Dear Douglas thanks a lot for this information. Indeed, I thought we are sampling our data on the own average!
Cheers Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology 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.haen...@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. ----------------------------------------------------------------------------------------------------- Am 09.03.2017 um 17:46 schrieb Douglas N Greve: > This was done to clear up a misunderstanding when using a target subject > other than fsaverage. The way that 5.3 worked is that the data were > actually sampled onto fsaverage through the ?h.sphere.reg. The target > subject was only used in the smoothing process (if you even specified > that as part of mris_preproc). This gave people the impression that they > were sampling their data onto the target subject. To replicate 5.3, just > specify fsaverage as the target and proceed as normal using your target > after those commands. If you want to sample onto your target subject, > then you will have to register each individual subject to the target, eg, > > surfreg --s individualsubject --t average_AN_FS6_long_split > > This will create ?h.average_AN_FS6_long_split.sphere.reg which can then > be used in mris_preproc > > > > On 03/09/2017 07:44 AM, Juergen Haenggi wrote: >> Dear FS experts >> >> we are trying to run statistics in FS6 Linux. Everthing worked fine >> until we applied the command >> mris_preproc that called mri_surf2surf and produced the following error: >> >> ############################################################# >> >> --------------------------------------------------- >> #@# 1/98 s1006_01.long.s1006_base Thu Mar 9 13:20:16 CET 2017 >> -------------- >> ----------------------- >> mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh >> --srcsurfreg average_AN_FS6_long_split.sphere.reg --trgsubject >> average_AN_FS6_long_split --trghemi rh --trgsurfreg sphere.reg --tval >> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh >> >> --sval >> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume >> --jac --sfmt curv --noreshape --cortex >> MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg): >> >> could not open file >> Source registration surface changed to >> average_AN_FS6_long_split.sphere.reg >> Target registration surface changed to sphere.reg >> >> $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ >> >> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects >> cd /usr/local/freesurfer/subjects >> mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh >> --srcsurfreg average_AN_FS6_long_split.sphere.reg --trgsubject >> average_AN_FS6_long_split --trghemi rh --trgsurfreg sphere.reg --tval >> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh >> >> --sval >> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume >> --jac --sfmt curv --noreshape --cortex >> >> sysname Linux >> hostname psy-neuro-clt-Monster >> machine x86_64 >> user ego >> srcsubject = s1006_01.long.s1006_base >> srcval = >> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume >> srctype = curv >> trgsubject = average_AN_FS6_long_split >> trgval = >> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh >> trgtype = >> srcsurfreg = average_AN_FS6_long_split.sphere.reg >> trgsurfreg = sphere.reg >> srchemi = rh >> trghemi = rh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 0 >> label-src = rh.cortex.label >> label-trg = rh.cortex.label >> OKToRevFaceOrder = 1 >> UseDualHemi = 0 >> Reading source surface reg >> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg >> No such file or directory >> mri_surf2surf: could not read surface >> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg >> No such file or directory >> >> ############################################################### >> >> this line is odd: >> >> MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg): >> >> could not open file >> >> we are wondering why FS6 introduced the name of the target average >> (average_AN_FS6_long_split) into the name of the individual subject >> (rh.average_AN_FS6_long_split.sphere.reg) when looking >> for s1006_01.long.s1006_base/surf/rh.sphere.reg. >> >> When using FS5.3.0 mris_preproc worked without this error. >> >> Any idea? >> >> Thanks in advance >> Best regards >> Jürgen >> >> >> ----------------------------------------------------------------------------------------------------- >> University of Zurich >> Dr. Jürgen Hänggi, Ph.D. >> Department of Psychology >> Division Neuropsychology >> 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.haen...@psychologie.uzh.ch <mailto:j.haen...@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 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.
