Dear Support,
I am trying to use fcseed-sess to create a ventricle and CSF regressor for
my resting state analysis. I have encountered an error running
fcseed-sess.
fcseed-config -vcsf -fsd Bold1 -mean -cfg vcsf_bold1_config -overwrite
works, but then the following command fails:
fcseed-sess -s AC30_1319 -cfg vcsf_bold1_config -overwrite
The above command worked for half my subjects and had the below error for
half with no discernible pattern. I've run it on jizo as well as my home
machine with the same error.
Cut-and-paste the following info into your FreeSurfer problem report:
---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
RedHat release: CentOS release 6.4 (Final)
Kernel info: Linux 2.6.32-358.2.1.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: jizo
SUBJECTS_DIR: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
PWD: /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
ssh jizo
setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
---------------------------------------------------------------------
I would appreciate any help. Let me know if anything is unclear.
Thank!
Best,
Omar
Error Message
*************
[jizo:fc_fs] (nmr-stable53-env) fcseed-sess -s AC30_1319 -cfg
vcsf_bold1_config -overwrite
Logfile is
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/log/fcseed-sess.vcsf_bold1_config.log.AC30_1319
Wed Aug 14 11:31:50 EDT 2013
Linux jizo 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
/usr/local/freesurfer/stable5_3_0/fsfast/bin/fcseed-sess
-s AC30_1319 -cfg vcsf_bold1_config -overwrite
freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
Wed Aug 14 11:31:50 EDT 2013
Linux jizo 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
cd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
/usr/local/freesurfer/stable5_3_0/fsfast/bin/fcseed-sess
-s AC30_1319 -cfg vcsf_bold1_config -overwrite
freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
mri_label2vol --seg
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/mri/aparc+aseg.mgz
--reg
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat
--temp
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/template.nii.gz
--fillthresh .95 --o
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz
--pvf
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz
PVF
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz
Number of labels: 0
Annot File: (null)
Template Volume:
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/template.nii.gz
Outut Volume:
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz
Registration File:
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat
Fill Threshold: 0.95
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: (null)
Hemi: (null)
UseNewASeg2Vol: 1
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: --------
-0.320 0.000 0.000 32.000;
-0.000 -0.000 -0.320 32.000;
-0.000 0.167 -0.000 12.500;
0.000 0.000 0.000 1.000;
Template Voxel Volume: 58.5938
nHits Thresh: 55.6641
Loading registration from
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/register.dof6.dat
RegMat: --------
-0.106 0.977 -0.185 7.376;
-0.994 -0.104 0.019 -0.687;
-0.000 0.186 0.983 -23.526;
0.000 0.000 0.000 1.000;
Label RAS-to-Vox: --------
0.034 -0.313 0.059 29.640;
0.000 -0.059 -0.314 39.528;
-0.166 -0.017 0.003 12.385;
0.000 0.000 0.000 1.000;
ASeg2Vol: Building LUT
ASeg2Vol: Sorting
ASeg2Vol: Mapping
ASeg2Vol: Reverse Map
nmisses = 1120 (0 filled)
ASeg2Vol: done
PVF
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/pvf.nii.gz
Computing PVF 58.5938
mri_binarize --i
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz
--o
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz
--match 4 --match 5 --match 43 --match 44 --match 31 --match 63
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs
cmdline mri_binarize --i
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz
--o
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz
--match 4 --match 5 --match 43 --match 44 --match 31 --match 63
sysname Linux
hostname jizo
machine x86_64
user osinglet
input
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/seg.nii.gz
frame 0
nErode3d 0
nErode2d 0
output
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz
Binarizing based on matching values
nMatch 6
0 4
1 5
2 43
3 44
4 31
5 63
binval 1
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 0 voxels in final mask
mri_binarize done
mri_segstats --i
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz
--seg
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz
--id 1 --sum
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/junk.sum
--avgwfvol
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz
--seg
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz
--id 1 --sum
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/junk.sum
--avgwfvol
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh
sysname Linux
hostname jizo
machine x86_64
user osinglet
UseRobust 0
Loading
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/mask.nii.gz
Loading
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/fmcpr.nii.gz
Voxel Volume is 58.5938 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 0 0.000
MRIalloc(0, 1, 1): bad parm
Reporting on 0 segmentations
Computing spatial average of each frame
Writing to
/autofs/cluster/lazar/projects/Omar/aging_conn/fc_fs/AC30_1319/Bold1/001/tmp.fcseed-sess.2081/avgwf.mgh
Segmentation fault (core dumped)