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 (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. -----------------------------------------------------------------------------------------------------
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)
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.
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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.haenggi@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.haenggi@psychologie.uzh.ch mailto:j.haenggi@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.
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