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?
- Versioin : FreeSurfer 5.1
- Platform : Linux
- 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