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
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
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 greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
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 greve@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 <greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 listFreesurfer@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_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 greve@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 greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 fischl@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 <
greve@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 greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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
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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 fischl@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 <greve@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 > <greve@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 > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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
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 corinnab83@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 fischl@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 <
greve@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 greve@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 subjectusing
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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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>
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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....
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer corinnab83@gmail.com wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve < greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 subjectusing
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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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>
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.... ?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer <corinnab83@gmail.com mailto:corinnab83@gmail.com> wrote:
Perfect. Thanks! On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> >> <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> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the >> person to whom it is >> addressed. If you believe this e-mail was sent to you in >> error and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was >> sent to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 <greve@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....
?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer <corinnab83@gmail.com mailto:corinnab83@gmail.com> wrote:
Perfect. Thanks! On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%3E
>> 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> >> <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> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only forthe
>> person to whom it is >> addressed. If you believe this e-mail was sent to you in >> error and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was >> sent to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contactthe
> sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <corinnab83@gmail.com <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com>>> wrote: > > Perfect. Thanks! > > > On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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>> > >> <mailto: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 > >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> > >> > >> Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the > >> person to whom it is > >> addressed. If you believe this e-mail was sent to > you in > >> error and the e-mail > >> contains patient information, please contact the > Partners > >> Compliance HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was > >> sent to you in error > >> but does not contain patient information, please > contact the > >> sender and properly > >> dispose of the e-mail. > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto: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 > > > > > > _______________________________________________ > > 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>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was > sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> > <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 derivedfrom
> mris_divide_parcellation, should mri_aparc2wmseg be used or shouldI
> follow the steps outlined in this posting >https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471....
> ? > > Thanks > > Corinna > > > On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer <corinnab83@gmail.com <mailto:corinnab83@gmail.com> > <mailto:corinnab83@gmail.com <mailto:corinnab83@gmail.com>>>wrote:
> > Perfect. Thanks! > > > On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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.mgz2035
> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii > > > > > > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 intodiffusion
> space). > >> Would a similar approach work for the new labels? > >> > >> Corinna > >> > >> > >> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 thedivided
> >> parcellations (which > >> > are currently done on the fsaverage brain)? > >> > > >> > If so, for extracting each label, what wouldbe
> 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>> > >> <mailto: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 > >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > >> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> > >> > >> Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the > >> person to whom it is > >> addressed. If you believe this e-mail was sentto
> you in > >> error and the e-mail > >> contains patient information, please contact the > Partners > >> Compliance HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was > >> sent to you in error > >> but does not contain patient information, please > contact the > >> sender and properly > >> dispose of the e-mail. > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto: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 > > > > > > _______________________________________________ > > 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>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mailwas
> sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> > <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 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>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Corinna Bauer -
Douglas Greve -
Douglas N Greve