yes, but not easily. You will have to create an annotation with your new label in it (and any other label for the other parts of cortex) (probably using mris_label2annot), then run mri_aparc2aseg to generate a new wmparc-style volume, then run mri_segstats. You can look in the recon-all.log file for example command lines for mri_aparc2aseg (used to generate the wmparc.mgz) doug On 03/03/2014 02:31 PM, Yang, Daniel wrote: > Sorry, I wasn't clear. It's a cortical label that I manually created, > based on the pial surface. > > Is it possible to generate the corresponding WM vol based on a new > label (not pre-defined)? > > > -- > Daniel (Yung-Jui) Yang, Ph.D. > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > Tel: (203) 737-5454 > E-mail: [email protected]_ > > On 3/3/14 2:17 PM, "Douglas N Greve" <[email protected] > <mailto:[email protected]>> wrote: > > > I don't understand. What label do you have? Do you mean a WM label > or a > cortical label that you want to find the WM under? > > On 03/03/2014 02:12 PM, Yang, Daniel wrote: > > Hi Doug, > > I am able to find wmparc.stats in stats. It shows WM vol based on > pre-defined ROIs. > > However, do you know how can we generate corresponding WM vol > for a > given label (not the D-K ROIs)? > > I'd like to use WM vol as DV but are limited to pre-defined ROIs. > > Best, > Daniel > > -- > Daniel (Yung-Jui) Yang, Ph.D. > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > Tel: (203) 737-5454 > E-mail: [email protected]_ <mailto:[email protected]_> > > On 3/3/14 1:14 PM, "Douglas N Greve" > <[email protected] <mailto:[email protected]> > <mailto:[email protected]> > <mailto:[email protected]%3E>> wrote: > > It should be there if the recon did not fail. The file is > called > wmparc.stats (not wmparc_stats.txt) > On 03/03/2014 01:07 PM, Yang, Daniel wrote: > > Thanks, Doug! But that is about using wmparc.stats as > IV or > continuous/covariate variables. I would like to use > WM vol as > the DV > (measure). > > -- > Daniel (Yung-Jui) Yang, Ph.D. > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > Tel: (203) 737-5454 > E-mail: [email protected]_ > <mailto:[email protected]_> > <mailto:[email protected]_> > > On 3/3/14 12:58 PM, "Douglas N Greve" > <[email protected] > <mailto:[email protected]> > <mailto:[email protected]> > <mailto:[email protected]> > <mailto:[email protected]%3E> > <mailto:[email protected]%3E%3E>> wrote: > > you can just add them into your qdec file (from > wmparc.stats) > doug > > On 03/02/2014 07:18 PM, Yang, Daniel wrote: > > Dear FreeSurfer Experts, > > FS provides thickness as the DV in qdec and > mri-glmfit. Do you > know how I can have WM vol as the DV in > these tools > with the > same GLM model? For example, I want to test > the WM > regions > that is most strongly positively correlated > with a > given factor. > > Thanks! > Daniel > _______________________________________________ > Freesurfer mailing list > [email protected] > <mailto:[email protected]> > <mailto:[email protected]> > <mailto:[email protected]> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > <mailto:[email protected]> > <mailto:[email protected]> > 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 > <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 > [email protected] > <mailto:[email protected]> > <mailto:[email protected]> > <mailto:[email protected]> > 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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > <mailto:[email protected]> > 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/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > 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/ > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
