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Hello,
I am Lili Jiang from Institute of Psychology Chinese Academy of Sciences. I used freesurfer to do MRI data analysis. When I used mri_preproc to extract morphology data, I always got log file writing 'Reading source surface reg ~/sub001/surf/rh.fsaverage5.sphere.reg No such file or directory mri_surf2surf: could not read surface ~/sub001/surf/rh.fsaverage6.sphere.reg No such file or directory'. It seemed that mri_surf2surf loaded by mris_preproc always wanted to load reg file with 'fsaverage5'. But when I extrated morphology data in the resolution of fsaverage, then everything went well. Could you tell me what's wrong with this?
ps. I just upgraded freesurfer to v6.0 last summer.
Best,
Lili
What is your command line and full terminal output?
On 9/24/2020 4:30 AM, 姜黎黎 wrote:
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Hello, I am Lili Jiang from Institute of Psychology Chinese Academy of Sciences. I used freesurfer to do MRI data analysis. When I used mri_preproc to extract morphology data, I always got log file writing 'Reading source surface reg ~/sub001/surf/rh.fsaverage5.sphere.reg No such file or directory mri_surf2surf: could not read surface ~/sub001/surf/rh.fsaverage6.sphere.reg No such file or directory'. It seemed that mri_surf2surf loaded by mris_preproc always wanted to load reg file with 'fsaverage5'. But when I extrated morphology data in the resolution of fsaverage, then everything went well. Could you tell me what's wrong with this? ps. I just upgraded freesurfer to v6.0 last summer. Best, Lili ------------------------------------------------------------------------
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hello,
my command line is
mris_preproc --s ${subject} --hemi ${hemi} --meas ${measure} --target ${fsaverage}5 --out ${measure}/${hemi}.${subject}.${fsaverage}5.sm0.mgz
and my terminal output is
Transfering area for sub1's lh hemisphere ... nsubjects = 1 INFO: turning on jacobican correction tmpdir is area/tmp.mris_preproc.4084 Log file is area/lh.sub1.fsaverage5.sm0.mris_preproc.log ~/Downloads/freesurfer/bin/mris_preproc --s sub1 --hemi lh --meas area --target fsaverage5 --out area/lh.sub1.fsaverage5.sm0.mgz
Linux localhost.localdomain 2.6.32-754.17.1.el6.x86_64 #1 SMP Tue Jul 2 12:42:48 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is area/tmp.mris_preproc.4084 Src lh fsaverage5.sphere.reg Trg lh sphere.reg
mri_surf2surf --srcsubject sub1 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval area/tmp.mris_preproc.4162/sub1.1.mgh --sval /sub1/surf/lh.area --jac --sfmt curv --noreshape --cortex MRISread(/sub1/surf/lh.fsaverage5.sphere.reg): could not open file Source registration surface changed to fsaverage5.sphere.reg Target registration surface changed to sphere.reg
$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
mri_surf2surf --srcsubject sub1 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval area/tmp.mris_preproc.4084/sub1.1.mgh --sval /sub1/surf/lh.area --jac --sfmt curv --noreshape --cortex
sysname Linux hostname localhost.localdomain machine x86_64 srcsubject = sub1 srcval = /sub1/surf/lh.area srctype = curv trgsubject = fsaverage5 trgval = area/tmp.mris_preproc.4084/sub1.1.mgh trgtype = srcsurfreg = fsaverage5.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /sub1/surf/lh.fsaverage5.sphere.reg No such file or directory mri_surf2surf: could not read surface /sub1/surf/lh.fsaverage5.sphere.reg No such file or directory
Appreciated for your help!
Lili
This is a bug. Try this cd $SUBJECTS_DIR/sub1/surf ln -s lh.sphere.reg lh.fsaverage5.sphere.reg ln -s rh.sphere.reg rh.fsaverage5.sphere.reg
On 9/28/2020 3:55 AM, 姜黎黎 wrote:
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Hello,
my command line is
mris_preproc --s ${subject} --hemi ${hemi} --meas ${measure} --target ${fsaverage}5 --out ${measure}/${hemi}.${subject}.${fsaverage}5.sm0.mgz
and my terminal output is
Transfering area for sub1's lh hemisphere ... nsubjects = 1 INFO: turning on jacobican correction tmpdir is area/tmp.mris_preproc.4084 Log file is area/lh.sub1.fsaverage5.sm0.mris_preproc.log ~/Downloads/freesurfer/bin/mris_preproc --s sub1 --hemi lh --meas area --target fsaverage5 --out area/lh.sub1.fsaverage5.sm0.mgz
Linux localhost.localdomain 2.6.32-754.17.1.el6.x86_64 #1 SMP Tue Jul 2 12:42:48 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is area/tmp.mris_preproc.4084 Src lh fsaverage5.sphere.reg Trg lh sphere.reg
mri_surf2surf --srcsubject sub1 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval area/tmp.mris_preproc.4162/sub1.1.mgh --sval /sub1/surf/lh.area --jac --sfmt curv --noreshape --cortex MRISread(/sub1/surf/lh.fsaverage5.sphere.reg): could not open file Source registration surface changed to fsaverage5.sphere.reg Target registration surface changed to sphere.reg
$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
mri_surf2surf --srcsubject sub1 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval area/tmp.mris_preproc.4084/sub1.1.mgh --sval /sub1/surf/lh.area --jac --sfmt curv --noreshape --cortex
sysname Linux hostname localhost.localdomain machine x86_64 srcsubject = sub1 srcval = /sub1/surf/lh.area srctype = curv trgsubject = fsaverage5 trgval = area/tmp.mris_preproc.4084/sub1.1.mgh trgtype = srcsurfreg = fsaverage5.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /sub1/surf/lh.fsaverage5.sphere.reg No such file or directory mri_surf2surf: could not read surface /sub1/surf/lh.fsaverage5.sphere.reg No such file or directory
Appreciated for your help!
Lili
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Okay, thanks a lot!
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-09-29 23:07:46 (星期二) 收件人: freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] extract morphology data
This is a bug. Try this cd $SUBJECTS_DIR/sub1/surf ln -s lh.sphere.reg lh.fsaverage5.sphere.reg ln -s rh.sphere.reg rh.fsaverage5.sphere.reg
On 9/28/2020 3:55 AM, 姜黎黎 wrote:
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Hello,
my command line is
mris_preproc --s ${subject} --hemi ${hemi} --meas ${measure} --target ${fsaverage}5 --out ${measure}/${hemi}.${subject}.${fsaverage}5.sm0.mgz
and my terminal output is
Transfering area for sub1's lh hemisphere ... nsubjects = 1 INFO: turning on jacobican correction tmpdir is area/tmp.mris_preproc.4084 Log file is area/lh.sub1.fsaverage5.sm0.mris_preproc.log ~/Downloads/freesurfer/bin/mris_preproc --s sub1 --hemi lh --meas area --target fsaverage5 --out area/lh.sub1.fsaverage5.sm0.mgz
Linux localhost.localdomain 2.6.32-754.17.1.el6.x86_64 #1 SMP Tue Jul 2 12:42:48 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is area/tmp.mris_preproc.4084 Src lh fsaverage5.sphere.reg Trg lh sphere.reg
mri_surf2surf --srcsubject sub1 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval area/tmp.mris_preproc.4162/sub1.1.mgh --sval /sub1/surf/lh.area --jac --sfmt curv --noreshape --cortex MRISread(/sub1/surf/lh.fsaverage5.sphere.reg): could not open file Source registration surface changed to fsaverage5.sphere.reg Target registration surface changed to sphere.reg
$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
mri_surf2surf --srcsubject sub1 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval area/tmp.mris_preproc.4084/sub1.1.mgh --sval /sub1/surf/lh.area --jac --sfmt curv --noreshape --cortex
sysname Linux hostname localhost.localdomain machine x86_64 srcsubject = sub1 srcval = /sub1/surf/lh.area srctype = curv trgsubject = fsaverage5 trgval = area/tmp.mris_preproc.4084/sub1.1.mgh trgtype = srcsurfreg = fsaverage5.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /sub1/surf/lh.fsaverage5.sphere.reg No such file or directory mri_surf2surf: could not read surface /sub1/surf/lh.fsaverage5.sphere.reg No such file or directory
Appreciated for your help!
Lili
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Lili Jiang Associate Research Professor Institute of Psychology
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
姜黎黎