Dear Douglas thanks a lot for your advice. I tried it, but only one volume of the stack was read. I tried to use the --frame option, but it does not work. How can I force mri_segstats with the --frame option so that all 53 volumes of the stack are read?
Thanks in advance Regards Jürgen Am 02.07.15 14:44 schrieb "Douglas N Greve" unter <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu>: > >There are inevitable issues around the boundaries of the cluster. For >small clusters, this can be a big deal. I would probably just use the >fsaverage clusters on the control group after they have been mapped to >fsaverage space (ie, run mris_preproc on the control group to get a >stack, smooth it, then run mri_segstats with the stack as the input and >the ocn.mgh file as the --seg. > >doug > > >On 07/02/2015 03:21 AM, Jürgen Hänggi wrote: >> Dear FS experts >> >> in a former email >> >> >> >>http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg23322.htm >>l >> >> >> it has been recommended that we should not map clusters found in an >> analysis in the standard space >> >> back to the individual space due to resampling issues. >> >> >> In one of our study, we computed a correlation across patients and >> controlls and get MC simulation corrected clusters, the individual >> values of it can be found in the .y.ocn.dat file. >> >> A reviewer suggested to do the correlation only across the patient >> group and then transform these clusters into the native space in >> >> order to extract the values within these clusters for the control group. >> >> >> Therefore we would like to know the exact reason why this resampling >> is not recommended. Is it related to the fact that the transform >> >> from the native to the standard space is not one-to-one? >> >> >> What you recommend to answer to this reviewer point? >> >> >> Thanks in advance >> >> Best regards >> >> Jürgen Hänggi >> >> >> >>------------------------------------------------------------------------- >>-- >> >> Jürgen Hänggi, Ph.D. >> >> Division Neuropsychology >> >> Institute of Psychology >> >> University of Zurich >> >> Binzmuehlestrasse 14, PO Box 25 >> >> 8050 Zurich, Switzerland >> >> 0041 44 635 73 97 (phone office) >> >> 0041 76 445 86 84 (phone mobile) >> >> 0041 44 635 74 09 (fax office) >> >> BIN 4.D.04 (office room number) >> >> j.haenggi[at]psychologie.uzh.ch (email) >> >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> >> http://www.juergenhaenggi.ch (private website) >> >> >> This e-mail (and any attachment/s) contains confidential >> >> and/or privileged information. If you are not the intended >> >> recipient (or have received this e-mail in error) please notify >> >> the sender immediately and destroy this e-mail. Any >> >> unauthorised copying, disclosure or distribution of the >> >> material in this e-mail is strictly forbidden. >> >> >>------------------------------------------------------------------------- >>-- >> >> >> >> >> >> _______________________________________________ >> 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 > > >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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
