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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