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
sysname Linux
hostname img-140.drc.ion.ucl.ac.uk
machine x86_64
user ebunting
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