I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time.
Cheers,
-Morgan
Hi Morgan,
yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall.
cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote:
I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time.
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old recon-all output?
Cheers,
-Morgan
Bruce Fischl wrote:
Hi Morgan,
yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall.
cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote:
I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time.
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
rerun mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote:
Hi Bruce,
These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old recon-all output?
Cheers,
-Morgan
Bruce Fischl wrote:
Hi Morgan,
yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall.
cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote:
I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time.
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Bruce,
From the ReconAllDevTable I see
mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi
which will produce new ?h.thickness, area, curv, white and pial surfaces as well. Are these the options I should rerun with?
Cheers,
-Morgan
Bruce Fischl wrote:
rerun mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote:
Hi Bruce,
These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old recon-all output?
Cheers,
-Morgan
Bruce Fischl wrote:
Hi Morgan,
yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall.
cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote:
I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time.
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Morgan,
Generally you would want to use:
recon-all -finalsurfs -s <subj> -hemi <hemi>
which will ensure calling mris_make_surfaces with the right parameters.
Nick
On Wed, 2007-07-25 at 16:59 +0100, Morgan Hough wrote:
Thanks Bruce,
From the ReconAllDevTable I see
mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi
which will produce new ?h.thickness, area, curv, white and pial surfaces as well. Are these the options I should rerun with?
Cheers,
-Morgan
Bruce Fischl wrote:
rerun mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote:
Hi Bruce,
These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old recon-all output?
Cheers,
-Morgan
Bruce Fischl wrote:
Hi Morgan,
yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall.
cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote:
I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time.
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, I think -aseg is the default now, so you don't need to specify it (it uses the aseg to figure out what's cortex and what's not) On Wed, 25 Jul 2007, Morgan Hough wrote:
Thanks Bruce,
From the ReconAllDevTable I see
mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi
which will produce new ?h.thickness, area, curv, white and pial surfaces as well. Are these the options I should rerun with?
Cheers,
-Morgan
Bruce Fischl wrote:
rerun mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote:
Hi Bruce,
These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old recon-all output?
Cheers,
-Morgan
Bruce Fischl wrote:
Hi Morgan,
yes, that seems reasonable. You can start with the ?h.cortex.label and subdivide it into sulcal and gyral to avoid the medial wall.
cheers, Bruce On Tue, 24 Jul 2007, Morgan Hough wrote:
I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time.
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Morgan Hough -
Nick Schmansky