9 Apr
2014
9 Apr
'14
10:09 a.m.
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