I'm not expecting it to advance.
Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around it?
Thanks,
Martin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin,
I will have to defer to Bruce or Doug regarding the validity of analyzing FreeSurfer output for your subject - although I would not recommend any analysis on the current state of your subject's surfaces. After glancing at your data, I have a few recommendations:
1. You seem to be using an excessive number of control points. Control points are designed for diffuse intensity normalize - using too many control points is unnecessary and possibly counterproductive. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0?highl... for more information on control points. 2. I've noticed that your brainmask.mgz is missing a large portion of your subject's cerebellum. This most likely caused some issues down the recon-all pipeline so you should address this issue first. You can change the watershed value to adjust the brain extraction. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0 for information of fixing a bad skull strip. 3. Since the wm.mgz has done such a poor job of identifying white matter, I would suggest directly editing the wm.mgz. Of course, only edit the wm.mgz after first attempting to use (fewer) control points on a better skull-stripped brainmask.mgz. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for information on editing the wm.mgz.
Best,
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loeffler, Martin martin.loeffler@zi-mannheim.de Sent: Saturday, December 23, 2017 4:26:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Dear Bruce,
Dear Bram,
Thanks a lot for having a look. Unfortunately the left hemisphere is equally important as the right one for our question of interest. With a lot of patience the recon-all has finished and the result looks surprisingly ok. I have additionally re-run it (recon-all -autorecon2-cp -autorecon3 -s Case) after setting control points to correct errors in the wm.mgz. Some errors were corrected, but not all. Next I would like to correct the surfaces.
My questions:
- I know that recon-all is not designed for such a subject. But is there any argument against continuing the analysis now?
- What can I do for those errors where the wm.mgz is still false, despite control points?
I have uploaded the respective files.
Best,
Martin
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram Ryder Gesendet: Mittwoch, 13. Dezember 2017 23:23 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin,
We've taken a look at the scans you uploaded, and unfortunately it won't be possible to run the standard recon-all on your subject. Recon-all is not designed to work on scans with such large lesions. If you are interested, there may be a way to generate a reasonable model of the right hemisphere.
Best,
Bram
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Loeffler, Martin <martin.loeffler@zi-mannheim.demailto:martin.loeffler@zi-mannheim.de> Sent: Tuesday, December 12, 2017 11:57:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Dear Bruce, I have uploaded the respective files. If there is something missing let me know. Cheers, Martin
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 12. Dezember 2017 16:35 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
we are happy to take a look, but can't really tell much from a screenshot. Feel free to upload the subject to our ftp site if you want us to help
cheers Bruce
On Tue, 12 Dec 2017, Loeffler, Martin wrote:
Dear Bruce,
thanks for the quick reply! You are right, of course. I do find errors in lh.inflated.nofix. I have attached a screenshot of the biggest errors I found.. Can you maybe guide me a little how to fix the issue? Do I just cancel the running recon-all process, and set control points and run again? Investing some time in manual editing would be fine as it's a case study...
Thanks for your help, Martin
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Dezember 2017 22:47 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9
cheers Bruce
On Mon, 11 Dec 2017, Loeffler, Martin wrote:
Dear FreeSurfer team,
For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I'm not expecting it to advance.
Following this post: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around it?
Thanks,
Martin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Diamond, Bram Ryder -
Loeffler, Martin