No. I'd write a script to do it
On 02/12/2018 12:17 PM, Michiko H. wrote: > Hi Doug, > > Thanks - this is extremely helpful! > > With regard to the first command: mri_binarize --replace 1001 3001 --i > aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz > Since I'd like to replace every cortical label with its corresponding > WM label on both hemispheres, is there a more efficient way of doing > this rather than having to manually write '--replace 10xx 30xx' > repetitively? > > Thanks very much again! > M. > > On Fri, Feb 9, 2018 at 12:53 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > On 2/6/18 5:26 PM, Michiko H. wrote: >> Hi Doug, >> >> That's very helpful, thank you! I have 2 follow-up questions though: >> >> 1. Is it possible to merge the cortical label (e.g. label 1001 >> ctx-lh-bankssts) with its corresponding label that extends into >> the WM (e.g. label 3001 wm-lh-bankssts)? I'm not completely sure >> but this may/may not give better results when tracking between >> labels as nodes. > You can use something like > mri_binarize --replaceonly 1001 3001 --i > aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz >> >> 2. Is it possible to include the subcortical structures in the >> final masked image? > Yes, use mri_binarize --i aparc+aseg+2mm.nii.gz --match 10 11 12 > ... --o aparc+aseg+2mm.subcort.nii.gz > where 10 11 12 is a list of the ids of the subcortical structures > you want > Then > fscalc aparc+aseg+2mm.subcort.nii.gz add > aparc+aseg+2mm.masked.nii.gz -o both.nii.gz > > >> >> Thank you so much! >> Michiko >> >> On Mon, Feb 5, 2018 at 12:30 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> You mean you want to remove everything but the WM labels? You >> can do it in two steps: >> >> 1. Create a mask of the wm labels: >> >> mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max >> 4035.5 --o wm.mask.nii.gz >> >> 2. Mask the wmparc: >> >> mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz >> aparc+aseg+2mm.masked.nii.gz >> >> >> >> >> On 2/4/18 5:28 PM, Michiko H. wrote: >>> Hi Freesurfer experts, >>> >>> I am wondering if it is possible to remove the original >>> labels after extending the parcellation by 2mm into the WM >>> for tractography? I don't wish to have tractography run on >>> both sets of labels considering the algorithm would take >>> into account the streamlines terminating at nodes defined by >>> the labels so it doesn't quite make sense to count >>> streamlines terminating at both the original label >>> separately from the new label extending into the WM. >>> >>> I used the following command for growing the parcellation >>> into WM: >>> >>> mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 >>> --labelwm --hypo-as-wm --o >>> $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz >>> >>> >>> Would appreciate help and suggestions! >>> >>> >>> Thanks, >>> >>> Michiko. >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <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 >> <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 >> <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 >> <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 > <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 > <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 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
