Yolanda, don't run mris_anatomical_stats on fsaverage. You should map the label to each individual with mri_label2label, then use mris_anatomical_stats. Sorry for not being clearer eariler. doug
Yolanda Vives wrote: > Hi Bruce, > > That's the error: > > limiting computations to label > fsaverage/label/grouplabel_concro_rh-0001.label. > reading volume > /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz... > ERROR: cannot find > /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz > mris_anatomical_stats: could not read input volume > /nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz > No such file or directory > > cheers, > yolanda > > 2011/7/28 Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > > Hi Yolanda, > > you need to email us the screen output with the error so we can > diagnose it. > > cheers > Bruce > > On Thu, 28 Jul 2011, Yolanda Vives wrote: > > Thank you Douglas for your suggestions! > > If I use mris_anatomical_stats, would I perform the following > procedure? > > - To run "mri_label2label" to all the subjects of my comparison > - To run mris_anatomical_stats. I would obtain the volume of > the labels in each subject > - Mean volume of all the subjects > > I have tried to map the label to fsaverage and ru run > mris_anatommical_stats but I have an error and I am not sure > if it is correct. > > Thanks again, > Yolanda > > 2011/7/26 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Hi Yolanda, don't use thmax (it will exclude everything > with a sig>7 -- not what you want I assume). That command > otherwise looks > right, but it won't correct for multiple comparisons. You > can run mris_anatomical_stats on the output label to give you > the stats > you want. > > doug > > > Yolanda Vives wrote: > Dear freesurfers, > > I would like to obtain the cluster size (in mm3) and > coordinates of the maxima of a cortical volume comparison using > mri_surfcluster. > > mri_surfcluster --in > > $PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh > --hemi rh --subject > fsaverage --thmin 2 --thmax 7 --sign pos --surf pial > --no-adjust --o ./concro --ocn ./cluster_number --olab > ./grouplabel_concro > --sd $SUBJ_DIR --sum ./concro_sum > > Would it be correct. > > Regarding the results that I obtain, I have some questions: > > - Which surface do I have to load? pial, orig? > - In the summary file, the cluster size is given in mm2, is it > possible to obtain it in mm3 (I am analysing cortical volume)? > > Thank you for your help, > Yolanda > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > > > > > > -- > Yolanda Vives > PIC (Port d'Informació CientÃfica) > Campus UAB, Edificio D > E-08193 Bellaterra, Barcelona > Telf. +34 93 586 8232 > http://www.pic.es > Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
