Hi everyone,
I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also applies to moving to v 6 when it is released).
If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted? Or does this "shortcut" not do what I think it does?
Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits?
Thank you again for the fantastic tools!
Kx
Thank you Michael!
So - just to be super sure I'm on the same page here. If I've run a subject using 5.3 I take that same subject directory (after backing it up somewhere) and then run the dev version of recon-all with the -all flag. After it's completed I (should - contingent on checking again as you recommend) have a well edited subject who can now be reported as having been processed with the dev version, right?
Thanks again Kx
On 22 June 2016 at 14:48, Harms, Michael mharms@wustl.edu wrote:
Hi, You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits. Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory under the new FS version.
And, if you want to preserve your results under FS 5.3, then you should make a copy of those results before rerunning recon-all.
cheers, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Kirstie Whitaker kw401@cam.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, June 22, 2016 at 1:28 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Quality control with different pipelines
Hi everyone,
I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also applies to moving to v 6 when it is released).
If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted? Or does this "shortcut" not do what I think it does?
Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits?
Thank you again for the fantastic tools!
Kx
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
*Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
*Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Brilliant - many thanks.
Kx
On 22 June 2016 at 14:57, Harms, Michael mharms@wustl.edu wrote:
Yes on all fronts.
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Kirstie Whitaker kw401@cam.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, June 22, 2016 at 8:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quality control with different pipelines
Thank you Michael!
So - just to be super sure I'm on the same page here. If I've run a subject using 5.3 I take that same subject directory (after backing it up somewhere) and then run the dev version of recon-all with the -all flag. After it's completed I (should - contingent on checking again as you recommend) have a well edited subject who can now be reported as having been processed with the dev version, right?
Thanks again Kx
On 22 June 2016 at 14:48, Harms, Michael mharms@wustl.edu wrote:
Hi, You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits. Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory under the new FS version.
And, if you want to preserve your results under FS 5.3, then you should make a copy of those results before rerunning recon-all.
cheers, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Kirstie Whitaker kw401@cam.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, June 22, 2016 at 1:28 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Quality control with different pipelines
Hi everyone,
I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also applies to moving to v 6 when it is released).
If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted? Or does this "shortcut" not do what I think it does?
Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits?
Thank you again for the fantastic tools!
Kx
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
*Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
*Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Kirstie Whitaker, PhD Research Associate
Department of Psychiatry University of Cambridge
*Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB
*Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
-
Harms, Michael -
Kirstie Whitaker