If you want to use a target other than fsaverage, then you need to register each subject to that target (eg, with surfreg). If you have found a problem with mris_make_subject, please document it in a separate post.
On 2/12/19 6:38 AM, Bunting, Emma wrote: > > External Email - Use Caution > > Hi Freesurfer Pros, > > I'm trying to perform mris_preproc with an average subject that I > created called 'avgsubject.Patients_EB', as my target. > > Although it appears to take avgsubject.Patients_EB as the target > subject, and VIPD_010 (the first subject in my fsgd file) as the > source subject, it then somehow swaps the target and source surfaces > (sphere.reg's) it is trying to call upon. I am therefore getting an > error because there is no avgsubject.Patients_EB.sphere.reg file > within the VIPD_010 subject folder. > > The commands I use for the mri_preproc are below, with the sections I > am referring to highlighted in bold. > > ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd > PDonly_Liu_EB.fsgd \ > > *> --target avgsubject.Patients_EB \* > > > --hemi lh \ > > > --meas thickness \ > > > --out lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mgh \ > > > > > nsubjects = 97 > > tmpdir is ./tmp.mris_preproc.12493 > > /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer > > Log file is > lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mris_preproc.log > > Tue Feb 12 11:20:49 GMT 2019 > > setenv SUBJECTS_DIR > /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer > > cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer > > /var/drc/software/64bit/freesurfer-6.0.0//bin/mris_preproc --fsgd > PDonly_Liu_EB.fsgd --target avgsubject.Patients_EB --hemi lh --meas > thickness --out lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mgh > > Linux img-140.drc.ion.ucl.ac.uk 2.6.32-279.el6.x86_64 #1 SMP Wed Jun > 13 18:24:36 EDT 2012 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.12493 > > Src lh avgsubject.Patients_EB.sphere.reg > > Trg lh sphere.reg > > --------------------------------------------------- > > #@# 1/97 VIPD_010 Tue Feb 12 11:20:49 GMT 2019 -------------- > > ----------------------- > > mri_surf2surf *--srcsubject VIPD_010* --srchemi lh -*-srcsurfreg > avgsubject.Patients_EB.sphere.reg* -*-trgsubject > avgsubject.Patients_EB* --trghemi lh *--trgsurfreg sphere.reg *--tval > ./tmp.mris_preproc.12493/VIPD_010.1.mgh --sval > /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness > > --sfmt curv --noreshape --cortex > > MRISread(/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg): > > could not open file > > *Source registration surface changed to avgsubject.Patients_EB.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 > /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer > > cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer > > mri_surf2surf -*-srcsubject VIPD_010 -*-srchemi lh *--srcsurfreg > avgsubject.Patients_EB.sphere.reg* *--trgsubject > avgsubject.Patients_EB* --trghemi lh *--trgsurfreg sphere.reg* --tval > ./tmp.mris_preproc.12493/VIPD_010.1.mgh --sval > /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness > > --sfmt curv --noreshape --cortex > > sysnameLinux > > hostname img-140.drc.ion.ucl.ac.uk > > machinex86_64 > > userebunting > > srcsubject = VIPD_010 > > srcval= > /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness > > srctype= curv > > *trgsubject = avgsubject.Patients_EB* > > trgval= ./tmp.mris_preproc.12493/VIPD_010.1.mgh > > trgtype= > > *srcsurfreg = avgsubject.Patients_EB.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 > /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg* > > *No such file or directory* > > *mri_surf2surf: could not read surface > /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg* > > *No such file or directory* > > n.b. that the lh.avgsubject.Patients_EB.sphere.reg file can be found > within the avgsubject.Patients_EB/surf folder, so I believe this is an > issue of simply mixing the target and source surfaces. > > It is also worth noting that I have found your bug fix for the > make_average_*surface *script, which now completes without errors. > However, the make_average_subject script still completes with errors, > and when I try to use the average_surface output as my target I get > the same errors. > > Please let me know if there is something I am doing wrong here, or if > there is a way to fix the error I am getting! > > > Many thanks, > > > Emma Bunting > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
