Hello Freesurfer Developers,

I'm working on group analysis, and I have done GLM analysis(mris_glmfit) on Linux. Next step is to visualize it, so I followed the instruction from the FsTutorial website. 

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d

Basically, I ran the commend above, and I got the effor "Unrecognized sub-option flag 'annot_outline'" or "unrecognized sub-opton flag 'overlay_threshold'." I think it's because I'm using old FS version which is 5.1, and the tutorial is based on FS 6.1 version. I tried to use tksurfer, but for some reason, it didn't work. I decided to use a freeview anyway.

On 5.1 version, what do I need to do to visualize them? How should I deal with overlay threshold and annot_outline? Please let me know.

Best regards,
Younghoon Kwon


2016-07-14 14:01 GMT-04:00 YoungHoon Kwon <yhkn11@gmail.com>:

---------- Forwarded message ----------
From: YoungHoon Kwon <yhkn11@gmail.com>
Date: 2016-07-13 21:10 GMT-04:00
Subject: mri_preproc error
To: freesurfer@nmr.mgh.harvard.edu


Hello FreeSurfer Developers,

I tried to assemble the data by using mri_preproc, then it shows segmentation fault (core dumped) after running. I searched for the solution, but I couldn't find it.

Here's information

Error : Segmentation fault (core dumped)

Input : FS.txt (FSGD file)
GroupDescriptorFile 1        
Title All        
Class Male        
Class Female        
Input    002_S_4213_A    Male
Input    002_S_4225_A    Male
Input    002_S_4262_A    Female

command:
[knho@in-rady-neuro11 test]$ mris_preproc --fsgd FS.txt \ --target fsaverage --hemi lh \ --meas thickness \ --out practice_result.mgh
nsubjects = 3
tmpdir is ./tmp.mris_preproc.2677
/localscratch3/test
Log file is practice_result.mris_preproc.log
Wed Jul 13 19:31:44 EDT 2016
setenv SUBJECTS_DIR /localscratch3/test
cd /localscratch3/test
/net/age3/DATA_from_AGE0/FREESURFER/freesurfer51/bin/mris_preproc --fsgd FS.txt --target fsaverage --hemi lh --meas thickness --out practice_result.mgh

Linux in-rady-neuro11.indyrad.iupui.edu 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
$Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
tmpdir is ./tmp.mris_preproc.2677
Src lh sphere.reg
Trg lh sphere.reg

---------------------------------------------------
#@# 1/3 002_S_4213_A Wed Jul 13 19:31:44 EDT 2016 --------------
-----------------------
mri_surf2surf --srcsubject 002_S_4213_A --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.2677/002_S_4213_A.1.mgh --sval /localscratch3/test/002_S_4213_A/surf/lh.thickness --sfmt curv --noreshape --no-cortex
Segmentation fault (core dumped)

I found some advice from online, and it suggested to run recon-all; however it didn't work. I really don't know what is wrong. Can anyone figure out this error?

1) Versioin : FreeSurfer 5.1
2) Platform : Linux
3) uname -a : Linux in-rady-neuro11.indyrad.iupui.edu 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux