Re: [Freesurfer] mris_divide_parcellation
Dear Bruce, Many thanks for quick reply. Actually, I meant doing the same thing as you explained with mris_make_face_parcellation command . with mris_divide_parcellation, I have done what you told me but the problem is that it only divide the labels perpendicular to the axis of the label which does not look nice. I prefer to use mris_make_face_parcellation and do for a certain label like superior temporal. Is that possible? Thanks, Fahimeh From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, October 06, 2016 4:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_divide_parcellation Hi Fahimeh you can also give mris_divide_parcellation a "splitfile" : rst, a splitfile can be specified as the fourth argument. The splitfile is a text file with two columns. The first column is the name of the label in the source annotation, and the second column is the number of units that label should be divided into. The names of the labels depends upon the source parcellation. For aparc.annot and aparc.a2005.annot, the names can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt. For aparc.annot, the labels are between the ranges of 1000-1034. For aparc.a2005s.annot, the labels are between the ranges of 1100-1181. The name for the label is the name of the segmentation without the 'ctx-lh'. Note that the name included in the splitfile does not indicate the hemisphere. For example, 1023 is 'ctx-lh-posteriorcingulate'. You should put 'posteriorcingulate' in the splitfile. Eg, to divide it into three segments, the following line should appear in the splitfile: posteriorcingulate 3 Only labels that should be split need be specified in the splitfile. cheers Bruce On Thu, 6 Oct 2016, Mamashli, Fahimeh wrote: > > Hi, > Thanks for your help. I tried and it worked. However, the problem is that > this is doing for all brain and it is very hard to find out which label > belongs to which parcellation in the brain. > For example, I am interested only to superior temporal area of the brain and > I don't need rest of the brain. How can I figure out which of these labels > belong to superior temporal? > is there any way to do this for a certain parcellation like lh.aparc.annot ? > > Thank you, > Fahimeh > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, September 16, 2016 6:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mris_divide_parcellation > > how would you like them divided? You can also use > mris_make_face_parcellation to make units of approximately equal area > (either in the individual or in the group) > On Fri, 16 Sep 2016, Mamashli, > Fahimeh wrote: > >> Dear Freesurfer group, >> I am going to divide a brain parcellation into divisions using >> mris_divide_parcellation. As far as I know from the help comment, this >> function "divides one or more parcellations into divisions perpendicular to >> the long axis of the label". Is there any other program that does not make >> the divisions perpendicular to the long axis? >> >> Thank you, >> Fahimeh >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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
Hi Fahimeh you can also give mris_divide_parcellation a "splitfile" : rst, a splitfile can be specified as the fourth argument. The splitfile is a text file with two columns. The first column is the name of the label in the source annotation, and the second column is the number of units that label should be divided into. The names of the labels depends upon the source parcellation. For aparc.annot and aparc.a2005.annot, the names can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt. For aparc.annot, the labels are between the ranges of 1000-1034. For aparc.a2005s.annot, the labels are between the ranges of 1100-1181. The name for the label is the name of the segmentation without the 'ctx-lh'. Note that the name included in the splitfile does not indicate the hemisphere. For example, 1023 is 'ctx-lh-posteriorcingulate'. You should put 'posteriorcingulate' in the splitfile. Eg, to divide it into three segments, the following line should appear in the splitfile: posteriorcingulate 3 Only labels that should be split need be specified in the splitfile. cheers Bruce On Thu, 6 Oct 2016, Mamashli, Fahimeh wrote: > > Hi, > Thanks for your help. I tried and it worked. However, the problem is that > this is doing for all brain and it is very hard to find out which label > belongs to which parcellation in the brain. > For example, I am interested only to superior temporal area of the brain and > I don't need rest of the brain. How can I figure out which of these labels > belong to superior temporal? > is there any way to do this for a certain parcellation like lh.aparc.annot ? > > Thank you, > Fahimeh > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, September 16, 2016 6:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mris_divide_parcellation > > how would you like them divided? You can also use > mris_make_face_parcellation to make units of approximately equal area > (either in the individual or in the group) > On Fri, 16 Sep 2016, Mamashli, > Fahimeh wrote: > >> Dear Freesurfer group, >> I am going to divide a brain parcellation into divisions using >> mris_divide_parcellation. As far as I know from the help comment, this >> function "divides one or more parcellations into divisions perpendicular to >> the long axis of the label". Is there any other program that does not make >> the divisions perpendicular to the long axis? >> >> Thank you, >> Fahimeh >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
Hi, Thanks for your help. I tried and it worked. However, the problem is that this is doing for all brain and it is very hard to find out which label belongs to which parcellation in the brain. For example, I am interested only to superior temporal area of the brain and I don't need rest of the brain. How can I figure out which of these labels belong to superior temporal? is there any way to do this for a certain parcellation like lh.aparc.annot ? Thank you, Fahimeh From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2016 6:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_divide_parcellation how would you like them divided? You can also use mris_make_face_parcellation to make units of approximately equal area (either in the individual or in the group) On Fri, 16 Sep 2016, Mamashli, Fahimeh wrote: > Dear Freesurfer group, > I am going to divide a brain parcellation into divisions using > mris_divide_parcellation. As far as I know from the help comment, this > function "divides one or more parcellations into divisions perpendicular to > the long axis of the label". Is there any other program that does not make > the divisions perpendicular to the long axis? > > Thank you, > Fahimeh > > ___ 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
how would you like them divided? You can also use mris_make_face_parcellation to make units of approximately equal area (either in the individual or in the group) On Fri, 16 Sep 2016, Mamashli, Fahimeh wrote: Dear Freesurfer group, I am going to divide a brain parcellation into divisions using mris_divide_parcellation. As far as I know from the help comment, this function "divides one or more parcellations into divisions perpendicular to the long axis of the label". Is there any other program that does not make the divisions perpendicular to the long axis? Thank you, Fahimeh ___ 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
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
___
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
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
___
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
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
___
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.
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.
___
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
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
___
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.
___
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
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
___
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.
___
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
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
___
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.
___
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,
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
___
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.
___
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
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
___
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
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.
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
___
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
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/
___
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
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
___
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
--
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
___
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
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/
___
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
listfreesur...@nmr.mgh.harvard.eduhttps://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
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.
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
___
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
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/
___
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
___
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
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
___
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
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/
___
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
___
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
___
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
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
___
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
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/
___
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
___
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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
___
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
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/
___
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
___
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
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
___
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
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/
___
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
___
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
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
___
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
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/
___
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
___
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
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
___
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
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/
___
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 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
___
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
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/
___
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.
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
___
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
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/
___
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
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
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 replication
Hi Bruce, Thanks for your reply. This makes sense. One remaining question is which surface is used to compute the eigen-axis, is it the white surface? Best, Martin On 02/03/14 15:27, Bruce Fischl wrote: Hi Christian and Martin mris_divide_parcellation finds the primary eigen-axis of the parcellation along the cortical surface, then splits it up into as many units as specified (either enough to get it under the area threshold, or explicitly specifed in a split file) cheers Bruce p.s. the code is open source so you are always welcome to grab it and take a look On Mon, 3 Feb 2014, Martin Luessi wrote: I'm wondering about this as well. It would be great if someone who is familiar with the FreeSurfer code could explain the split algorithm. Best, Martin On 01/29/14 14:36, Christian Brodbeck wrote: Dear Freesurfer developers, I am trying to replicate mris_divide_parcellation for mne-python (https://github.com/mne-tools/mne-python/pull/1085). I think I am doing the same as the MRISdivideAnnotationUnit function (https://github.com/neurodebian/freesurfer/blob/master/utils/annotation.c#L473), but the result still looks different. Could someone point out how exactly the split is done, and if there are any steps in addition to the function? Are there any measures that are taken when the split would result in two disconnected regions belonging to the same label? And what surface is the split performed on (I would assume that would be “white”)? Thank you! Christian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Luessi, Ph.D. Research Fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 Fax: +1 617 726-7422 ___ 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 replication
Thanks a lot Bruce! Using the sphere surface was what I was missing. Christian On Feb 4, 2014, at 12:16, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: it's the ?h.sphere so that folding isn't an issue On Tue, 4 Feb 2014, Martin Luessi wrote: Hi Bruce, Thanks for your reply. This makes sense. One remaining question is which surface is used to compute the eigen-axis, is it the white surface? Best, Martin On 02/03/14 15:27, Bruce Fischl wrote: Hi Christian and Martin mris_divide_parcellation finds the primary eigen-axis of the parcellation along the cortical surface, then splits it up into as many units as specified (either enough to get it under the area threshold, or explicitly specifed in a split file) cheers Bruce p.s. the code is open source so you are always welcome to grab it and take a look On Mon, 3 Feb 2014, Martin Luessi wrote: I'm wondering about this as well. It would be great if someone who is familiar with the FreeSurfer code could explain the split algorithm. Best, Martin On 01/29/14 14:36, Christian Brodbeck wrote: Dear Freesurfer developers, I am trying to replicate mris_divide_parcellation for mne-python (https://github.com/mne-tools/mne-python/pull/1085). I think I am doing the same as the MRISdivideAnnotationUnit function (https://github.com/neurodebian/freesurfer/blob/master/utils/annotation.c#L473), but the result still looks different. Could someone point out how exactly the split is done, and if there are any steps in addition to the function? Are there any measures that are taken when the split would result in two disconnected regions belonging to the same label? And what surface is the split performed on (I would assume that would be “white”)? Thank you! Christian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
Re: [Freesurfer] mris_divide_parcellation replication
Hi Christian and Martin mris_divide_parcellation finds the primary eigen-axis of the parcellation along the cortical surface, then splits it up into as many units as specified (either enough to get it under the area threshold, or explicitly specifed in a split file) cheers Bruce p.s. the code is open source so you are always welcome to grab it and take a look On Mon, 3 Feb 2014, Martin Luessi wrote: I'm wondering about this as well. It would be great if someone who is familiar with the FreeSurfer code could explain the split algorithm. Best, Martin On 01/29/14 14:36, Christian Brodbeck wrote: Dear Freesurfer developers, I am trying to replicate mris_divide_parcellation for mne-python (https://github.com/mne-tools/mne-python/pull/1085). I think I am doing the same as the MRISdivideAnnotationUnit function (https://github.com/neurodebian/freesurfer/blob/master/utils/annotation.c#L473), but the result still looks different. Could someone point out how exactly the split is done, and if there are any steps in addition to the function? Are there any measures that are taken when the split would result in two disconnected regions belonging to the same label? And what surface is the split performed on (I would assume that would be “white”)? Thank you! Christian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 color table error
I am running version 5.3- the latest version. I also tried running the codes on v5.0 and got the same result. Is there any way I can change the color table so that the colors of the parcellation are unique? Thanks, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:41 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error Sure On May 29, 2013, at 9:36 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: The colors are visually different by a shade then loop every 4 or so colors. I think the color table may be running on a loop? I can send the annot and surface file if you need that as well. Best, Tina From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:02 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error p.s. can you send me the splittable text file ? I seem to have deleted it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 -03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 _ ___ UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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. splittable.txt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_divide_parcellation color table error (fwd)
Yes it worked. Thank you that is exactly what I needed. Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 12:36 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error (fwd) Hi Tina is this (attached) more what you wanted? If so, then I think you want to use mris_make_face_parcellation instead of mris_divide_parcellation. I can't remember what they used in that paper, but in mris_divide_parcellation I try to have the different units within a parcel have similar colors (which evidentally fails when you split it so finely) Bruce On Thu, 30 May 2013, Tina Jeon wrote: I am running version 5.3- the latest version. I also tried running the codes on v5.0 and got the same result. Is there any way I can change the color table so that the colors of the parcellation are unique? Thanks, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:41 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error Sure On May 29, 2013, at 9:36 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: The colors are visually different by a shade then loop every 4 or so colors. I think the color table may be running on a loop? I can send the annot and surface file if you need that as well. Best, Tina From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:02 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error p.s. can you send me the splittable text file ? I seem to have deleted it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 -03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 _ ___ UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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. splittable.txt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_divide_parcellation color table error
Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010-03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 color table error
Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edumailto:tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010-03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
Re: [Freesurfer] mris_divide_parcellation color table error
hmmm, I haven't run that code in a long time. Are the colors different but not visually so? That is, do the rgb values differ by 1 or 2 or something like that? Or are they actualy identical? On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 -03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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.
Re: [Freesurfer] mris_divide_parcellation
Hi Mario, I don't think we've ever written such a thing but it would be pretty straightfoward in matlab. sorry Bruce On Tue, 24 Apr 2012, Mario Ortega wrote: Hi Freesurfer users, Does anyone have a method to divide aseg.mgz volumetric regions along a longitudinal axis? Or a simple split after finding a center of mass of an ROI? I found that mris_divide_parcellation only splits up regions from the surface based segmentation as found in the desikan killiany label file. Thanks, Mario ___ 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
Thank you Bruce, the parcellation looks good, as you say, I think that it doesn't affect me. yolanda 2012/2/7 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Yolanda does the resulting parcellation look ok? I think that's a small bug that may not have any effect on you (there will just be extra, unused color table entries) Bruce On Tue, 7 Feb 2012, Yolanda Vives wrote: Dear Freesurfer experts, I have a question regarding mris_divide_parcellation. I have created a file containing the parcels from aparc.annot that I want to split and I have run the following command. Why is Freesurfer allocating 36 additional units? When I open the new annotation file (rh.aparc.splitted) with matlab (using read_annotation), I can see that at the end of colortable.struct_names there are a lot of parcels called cluster38, cluster39, ..., cluster71. What are exactly these clusters? Many thanks, Yolanda In splittable.txt file precentral 2 Command ./mris_divide_parcellation fsaverage rh aparc.annot splittable.txt rh.aparc.splitted Output reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/** users/buckner_cortical_atlas/**scripts/colortable_final.txt) interpreting 4th command line arg as split file name dividing precentral into 2 parts allocating new colortable with 36 additional units... saving annotation to rh.aparc.splitted writing colortable into annotation file... 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/**compliancelinehttp://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. -- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ 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
Hi Yolanda does the resulting parcellation look ok? I think that's a small bug that may not have any effect on you (there will just be extra, unused color table entries) Bruce On Tue, 7 Feb 2012, Yolanda Vives wrote: Dear Freesurfer experts, I have a question regarding mris_divide_parcellation. I have created a file containing the parcels from aparc.annot that I want to split and I have run the following command. Why is Freesurfer allocating 36 additional units? When I open the new annotation file (rh.aparc.splitted) with matlab (using read_annotation), I can see that at the end of colortable.struct_names there are a lot of parcels called cluster38, cluster39, ..., cluster71. What are exactly these clusters? Many thanks, Yolanda In splittable.txt file precentral 2 Command ./mris_divide_parcellation fsaverage rh aparc.annot splittable.txt rh.aparc.splitted Output reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) interpreting 4th command line arg as split file name dividing precentral into 2 parts allocating new colortable with 36 additional units... saving annotation to rh.aparc.splitted writing colortable into annotation file... ___ 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
I'm surprised that the divisions are not roughly equal in area. How much different are they? You can also spec an area threshold instead of a number of subdivisions, but that just keeps dividing until all subdivisions are below that area. I don't think we have anything that will divide them into equal sizes, though I think bruce is working on something like that. doug Jose Luis Cantero Lorente wrote: Dear FS Team, I used mris_divide_parcellation to create a new parcelation with smaller regions, but all these regions seem to have a different size. I am interested to get smaller cortical parcellated regions, but all of them with the same area. How can I get it? Could I decide the area size? Thank you in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcan...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_divide_parcellation
Hi Jose, I have another tool that we haven't released that will do this more closely. You can't do that with mris_divide_parcellation since the units don't start with equal area (or multiples thereof) cheers, Bruce On Thu, 19 Feb 2009, Jose Luis Cantero Lorente wrote: Dear FS Team, I used mris_divide_parcellation to create a new parcelation with smaller regions, but all these regions seem to have a different size. I am interested to get smaller cortical parcellated regions, but all of them with the same area. How can I get it? Could I decide the area size? Thank you in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcan...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_divide_parcellation output problem
Hi Jürgen, turns out this was a display but in tksurfer, which I fixed. It would stop displaying after the 3000th annotation unit. If you tell us what os/hardware you are running on we can send you a new version. cheers, Bruce On Sat, 17 Jan 2009, Jürgen Hänggi wrote: Dear FS experts I have run the following command: mris_divide_parcellation Ego_Mean3_FineParc rh aparc.annot 100 rh_annot_100 But cannot read the output file (see attachment) with tksurfer % [juergen-haenggis-mac-pro:subjects/Ego_Mean3_FineParc/label] juergenhaenggi% tksurfer Ego_Mean3_FineParc rh inflated -annot rh_annot_100 surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects/Ego_Mean3_FineParc/label surfer: Reading header info from /Applications/freesurfer/subjects/Ego_Mean3_FineParc/mri/T1.mgz surfer: vertices=151401, faces=302798 could not read annot file /Applications/freesurfer/subjects/Ego_Mean3_FineParc/surf/../label/rh.rh_ann ot_100.annot No such file or directory ERROR: could not load rh_annot_100 surfer: single buffered window surfer: tkoInitWindow(Ego_Mean3_FineParc) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... If I provided tksurfer the whole path to the annot file, the error still occurred. Thanks in advance Regards Juergen -- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_divide_parcellation
Hi Jürgen, the cmdline you gave will only divide units bigger than 100 mm^2. Is that what you want? cheers, Bruce On Sat, 17 Jan 2009, Jürgen Hänggi wrote: Daer FS experts When using the command: mris_divide_parcellation Ego_Mean3_FineParc rh aparc.annot 100 rh_annot_100 Only some posterior brain areas (see attachment) were further divided, not the whole hemisphere. Why? Thanks Regards Juergen -- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Mris_divide_parcellation II
Hi Jürgen, it will pick a random (unique) color for each new parcellation unit. cheers, Bruce On Sat, 17 Jan 2009, Jürgen Hänggi wrote: Dear FS experts Sorry, me again. If I divide the parcellations into areas of 100 mm2 only the most posterior part of the parcellations will be divided. Only with a threshold of about 500 mm2, the whole hemisphere's parcellations will be divided. Are there not enough labels resp. colors available? Thanks Regards Jürgen -- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_divide_parcellation
perfect. thanks, all of you, for your help. On May 10, 2007, at 7:55 PM, Nick Schmansky wrote: Catherine, It looks like you have a Mac. You can get mris_divide_parcellation for that here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev macppc directory is for the PowerPC, macintel dir is for the new Intel Macs. Nick On Thu, 2007-05-10 at 19:45 -0400, Catherine Hartley wrote: From: Catherine Hartley [EMAIL PROTECTED] Date: May 10, 2007 7:10:19 PM EDT To: Doug Greve [EMAIL PROTECTED] Subject: Re: [Freesurfer] mris_divide_parcellation then i get: Exec format error. Binary file not executable. [catemac:/Applications] cate% cd freesurfer/bin [catemac:/Applications/freesurfer/bin] cate% chmod a+x mris_divide_parcellation [catemac:/Applications/freesurfer/bin] cate% mris_divide_parcellation tcsh: /Applications/freesurfer/bin/mris_divide_parcellation: Exec format error. Binary file not executable. [catemac:/Applications/freesurfer/bin] cate% On May 10, 2007, at 6:58 PM, Doug Greve wrote: try chmod a+x mris_divide_parcellation Catherine Hartley wrote: Thanks! However when i try to execute the command, i get a message saying Permission denied. Any ideas? Thanks, Cate On May 10, 2007, at 5:30 PM, Doug Greve wrote: here you go ... ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ mris_divide_parcellation Catherine Hartley wrote: Hi, I'm hoping to get a hold of the function mris_divide_parcellation which automatically subdivides the cortical parcellations for a region into sub-regions. It's not a part of the current Freesurfer release but would it be possible to get a copy of the development version? Thanks, Cate ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_divide_parcellation
try chmod a+x mris_divide_parcellation Catherine Hartley wrote: Thanks! However when i try to execute the command, i get a message saying Permission denied. Any ideas? Thanks, Cate On May 10, 2007, at 5:30 PM, Doug Greve wrote: here you go ... ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ mris_divide_parcellation Catherine Hartley wrote: Hi, I'm hoping to get a hold of the function mris_divide_parcellation which automatically subdivides the cortical parcellations for a region into sub-regions. It's not a part of the current Freesurfer release but would it be possible to get a copy of the development version? Thanks, Cate ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
