hello, I was wondering if it was possible to use mris_divide_parcellation on white matter labels.
Thanks,
Corinna
Hi Corinna
not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want.
cheers Bruce
On Tue, 1 Jul 2014, Corinna Bauer wrote:
hello, I was wondering if it was possible to use mris_divide_parcellation on white matter labels.
Thanks,
Corinna
Hi Bruce,
I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split
After the slice labeling, I get the following:
Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white
Any suggestions?
Thanks, Corinna
On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Corinna
not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want.
cheers Bruce
On Tue, 1 Jul 2014, Corinna Bauer wrote:
hello, I was wondering if it was possible to use mris_divide_parcellation on
white
matter labels.
Thanks,
Corinna
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Hi Corinna
you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...)
cheers Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
Hi Bruce,
I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split
After the slice labeling, I get the following:
Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white
Any suggestions?
Thanks, Corinna
On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Corinna
not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want. cheers Bruce On Tue, 1 Jul 2014, Corinna Bauer wrote: > hello, > I was wondering if it was possible to use mris_divide_parcellation on white > matter labels. > > Thanks, > > Corinna > >
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And then for breaking the individual labels up, would mri_extract_label be the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Corinna
you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...)
cheers Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
Hi Bruce,
I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split
After the slice labeling, I get the following:
Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white
Any suggestions?
Thanks, Corinna
On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Corinna
not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want. cheers Bruce On Tue, 1 Jul 2014, Corinna Bauer wrote: > hello, > I was wondering if it was possible to use mris_divide_parcellation on white > matter labels. > > Thanks, > > Corinna > >
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yes, or mri_binarize --match
cheers Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
And then for breaking the individual labels up, would mri_extract_label be the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Corinna
you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: Hi Bruce, I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split After the slice labeling, I get the following: Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white Any suggestions? Thanks, Corinna On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Corinna not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want. cheers Bruce On Tue, 1 Jul 2014, Corinna Bauer wrote: > hello, > I was wondering if it was possible to use mris_divide_parcellation on white > matter labels. > > Thanks, > > Corinna > > _______________________________________________ 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.
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Whereby the label name is derived from which, the GM labels? i.e. lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, or mri_binarize --match
cheers Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
And then for breaking the individual labels up, would mri_extract_label be
the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Corinna
you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: Hi Bruce, I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split After the slice labeling, I get the following: Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white Any suggestions? Thanks, Corinna On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Corinna not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want. cheers Bruce On Tue, 1 Jul 2014, Corinna Bauer wrote: > hello, > I was wondering if it was possible to use mris_divide_parcellation on white > matter labels. > > Thanks, > > Corinna > > _______________________________________________ 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.
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I figured it out. Thanks for your help!
On Wed, Jul 2, 2014 at 2:00 PM, Corinna Bauer corinnab83@gmail.com wrote:
Whereby the label name is derived from which, the GM labels? i.e. lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, or mri_binarize --match
cheers Bruce
On Wed, 2 Jul 2014, Corinna Bauer wrote:
And then for breaking the individual labels up, would mri_extract_label
be the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Corinna
you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: Hi Bruce, I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split After the slice labeling, I get the following: Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white Any suggestions? Thanks, Corinna On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Corinna not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want. cheers Bruce On Tue, 1 Jul 2014, Corinna Bauer wrote: > hello, > I was wondering if it was possible to use mris_divide_parcellation on white > matter labels. > > Thanks, > > Corinna > > _______________________________________________ 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.
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yes On Wed, 2 Jul 2014, Corinna Bauer wrote:
Whereby the label name is derived from which, the GM labels? i.e. lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: yes, or mri_binarize --match
cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: And then for breaking the individual labels up, would mri_extract_label be the best option? On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Corinna you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: Hi Bruce, I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split After the slice labeling, I get the following: Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white Any suggestions? Thanks, Corinna On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Corinna not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want. cheers Bruce On Tue, 1 Jul 2014, Corinna Bauer wrote: > hello, > I was wondering if it was possible to use mris_divide_parcellation on white > matter labels. > > Thanks, > > Corinna > > _______________________________________________ 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 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.
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The name of which label?
On 07/02/2014 02:00 PM, Corinna Bauer wrote:
Whereby the label name is derived from which, the GM labels? i.e. lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
yes, or mri_binarize --match cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: And then for breaking the individual labels up, would mri_extract_label be the best option? On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Corinna you need to give some output extension so it knows what file type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: Hi Bruce, I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split After the slice labeling, I get the following: Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white Any suggestions? Thanks, Corinna On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Corinna not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want. cheers Bruce On Tue, 1 Jul 2014, Corinna Bauer wrote: > hello, > I was wondering if it was possible to use mris_divide_parcellation on white > matter labels. > > Thanks, > > Corinna > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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the new white matter divided labels. I was not able to extract the labels using the matching grey matter names, but was able to do so using the label number seen in the tools from tkmedit. Seeing as there are over 100 labels, is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The name of which label?
On 07/02/2014 02:00 PM, Corinna Bauer wrote:
Whereby the label name is derived from which, the GM labels? i.e. lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
yes, or mri_binarize --match cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: And then for breaking the individual labels up, would mri_extract_label be the best option? On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Corinna you need to give some output extension so it knows whatfile
type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) cheers Bruce On Wed, 2 Jul 2014, Corinna Bauer wrote: Hi Bruce, I am trying to do just that using the following command line: mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split After the slice labeling, I get the following: Used brute-force search on 872 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided unknown file type for file (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) subject = FSH_09062013 annotation = wmdivided hemi = lh outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels surface = white Any suggestions? Thanks, Corinna On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Corinna not really, as that is a surface-based utility. You could divide the cortical labels and then recrate the wmparc from it, which might do what you want. cheers Bruce On Tue, 1 Jul 2014, Corinna Bauer wrote: > hello, > I was wondering if it was possible to use mris_divide_parcellation on white > matter labels. > > Thanks, > > Corinna > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Right, this is going to be a problem. One of the things you can do is to use the --ctab option of mri_annotation2label to create a colortable, something like
mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh --annotation newannot --outdir junk
You can do this for both hemis, then concatenate them together along with the ROIs from the subcortical. Then take the two new.?h.ctabs and add 3000 to the indices and change the name to be wm- instead of ctx- and include those in the new ctab
clunky, but it should work
doug
On 07/07/2014 12:29 PM, Corinna Bauer wrote:
the new white matter divided labels. I was not able to extract the labels using the matching grey matter names, but was able to do so using the label number seen in the tools from tkmedit. Seeing as there are over 100 labels, is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The name of which label? On 07/02/2014 02:00 PM, Corinna Bauer wrote: > Whereby the label name is derived from which, the GM labels? i.e. > lh.rostralmiddlefrontal_div3 > > > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > yes, or mri_binarize --match > > > cheers > Bruce > > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > And then for breaking the individual labels up, would > mri_extract_label be > the best option? > > > On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > wrote: > Hi Corinna > > you need to give some output extension so it knows what file > type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) > > cheers > Bruce > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > Hi Bruce, > > I am trying to do just that using the following > command line: > mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm > --rip-unknown --volmask > --o ${subj_dir}/mri/wmdivided --annot aparc.split > > After the slice labeling, I get the following: > > Used brute-force search on 872 voxels > Fixing Parahip LH WM > Found 0 clusters > Fixing Parahip RH WM > Found 0 clusters > Writing output aseg to > > /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided > unknown file type for file > > (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) > subject = FSH_09062013 > annotation = wmdivided > hemi = lh > outdir = > > /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels > surface = white > > Any suggestions? > > Thanks, > Corinna > > > > On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > wrote: > Hi Corinna > > not really, as that is a surface-based > utility. You could divide > the > cortical labels and then recrate the wmparc > from it, which might > do what > you want. > > cheers > Bruce > > > On Tue, 1 Jul 2014, Corinna > Bauer wrote: > > > hello, > > I was wondering if it was possible to use > mris_divide_parcellation on white > > matter labels. > > > > Thanks, > > > > Corinna > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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great, thanks! I'll give that a try and let you know how it goes.
On Mon, Jul 7, 2014 at 12:50 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Right, this is going to be a problem. One of the things you can do is to use the --ctab option of mri_annotation2label to create a colortable, something like
mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh --annotation newannot --outdir junk
You can do this for both hemis, then concatenate them together along with the ROIs from the subcortical. Then take the two new.?h.ctabs and add 3000 to the indices and change the name to be wm- instead of ctx- and include those in the new ctab
clunky, but it should work
doug
On 07/07/2014 12:29 PM, Corinna Bauer wrote:
the new white matter divided labels. I was not able to extract the labels using the matching grey matter names, but was able to do so using the label number seen in the tools from tkmedit. Seeing as there are over 100 labels, is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The name of which label? On 07/02/2014 02:00 PM, Corinna Bauer wrote: > Whereby the label name is derived from which, the GM labels? i.e. > lh.rostralmiddlefrontal_div3 > > > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > yes, or mri_binarize --match > > > cheers > Bruce > > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > And then for breaking the individual labels up, would > mri_extract_label be > the best option? > > > On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > wrote: > Hi Corinna > > you need to give some output extension so it knows what file > type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) > > cheers > Bruce > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > Hi Bruce, > > I am trying to do just that using the following > command line: > mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm > --rip-unknown --volmask > --o ${subj_dir}/mri/wmdivided --annot aparc.split > > After the slice labeling, I get the following: > > Used brute-force search on 872 voxels > Fixing Parahip LH WM > Found 0 clusters > Fixing Parahip RH WM > Found 0 clusters > Writing output aseg to > > /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided > unknown file type for file > > (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) > subject = FSH_09062013 > annotation = wmdivided > hemi = lh > outdir = > > /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels > surface = white > > Any suggestions? > > Thanks, > Corinna > > > > On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > wrote: > Hi Corinna > > not really, as that is a surface-based > utility. You could divide > the > cortical labels and then recrate the wmparc > from it, which might > do what > you want. > > cheers > Bruce > > > On Tue, 1 Jul 2014, Corinna > Bauer wrote: > > > hello, > > I was wondering if it was possible to use > mris_divide_parcellation on white > > matter labels. > > > > Thanks, > > > > Corinna > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 contactthe
> 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 mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 contactthe
> sender > and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Doug, that worked very well, thanks.
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown --volmask --wmparc-dmax 2 --o ${subj_dir}/mri/wmdivided.nii --annot aparc.split mri_annotation2label --ctab new.rh.ctab --subject ${subject} --hemi rh --annotation aparc.split --outdir ${subj_dir}/smaller_labels mri_extract_label ${subj_dir}/mri/wmdivided.nii 3001 ${subj_dir}/smaller_labels/wm-lh-bankssts.nii
On Mon, Jul 7, 2014 at 1:05 PM, Corinna Bauer corinnab83@gmail.com wrote:
great, thanks! I'll give that a try and let you know how it goes.
On Mon, Jul 7, 2014 at 12:50 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Right, this is going to be a problem. One of the things you can do is to use the --ctab option of mri_annotation2label to create a colortable, something like
mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh --annotation newannot --outdir junk
You can do this for both hemis, then concatenate them together along with the ROIs from the subcortical. Then take the two new.?h.ctabs and add 3000 to the indices and change the name to be wm- instead of ctx- and include those in the new ctab
clunky, but it should work
doug
On 07/07/2014 12:29 PM, Corinna Bauer wrote:
the new white matter divided labels. I was not able to extract the labels using the matching grey matter names, but was able to do so using the label number seen in the tools from tkmedit. Seeing as there are over 100 labels, is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The name of which label? On 07/02/2014 02:00 PM, Corinna Bauer wrote: > Whereby the label name is derived from which, the GM labels? i.e. > lh.rostralmiddlefrontal_div3 > > > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > yes, or mri_binarize --match > > > cheers > Bruce > > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > And then for breaking the individual labels up, would > mri_extract_label be > the best option? > > > On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > wrote: > Hi Corinna > > you need to give some output extension so it knows what file > type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...) > > cheers > Bruce > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > Hi Bruce, > > I am trying to do just that using thefollowing
> command line: > mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm > --rip-unknown --volmask > --o ${subj_dir}/mri/wmdivided --annot aparc.split > > After the slice labeling, I get the following: > > Used brute-force search on 872 voxels > Fixing Parahip LH WM > Found 0 clusters > Fixing Parahip RH WM > Found 0 clusters > Writing output aseg to > > /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided > unknown file type for file > > (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided) > subject = FSH_09062013 > annotation = wmdivided > hemi = lh > outdir = > > /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels > surface = white > > Any suggestions? > > Thanks, > Corinna > > > > On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > wrote: > Hi Corinna > > not really, as that is a surface-based > utility. You could divide > the > cortical labels and then recrate the wmparc > from it, which might > do what > you want. > > cheers > Bruce > > > On Tue, 1 Jul 2014, Corinna > Bauer wrote: > > > hello, > > I was wondering if it was possible to use > mris_divide_parcellation on white > > matter labels. > > > > Thanks, > > > > Corinna > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 contactthe
> 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 mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 contactthe
> sender > and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 sentto
> you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 -
Corinna Bauer -
Douglas N Greve