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We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution
We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi there, Here's an issue that keeps coming up:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh
Could you help with this? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, February 17, 2022 6:06 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution
We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Cp3K814P0MwvELKUWzLxwTUY2oX1XGj8_uwarvyLEVGANH...
Hi Anna
Where did you install FreeSurfer? That is where the env variable FREESURFER_HOME should point. What does:
ls $FREESURFER_HOME
show you?
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Pusok, Anna Sent: Thursday, February 17, 2022 6:40 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution Hi there, Here's an issue that keeps coming up:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh
Could you help with this? ________________________________ 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 Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Sent: Thursday, February 17, 2022 6:06 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6. On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it's largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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- Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. - ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent). white.preaparc does NOT. - We noticed that the placement is very stubborn and we were not able to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either.
Is there any way we can overcome this stubbornness?
Many thanks! Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use CautionWe have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1BhcjfvnDAXHKeDR6R-iodPMLY3xi6xzTIkDcLTzdfO3AL0...
Hi Edan
Sometimes control points can be more effective than editing the wm, particularly if the intensities in that region are not what we expect (like if the wm and gm are darker than what we try to set them to). Can you post an image or two?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Edan Daniel Sent: Thursday, February 17, 2022 6:51 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
External Email - Use Caution
* Different data, same pipeline. In v6 our changes were included in the final white surface segmentation, whereas in v7 they are overwritten during the placement 'refining'. * ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent). white.preaparc does NOT. * We noticed that the placement is very stubborn and we were not able to overcome this. Methods like manually editing the wm surface worked well with v6 and do not work now with v7. We have also tried editing the filled.mgz with v7.2 following the new tutorial, and that did not work either. Is there any way we can overcome this stubbornness?
Many thanks! Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: The edits you are making only change the initial surface; the surface placement then refines the placement. Sometimes the surface placement can be quite stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent). Also check the the white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different data? The surface placement has not changed that much since v6. On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!! Edan, Braindevlab@Princeton
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Edan Daniel -
Fischl, Bruce -
Pusok, Anna