Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I follow
the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer corinna...@gmail.com wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
you'll need to figure it out from the volume itself by loading the seg
with both -seg and -aux. When you find the label you want, click on it
and the aux value in the control window will tell you what the id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there is a label number. Where would I find
this for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will
need to then put them into diffusion and resting state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using bbregister,
tkregister2, mri_vol2vol (using the inverse registration from
bbregister to put the T1 into diffusion space), mri_extract_label
(extract labels from aparc+aseg.mgz), and then mri_label2vol
(register each of the extracted labels into diffusion space).
Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
wrote:
Exactly what you have described won't work very well because
it would be
in the volume. I would divide up the parcellations in
fsaverage space
like you've done, then map the parcellation to each subject
using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the
Desikan
atlas into smaller ROIs, but will need the new ROIs to be
consistent
between subjects.
Can I achieve this if I register each subject to fsaverage
space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for
the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu mailto:gr...@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/
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The information in this e-mail is intended only for the
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log
file for an example command line that generates wmparc.mgz
doug
On 04/10/2014 09:52 AM, Corinna Bauer wrote:
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I
follow the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer corinna...@gmail.com
mailto:corinna...@gmail.com wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
you'll need to figure it out from the volume itself by loading
the seg
with both -seg and -aux. When you find the label you want,
click on it
and the aux value in the control window will tell you what the
id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there is a label number. Where
would I find
this for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1
space, I will
need to then put them into diffusion and resting state
space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister,
tkregister2, mri_vol2vol (using the inverse
registration from
bbregister to put the T1 into diffusion space),
mri_extract_label
(extract labels from aparc+aseg.mgz), and then
mri_label2vol
(register each of the extracted labels into diffusion
space).
Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very
well because
it would be
in the volume. I would divide up the parcellations in
fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the
Desikan
atlas into smaller ROIs, but will need the new
ROIs to be
consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage
space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for
the label
number?
(i.e. mri_extract_label
${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Hi Doug,
Following the example in recon-all.log, I tried this: mri_aparc2aseg --s
FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o
mri/wmdivided.mgz --annot aparc.split
and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1): could not
open file
On Thu, Apr 10, 2014 at 11:11 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log
file for an example command line that generates wmparc.mgz
doug
On 04/10/2014 09:52 AM, Corinna Bauer wrote:
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I
follow the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer corinna...@gmail.com
mailto:corinna...@gmail.com wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
wrote:
you'll need to figure it out from the volume itself by loading
the seg
with both -seg and -aux. When you find the label you want,
click on it
and the aux value in the control window will tell you what the
id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there is a label number. Where
would I find
this for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1
space, I will
need to then put them into diffusion and resting state
space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister,
tkregister2, mri_vol2vol (using the inverse
registration from
bbregister to put the T1 into diffusion space),
mri_extract_label
(extract labels from aparc+aseg.mgz), and then
mri_label2vol
(register each of the extracted labels into diffusion
space).
Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very
well because
it would be
in the volume. I would divide up the parcellations in
fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the
Desikan
atlas into smaller ROIs, but will need the new
ROIs to be
consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage
space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for
the label
number?
(i.e. mri_extract_label
${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
no, I was in subjects_dir. Updated the command to this and it works now.
thanks.
mri_aparc2aseg --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown
--volmask --o FGH_09112013/mri/wmdivided.mgz --annot aparc.split
On Thu, Apr 10, 2014 at 11:24 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Are you in the folder just above the mri folder?
On 04/10/2014 11:20 AM, Corinna Bauer wrote:
Hi Doug,
Following the example in recon-all.log, I tried this: mri_aparc2aseg
--s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o
mri/wmdivided.mgz --annot aparc.split
and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1):
could not open file
On Thu, Apr 10, 2014 at 11:11 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
Use mri_aparc2aseg with the --labelwm option. Look in the
recon-all.log
file for an example command line that generates wmparc.mgz
doug
On 04/10/2014 09:52 AM, Corinna Bauer wrote:
For creating corresponding wm segmentations to the rois derived
from
mris_divide_parcellation, should mri_aparc2wmseg be used or should
I
follow the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer
corinna...@gmail.com mailto:corinna...@gmail.com
mailto:corinna...@gmail.com mailto:corinna...@gmail.com
wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
you'll need to figure it out from the volume itself by
loading
the seg
with both -seg and -aux. When you find the label you want,
click on it
and the aux value in the control window will tell you
what the
id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there is a label number. Where
would I find
this for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1
space, I will
need to then put them into diffusion and resting
state
space.
I already have scripts that put the parcellations
into
subject-specific diffusion/resting state space
(using
bbregister,
tkregister2, mri_vol2vol (using the inverse
registration from
bbregister to put the T1 into diffusion space),
mri_extract_label
(extract labels from aparc+aseg.mgz), and then
mri_label2vol
(register each of the extracted labels into
diffusion
space).
Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very
well because
it would be
in the volume. I would divide up the
parcellations in
fsaverage space
like you've done, then map the parcellation
to each
subject using
mri_surf2surf (--sval-annot, see example 6)
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
In the mri_extract_label, there is a label number. Where would I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will need to
then put them into diffusion and resting state space.
I already have scripts that put the parcellations into subject-specific
diffusion/resting state space (using bbregister, tkregister2, mri_vol2vol
(using the inverse registration from bbregister to put the T1 into
diffusion space), mri_extract_label (extract labels from aparc+aseg.mgz),
and then mri_label2vol (register each of the extracted labels into
diffusion space). Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Exactly what you have described won't work very well because it would be
in the volume. I would divide up the parcellations in fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the Desikan
atlas into smaller ROIs, but will need the new ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to fsaverage space and
then apply the inverse transform to the divided parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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The information in this e-mail is intended only for the person to whom it
is
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contains patient information, please contact the Partners Compliance
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 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
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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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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I
will need to then put them into diffusion and resting
state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister, tkregister2, mri_vol2vol (using the inverse
registration from bbregister to put the T1 into diffusion
space), mri_extract_label (extract labels from
aparc+aseg.mgz), and then mri_label2vol (register each of
the extracted labels into diffusion space). Would a
similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well
because it would be
in the volume. I would divide up the parcellations
in fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the Desikan
atlas into smaller ROIs, but will need the new
ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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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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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would I find
this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I
will need to then put them into diffusion and resting
state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister, tkregister2, mri_vol2vol (using the inverse
registration from bbregister to put the T1 into diffusion
space), mri_extract_label (extract labels from
aparc+aseg.mgz), and then mri_label2vol (register each of
the extracted labels into diffusion space). Would a
similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well
because it would be
in the volume. I would divide up the parcellations
in fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the Desikan
atlas into smaller ROIs, but will need the new
ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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MGH-NMR Center
gr...@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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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Should I make up my own LUT for the new ROIs that specifies some colour and
label number?
On Wed, Apr 9, 2014 at 10:00 AM, Corinna Bauer corinna...@gmail.com wrote:
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would I find
this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I
will need to then put them into diffusion and resting
state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister, tkregister2, mri_vol2vol (using the inverse
registration from bbregister to put the T1 into diffusion
space), mri_extract_label (extract labels from
aparc+aseg.mgz), and then mri_label2vol (register each of
the extracted labels into diffusion space). Would a
similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well
because it would be
in the volume. I would divide up the parcellations
in fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the Desikan
atlas into smaller ROIs, but will need the new
ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
oh, those should be embedded in the .annot file it creates
On Wed, 9 Apr
2014, Corinna Bauer wrote:
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would
I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space,
I
will need to then put them into diffusion and resting
state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister, tkregister2, mri_vol2vol (using the inverse
registration from bbregister to put the T1 into
diffusion
space), mri_extract_label (extract labels from
aparc+aseg.mgz), and then mri_label2vol (register each
of
the extracted labels into diffusion space). Would a
similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well
because it would be
in the volume. I would divide up the parcellations
in fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the Desikan
atlas into smaller ROIs, but will need the new
ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
you'll need to figure it out from the volume itself by loading the seg
with both -seg and -aux. When you find the label you want, click on it
and the aux value in the control window will tell you what the id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there is a label number. Where would I find
this for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will
need to then put them into diffusion and resting state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using bbregister,
tkregister2, mri_vol2vol (using the inverse registration from
bbregister to put the T1 into diffusion space), mri_extract_label
(extract labels from aparc+aseg.mgz), and then mri_label2vol
(register each of the extracted labels into diffusion space).
Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well because
it would be
in the volume. I would divide up the parcellations in
fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the
Desikan
atlas into smaller ROIs, but will need the new ROIs to be
consistent
between subjects.
Can I achieve this if I register each subject to fsaverage
space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for
the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu mailto:gr...@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/
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
you'll need to figure it out from the volume itself by loading the seg
with both -seg and -aux. When you find the label you want, click on it
and the aux value in the control window will tell you what the id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there is a label number. Where would I find
this for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will
need to then put them into diffusion and resting state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using bbregister,
tkregister2, mri_vol2vol (using the inverse registration from
bbregister to put the T1 into diffusion space), mri_extract_label
(extract labels from aparc+aseg.mgz), and then mri_label2vol
(register each of the extracted labels into diffusion space).
Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
wrote:
Exactly what you have described won't work very well because
it would be
in the volume. I would divide up the parcellations in
fsaverage space
like you've done, then map the parcellation to each subject
using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the
Desikan
atlas into smaller ROIs, but will need the new ROIs to be
consistent
between subjects.
Can I achieve this if I register each subject to fsaverage
space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for
the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu mailto:gr...@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/
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[Freesurfer] mris_divide_parcellation same divisions between subjects
Hello all,
I am planning to use mris_divide_parcellation to split the Desikan atlas
into smaller ROIs, but will need the new ROIs to be consistent between
subjects.
Can I achieve this if I register each subject to fsaverage space and then
apply the inverse transform to the divided parcellations (which are
currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for the label number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Exactly what you have described won't work very well because it would be
in the volume. I would divide up the parcellations in fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the Desikan
atlas into smaller ROIs, but will need the new ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to fsaverage space and
then apply the inverse transform to the divided parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Hi Doug,
After I have the labels then in each subject's T1 space, I will need to
then put them into diffusion and resting state space.
I already have scripts that put the parcellations into subject-specific
diffusion/resting state space (using bbregister, tkregister2, mri_vol2vol
(using the inverse registration from bbregister to put the T1 into
diffusion space), mri_extract_label (extract labels from aparc+aseg.mgz),
and then mri_label2vol (register each of the extracted labels into
diffusion space). Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Exactly what you have described won't work very well because it would be
in the volume. I would divide up the parcellations in fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the Desikan
atlas into smaller ROIs, but will need the new ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to fsaverage space and
then apply the inverse transform to the divided parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will need
to then put them into diffusion and resting state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using bbregister,
tkregister2, mri_vol2vol (using the inverse registration from
bbregister to put the T1 into diffusion space), mri_extract_label
(extract labels from aparc+aseg.mgz), and then mri_label2vol (register
each of the extracted labels into diffusion space). Would a similar
approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well because it
would be
in the volume. I would divide up the parcellations in fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the Desikan
atlas into smaller ROIs, but will need the new ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to fsaverage space and
then apply the inverse transform to the divided parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu mailto:gr...@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
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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/
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the e-mail
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