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
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