Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
Thank you for the help and for getting back to me,
After using the custom-fill option and labelling the central sulcus (yellow), I've been running the following code: "mris_register -L subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif subject/surf/?h.sphere.reg".
Which is followed by "mris_ca_label subject ?h subject/surf/?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs subject/label/?h.aparc.a2009s.annot" or "recon-all -make all -subject". For some reason, I don't see any difference in the subject Destrieux-labelling (the incorrect shift is still there) and I suspect that I'm not doing this correctly. Would it be possible for you to check if I'm using the wrong syntax or if I might have missed out on some parts necessary for this solution to work?
Kind regards,
Carl
What is the output of the first command? And if you bring up the ?h.sphere.reg does it align better with the atlas? You can use mrisp_paint or just look at fsaverage on the sphere
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Trolle, Carl Sent: Wednesday, August 3, 2022 9:25 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
Thank you for the help and for getting back to me,
After using the custom-fill option and labelling the central sulcus (yellow), I've been running the following code: "mris_register -L subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif subject/surf/?h.sphere.reg".
Which is followed by "mris_ca_label subject ?h subject/surf/?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs subject/label/?h.aparc.a2009s.annot" or "recon-all -make all -subject". For some reason, I don't see any difference in the subject Destrieux-labelling (the incorrect shift is still there) and I suspect that I'm not doing this correctly. Would it be possible for you to check if I'm using the wrong syntax or if I might have missed out on some parts necessary for this solution to work?
Kind regards,
Carl
Sorry, been trying to get this right for some time before getting back to you, but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for the original, processed and the fsaverage-subjects with the destrieux-annotation. To me, it looks slightly worse after the mris_register command. Not sure that I've managed correctly with the mrisp_paint (mrisp_paint $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif surf/?h.sphere.reg ?h.sulc_test) but attaching a screenshot from there as well.
Would be happy to know what I could alter to get it more accurate!
Kind regards,
Carl
Yes, definitely something wrong. For the paint you want to specify which frame in the tiff with #3 I believe (so $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#3). We store information in 3-frame sets, with means, variances and dofs in that order for each of inflated, sulc and curv. So what you are showing is the inflated curvature whereas what you probably want is the sulc. Something also wrong with the registration though. Can you bounce that command line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Trolle, Carl Sent: Tuesday, August 9, 2022 12:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
Sorry, been trying to get this right for some time before getting back to you, but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for the original, processed and the fsaverage-subjects with the destrieux-annotation. To me, it looks slightly worse after the mris_register command. Not sure that I've managed correctly with the mrisp_paint (mrisp_paint $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif surf/?h.sphere.reg ?h.sulc_test) but attaching a screenshot from there as well.
Would be happy to know what I could alter to get it more accurate!
Kind regards,
Carl
I apologize but I'm not familiar with the term bounce; do you want me to re-run the mrisp_paint-command but with specifying the optional #3 parameter for the <template_fname> argument? The sphere and the inflated surface look more similar but still seem to differ from the fsaverage that way.
Kind regards,
Carl
________________________________ From: Trolle, Carl CTROLLE@PARTNERS.ORG Sent: 09 August 2022 12:37 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
Sorry, been trying to get this right for some time before getting back to you, but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for the original, processed and the fsaverage-subjects with the destrieux-annotation. To me, it looks slightly worse after the mris_register command. Not sure that I've managed correctly with the mrisp_paint (mrisp_paint $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif surf/?h.sphere.reg ?h.sulc_test) but attaching a screenshot from there as well.
Would be happy to know what I could alter to get it more accurate!
Kind regards,
Carl
You should paint the template onto the sphere that is registered (i.e. sphere.reg), at which point it should look similar to the individual subject's sulc pattern.
And by "bounce" I just meant send it to me Cheers, Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Trolle, Carl Sent: Tuesday, August 9, 2022 6:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
I apologize but I'm not familiar with the term bounce; do you want me to re-run the mrisp_paint-command but with specifying the optional #3 parameter for the <template_fname> argument? The sphere and the inflated surface look more similar but still seem to differ from the fsaverage that way.
Kind regards,
Carl
________________________________ From: Trolle, Carl <CTROLLE@PARTNERS.ORGmailto:CTROLLE@PARTNERS.ORG> Sent: 09 August 2022 12:37 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
Sorry, been trying to get this right for some time before getting back to you, but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for the original, processed and the fsaverage-subjects with the destrieux-annotation. To me, it looks slightly worse after the mris_register command. Not sure that I've managed correctly with the mrisp_paint (mrisp_paint $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif surf/?h.sphere.reg ?h.sulc_test) but attaching a screenshot from there as well.
Would be happy to know what I could alter to get it more accurate!
Kind regards,
Carl
freesurfer@nmr.mgh.harvard.edu
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Fischl, Bruce -
Trolle, Carl