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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 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: 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