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Hello, I am running into an error while running the LGI analyses using FreeSurfer 6.0 following Jove article recommendations ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). The error is occuring when I try to run the following command: mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh
Here is the error message: nsubjects = 57tmpdir is ./tmp.mris_preproc.174575 /data/EDresearch/AdolAN_All/enigma/output Log file is lh.lgi.mris_preproc.log Mon Aug 31 08:25:13 PDT 2020 setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output /usr/local/freesurfer/bin/mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh
Linux induction3.sdsc.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 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 ./tmp.mris_preproc.174575 Src lh average.sphere.reg Trg lh sphere.reg
--------------------------------------------------- #@# 1/57 541202132011 Mon Aug 31 08:25:13 PDT 2020 -------------- ----------------------- mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex MRISread(/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg): could not open file Source registration surface changed to average.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 /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex
sysname Linux hostname induction3.sdsc.edu machine x86_64 user chays srcsubject = 541202132011 srcval = /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi srctype = curv trgsubject = average trgval = ./tmp.mris_preproc.174575/541202132011.1.mgh trgtype = srcsurfreg = average.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 /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory mri_surf2surf: could not read surface /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory
Of note, this command works fine when substituting the fsaverage rather than study average template, however this is an adolescent sample so we are not able to use the fsaverage. Any help would be greatly appreciated! Best, Chelsea
Chelsea C. Hays, Ph.D. Neuropsychology Postdoctoral Fellow Center of Excellence in Stress and Mental Health UC San Diego|VA San Diego Healthcare Systemchays@ucsd.edu|chelsea.hays2@va.gov
Why are you specifying the target as average instead of fsaverage?
On 8/31/20 12:13 PM, chelseachays@yahoo.com wrote:
External Email - Use Caution
Hello, I am running into an error while running the LGI analyses using FreeSurfer 6.0 following Jove article recommendations ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). The error is occuring when I try to run the following command:
mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh
Here is the error message:
nsubjects = 57 tmpdir is ./tmp.mris_preproc.174575 /data/EDresearch/AdolAN_All/enigma/output Log file is lh.lgi.mris_preproc.log Mon Aug 31 08:25:13 PDT 2020 setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output /usr/local/freesurfer/bin/mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh
Linux induction3.sdsc.edu http://induction3.sdsc.edu/ 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 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 ./tmp.mris_preproc.174575 Src lh average.sphere.reg Trg lh sphere.reg
#@# 1/57 541202132011 Mon Aug 31 08:25:13 PDT 2020 --------------
mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex MRISread(/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg): could not open file Source registration surface changed to average.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 /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex
sysname Linux hostname induction3.sdsc.edu http://induction3.sdsc.edu/ machine x86_64 user chays srcsubject = 541202132011 srcval = /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi srctype = curv trgsubject = average trgval = ./tmp.mris_preproc.174575/541202132011.1.mgh trgtype = srcsurfreg = average.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 /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory mri_surf2surf: could not read surface /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory / /
Of note, this command works fine when substituting the fsaverage rather than study average template, however this is an adolescent sample so we are not able to use the fsaverage. Any help would be greatly appreciated!
Best, Chelsea
Chelsea C. Hays, Ph.D. Neuropsychology Postdoctoral Fellow Center of Excellence in Stress and Mental Health UC San Diego|VA San Diego Healthcare System chays@ucsd.edu mailto:chays@ucsd.edu|chelsea.hays2@va.gov mailto:chelsea.hays2@va.gov
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Douglas, Because the Jove article recommends using a study-specific template (cited the article in the original post) and our analyses is being run on an adolescent sample. Therefore, "average" corresponds to the average template for our current sample. Let me know if you have any other questions! Best, Chelsea Chelsea C. Hays, Ph.D. Neuropsychology Postdoctoral Fellow Center of Excellence in Stress and Mental Health UC San Diego|VA San Diego Healthcare Systemchays@ucsd.edu|chelsea.hays2@va.gov
On Tuesday, September 1, 2020, 07:33:34 AM PDT, Douglas Greve dgreve@mgh.harvard.edu wrote:
Why are you specifying the target as average instead of fsaverage?
On 8/31/20 12:13 PM, chelseachays@yahoo.com wrote:
External Email - Use Caution Hello, I am running into an error while running the LGI analyses using FreeSurfer 6.0 following Jove article recommendations ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). The error is occuring when I try to run the following command: mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh
Here is the error message: nsubjects = 57 tmpdir is ./tmp.mris_preproc.174575 /data/EDresearch/AdolAN_All/enigma/output Log file is lh.lgi.mris_preproc.log Mon Aug 31 08:25:13 PDT 2020 setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output /usr/local/freesurfer/bin/mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh
Linux induction3.sdsc.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 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 ./tmp.mris_preproc.174575 Src lh average.sphere.reg Trg lh sphere.reg
--------------------------------------------------- #@# 1/57 541202132011 Mon Aug 31 08:25:13 PDT 2020 -------------- ----------------------- mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex MRISread(/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg): could not open file Source registration surface changed to average.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 /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex
sysname Linux hostname induction3.sdsc.edu machine x86_64 user chays srcsubject = 541202132011 srcval = /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi srctype = curv trgsubject = average trgval = ./tmp.mris_preproc.174575/541202132011.1.mgh trgtype = srcsurfreg = average.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/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory mri_surf2surf: could not read surface/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory
Of note, this command works fine when substituting the fsaverage rather than study average template, however this is an adolescent sample so we are not able to use the fsaverage. Any help would be greatly appreciated! Best, Chelsea
Chelsea C. Hays, Ph.D. Neuropsychology Postdoctoral Fellow Center of Excellence in Stress and Mental Health UC San Diego|VA San Diego Healthcare System chays@ucsd.edu|chelsea.hays2@va.gov
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ah, I see. Um. Well, at the time of that publication, mris_preproc had a bug in that it was actually sampling onto fsaverage and not truly the target subject (though it was smoothing on the target subject). So, in version 6, I changed it to sample to the target subject by requiring that the input subject be registered to the target. For fsaverage, this is done as part of recon-all. Since you have your own average, you will need to do it yourself with
surfreg --s subject --t average
for each subject (probably 1-2 hours per subject). Then when you run mris_preproc, it should find that registration and run properly. Now, having said all that, it was probably an incomplete conclusion from the paper that a custom template is needed, so I don't know if you need to do it or not. Probably makes it easier to publish to just do it the way in the paper.
On 9/1/2020 3:24 PM, chelseachays@yahoo.com wrote:
External Email - Use Caution
Hi Douglas, Because the Jove article recommends using a study-specific template (cited the article in the original post) and our analyses is being run on an adolescent sample. Therefore, "average" corresponds to the average template for our current sample. Let me know if you have any other questions!
Best, Chelsea
Chelsea C. Hays, Ph.D. Neuropsychology Postdoctoral Fellow Center of Excellence in Stress and Mental Health UC San Diego|VA San Diego Healthcare System chays@ucsd.edu mailto:chays@ucsd.edu|chelsea.hays2@va.gov mailto:chelsea.hays2@va.gov
On Tuesday, September 1, 2020, 07:33:34 AM PDT, Douglas Greve dgreve@mgh.harvard.edu wrote:
Why are you specifying the target as average instead of fsaverage?
On 8/31/20 12:13 PM, chelseachays@yahoo.com mailto:chelseachays@yahoo.com wrote:
External Email - Use Caution
Hello, I am running into an error while running the LGI analyses using FreeSurfer 6.0 following Jove article recommendations ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). The error is occuring when I try to run the following command:
mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh
Here is the error message:
nsubjects = 57 tmpdir is ./tmp.mris_preproc.174575 /data/EDresearch/AdolAN_All/enigma/output Log file is lh.lgi.mris_preproc.log Mon Aug 31 08:25:13 PDT 2020 setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output /usr/local/freesurfer/bin/mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out lh.lgi.mgh
Linux induction3.sdsc.edu http://induction3.sdsc.edu/ 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 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 ./tmp.mris_preproc.174575 Src lh average.sphere.reg Trg lh sphere.reg
#@# 1/57 541202132011 Mon Aug 31 08:25:13 PDT 2020 --------------
mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex MRISread(/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg): could not open file Source registration surface changed to average.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 /data/EDresearch/AdolAN_All/enigma/output cd /data/EDresearch/AdolAN_All/enigma/output mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt curv --noreshape --cortex
sysname Linux hostname induction3.sdsc.edu http://induction3.sdsc.edu/ machine x86_64 user chays srcsubject = 541202132011 srcval = /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi srctype = curv trgsubject = average trgval = ./tmp.mris_preproc.174575/541202132011.1.mgh trgtype = srcsurfreg = average.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 /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory mri_surf2surf: could not read surface /data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg No such file or directory / /
Of note, this command works fine when substituting the fsaverage rather than study average template, however this is an adolescent sample so we are not able to use the fsaverage. Any help would be greatly appreciated!
Best, Chelsea
Chelsea C. Hays, Ph.D. Neuropsychology Postdoctoral Fellow Center of Excellence in Stress and Mental Health UC San Diego|VA San Diego Healthcare System chays@ucsd.edu mailto:chays@ucsd.edu|chelsea.hays2@va.gov mailto:chelsea.hays2@va.gov
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