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.haenggi@psychologie.uzh.ch <mailto:j.haenggi@psychologie.uzh.ch> (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
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