Re: [Freesurfer] mris_divide_parcellation for white matter
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
fis...@nmr.mgh.harvard.edu mailto:fis...@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
fis...@nmr.mgh.harvard.edu mailto:fis...@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
fis...@nmr.mgh.harvard.edu
mailto:fis...@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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Re: [Freesurfer] mris_divide_parcellation for white matter
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 gr...@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
fis...@nmr.mgh.harvard.edu mailto:fis...@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
fis...@nmr.mgh.harvard.edu mailto:fis...@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
fis...@nmr.mgh.harvard.edu
mailto:fis...@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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The information in this e-mail is intended only for
the person to whom
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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
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e-mail was sent to you
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but does not contain patient information, please
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Re: [Freesurfer] mris_divide_parcellation for white matter
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
gr...@nmr.mgh.harvard.edu mailto:gr...@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
fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
Re: [Freesurfer] mris_divide_parcellation for white matter
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 gr...@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
gr...@nmr.mgh.harvard.edu mailto:gr...@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
fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
Re: [Freesurfer] mris_divide_parcellation for white matter
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 corinna...@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
gr...@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
gr...@nmr.mgh.harvard.edu mailto:gr...@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
fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@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
Re: [Freesurfer] mris_divide_parcellation for white matter
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 fis...@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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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
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but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
___
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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.
Re: [Freesurfer] mris_divide_parcellation for white matter
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 fis...@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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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.
Re: [Freesurfer] mris_divide_parcellation for white matter
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 fis...@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 fis...@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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Re: [Freesurfer] mris_divide_parcellation for white matter
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 fis...@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
fis...@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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HelpLine at
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Re: [Freesurfer] mris_divide_parcellation for white matter
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 fis...@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 fis...@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
fis...@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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addressed. If you believe this e-mail was sent to
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contains patient information, please contact the
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HelpLine at
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Re: [Freesurfer] mris_divide_parcellation for white matter
I figured it out. Thanks for your help!
On Wed, Jul 2, 2014 at 2:00 PM, Corinna Bauer corinna...@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 fis...@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
fis...@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
fis...@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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addressed. If you believe this e-mail was sent to
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e-mail
contains patient information, please contact the
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HelpLine at
http://www.partners.org/complianceline . If the
e-mail was sent to you
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but does not contain patient information, please
contact the sender
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Re: [Freesurfer] mris_divide_parcellation for white matter
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 fis...@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
fis...@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
fis...@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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[Freesurfer] mris_divide_parcellation for white matter
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.
Re: [Freesurfer] mris_divide_parcellation for white matter
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.
