on one group of subjects i ran "recon-all -all -clean -wsthresh n", which according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags includes what "-clean-bm" does.
on the other group i ran "recon-all -all -wshthresh n" after deleting everything and converting them from raw invol data to freesurfer format again. as i understand it, "-clean" is not required because no previous data is there to be overwritten/cleaned.
to prevent confusion, i am not comparing these two groups, it's just that we have a separate group of subjects of which whe don't have the raw data, so i had to use -clean. i compared using "-wsthresh" against not using it in a few subjects from both groups. as far as the "-clean" flags are concerned, there is no bug: they do change the result, so i assume the previous volume is overwritten as it should, however the results are no improvement (see screenshots).
On Mon, 12 Apr 2010 15:54:47 -0400 (EDT) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Andreas, I'm not very clear on your response. Did using -clean-bm on the subjects you had used -clean on when running with -wsthresh, change the skull strip for the better?
when you ran it on the already clean data set, you said using -wsthresh 0 still did not get a good skull strip? Allison
--
On Fri, 9 Apr 2010, Andreas Berger wrote:
Sorry for the slow response,
yes, the "-clean" flag should imply "-clean-bm" (among others)
besides, on one group of the subjects i ran "recon-all -all -wsthresh n" after converting them from invol data again, everything from scratch (no cleaning required), with the same result. also, the fact that the surfaces did change (however not as i hoped) indicates that it's not a problem with the flags.
On Wed, 31 Mar 2010 13:01:32 -0400 (EDT) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Andreas, Did using -clean-bm work? Allison
--
On Mon, 29 Mar 2010, Allison Stevens wrote:
Andreas, Let me know how this turns out. The response you got about the command (using -clean-bm) is correct but since you used -clean, that should have worked just as well. Can you please let me know if using -clean-bm does anything differently from -clean? If so, we'll have to investigate this as a potential bug. Thanks, Allison
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thanks, Andreas. That clears it up.
There was no attachment though. Can you send me the screenshots?
thank you for replying,
i reattached the screenshots. they were in my first mail but i think i broke the thread by replying to the wrong adress once, sorry. screenshot 1 is result of "recon-all -all", screenshot 2 is result of "recon-all -all -wsthresh 0". what's weird is that next to the left hemisphere there's some skull left that wasn't even there with default settings.
On Tue, 13 Apr 2010 08:20:40 -0400 (EDT) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Thanks, Andreas. That clears it up.
There was no attachment though. Can you send me the screenshots?
--
On Tue, 13 Apr 2010, Andreas Berger wrote:
on one group of subjects i ran "recon-all -all -clean -wsthresh n", which according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags includes what "-clean-bm" does.
on the other group i ran "recon-all -all -wshthresh n" after deleting everything and converting them from raw invol data to freesurfer format again. as i understand it, "-clean" is not required because no previous data is there to be overwritten/cleaned.
to prevent confusion, i am not comparing these two groups, it's just that we have a separate group of subjects of which whe don't have the raw data, so i had to use -clean. i compared using "-wsthresh" against not using it in a few subjects from both groups. as far as the "-clean" flags are concerned, there is no bug: they do change the result, so i assume the previous volume is overwritten as it should, however the results are no improvement (see screenshots).
On Mon, 12 Apr 2010 15:54:47 -0400 (EDT) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Andreas, I'm not very clear on your response. Did using -clean-bm on the subjects you had used -clean on when running with -wsthresh, change the skull strip for the better?
when you ran it on the already clean data set, you said using -wsthresh 0 still did not get a good skull strip? Allison
--
On Fri, 9 Apr 2010, Andreas Berger wrote:
Sorry for the slow response,
yes, the "-clean" flag should imply "-clean-bm" (among others)
besides, on one group of the subjects i ran "recon-all -all -wsthresh n" after converting them from invol data again, everything from scratch (no cleaning required), with the same result. also, the fact that the surfaces did change (however not as i hoped) indicates that it's not a problem with the flags.
On Wed, 31 Mar 2010 13:01:32 -0400 (EDT) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Andreas, Did using -clean-bm work? Allison
--
On Mon, 29 Mar 2010, Allison Stevens wrote:
Andreas, Let me know how this turns out. The response you got about the command (using -clean-bm) is correct but since you used -clean, that should have worked just as well. Can you please let me know if using -clean-bm does anything differently from -clean? If so, we'll have to investigate this as a potential bug. Thanks, Allison
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
thank you for replying,
i reattached the screenshots. they were in my first mail but i think i broke the thread by replying to the wrong adress once, sorry. screenshot 1 is result of "recon-all -all", screenshot 2 is result of "recon-all -all -wsthresh 0". what's weird is that next to the left hemisphere there's some skull left that wasn't even there with default settings.
EDIT: forgot to attach the screenshots, sorry once more...
On Tue, 13 Apr 2010 08:20:40 -0400 (EDT) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Thanks, Andreas. That clears it up.
There was no attachment though. Can you send me the screenshots?
--
On Tue, 13 Apr 2010, Andreas Berger wrote:
on one group of subjects i ran "recon-all -all -clean -wsthresh n", which according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags includes what "-clean-bm" does.
on the other group i ran "recon-all -all -wshthresh n" after deleting everything and converting them from raw invol data to freesurfer format again. as i understand it, "-clean" is not required because no previous data is there to be overwritten/cleaned.
to prevent confusion, i am not comparing these two groups, it's just that we have a separate group of subjects of which whe don't have the raw data, so i had to use -clean. i compared using "-wsthresh" against not using it in a few subjects from both groups. as far as the "-clean" flags are concerned, there is no bug: they do change the result, so i assume the previous volume is overwritten as it should, however the results are no improvement (see screenshots).
On Mon, 12 Apr 2010 15:54:47 -0400 (EDT) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Andreas, I'm not very clear on your response. Did using -clean-bm on the subjects you had used -clean on when running with -wsthresh, change the skull strip for the better?
when you ran it on the already clean data set, you said using -wsthresh 0 still did not get a good skull strip? Allison
--
On Fri, 9 Apr 2010, Andreas Berger wrote:
Sorry for the slow response,
yes, the "-clean" flag should imply "-clean-bm" (among others)
besides, on one group of the subjects i ran "recon-all -all -wsthresh n" after converting them from invol data again, everything from scratch (no cleaning required), with the same result. also, the fact that the surfaces did change (however not as i hoped) indicates that it's not a problem with the flags.
On Wed, 31 Mar 2010 13:01:32 -0400 (EDT) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Andreas, Did using -clean-bm work? Allison
--
On Mon, 29 Mar 2010, Allison Stevens wrote:
Andreas, Let me know how this turns out. The response you got about the command (using -clean-bm) is correct but since you used -clean, that should have worked just as well. Can you please let me know if using -clean-bm does anything differently from -clean? If so, we'll have to investigate this as a potential bug. Thanks, Allison
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Your surfaces look fine (at least in that slice). Why do you feel you need to strip away more skull?
freesurfer@nmr.mgh.harvard.edu
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Allison Stevens -
Andreas Berger