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
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