I meant this file: cache.th40.pos.sig.y.ocn.dat - it should contain the average value of each subject in each cluster. Are we writing about the same file?
2017-08-21 22:07 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
The numbers in that file are just indices indicating the cluster number (eg, 1=cluster1, 2=cluster2, etc). They are the output of the multiple comparisons correction, so they are gennerated from all the input
On 08/18/2017 03:28 PM, Patrícia Klobušiaková wrote:
OK, this works now, when I map the label on subject and use rh.thickness as an input. Don't you know why it didn't work before, when I had label from fsaverage and was trying to use rh.thickness.fwhm10.fsaverage.mgh? Aren't they both in fsaverage space?
And can I ask you one more question - how exactly are numbers iny.ocn.dat calculated (which files are used as a input)?
2017-08-18 21:14 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
if you want to apply it to an individual you could map the label from fsaverage to that subject using mri_label2label On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: Yes, it was. I just don't know, how to apply that on individual subjects. Thanks! 2017-08-18 21:06 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu:
I'll defer to Doug on this, but it looks like your labelwas
created on fsaverage On Fri, 18 Aug 2017, Patrícia Klobušiaková wrote: Hi Bruce, so I tried fmri/galadriel/_personal/riha_klobusiakova$ mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness s0110B rh but I get the same error - label point 178 has vertex number = 154391, but surface only has 140611 vertices My labels were created by mri_surfcluster--in$SUBJECTS_DIR/glm/rh.Apgem1_FSGD_HCvsPD-MCIreal.glmdir/Apgem1_FSGD_HCvs
PD-M CIreal/sig.mgh --subject fsaverage --hemi rh --thmin 4 --thmax 5 --thsign pos --sign pos --sum $SUBJECTS_DIR/glm/analyza/HCvsPD-MCIunc_rh --o /$SUBJECTS_DIR/glm/analyza/clvals --ocn /$SUBJECTS_DIR/glm/analyza/clnums --olab /$SUBJECTS_DIR/glm/analyza/cllabel Am I missing something here? Should I create labels for every subject? I thought sig.mgh belongs to fsaverage, that's why I wanted to use rh.thickness.fwhm10.fsaverage.mgh. I wanted to create something similar to y.ocn.dat which I get after multiple comparisons correction (but for clusters significant at lower threshold). Thanks, Patricia 2017-08-18 2:58 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Patricia try using the subject's rh.thickness instead (it is in subject space, as I think is your label) cheers Bruce On Thu, 17 Aug 2017, Patrícia Klobušiaková wrote: Dear Freesurfer experts, I have labels representing clusters that I created using mri_surfcluster on sig.mgh file using a specific threshold. Now I want to use these labels to extract average thickness values for every subject. I tried to use mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh s0110B rh to calculate it for one subject, but it doesn't work - I get error because the number of vertices in subject's file rh.thickness.fwhm10.fsaverage.mgh doesn't match surface. I should use fsaverage as a subject, right? So I tried mris_anatomical_stats -l $SUBJECTS_DIR/glm/analyza/cllabel-0001.label -t $SUBJECTS_DIR/s0110B/surf/rh.thickness.fwhm10.fsaverage.mgh fsaverage rh but then I get error, that it cannot read fsaverage/mri/wm.mgz file. The wm.mgz file isn't in fsaverage folder. How can I calculate this? Thanks for your help! Patricia _______________________________________________ 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> 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>
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