New subject: fcseed-sess error

19 Aug 2013

      Sorry about that. I must have clicked 'reply' by mistake rather than
'reply all'. I wouldn't want to deprive anyone of the opportunity to help
me resolve this issue.
--The issue--
I looked at the segmentation in tkmedit and the labels for the ventricles
showed up the same as in subjects that worked. I checked registration by
eye and used this command from the tutorial:
tkregister-sess -s AC30_1319 -fsd Bold1 -per-run -bbr-sum
Which output:
AC30_1319  001 0.4437
I'm not sure what the problem is with these subjects. Is there another way
I should check the data? Any suggestions?
-Omar
...
Hi Omar, can you post questions to the list instead of us personally?
thanks!
doug
On 08/19/2013 09:41 AM, Omar Singleton wrote:
...
Hi Doug,
Thanks for the help. I looked at the segmentation in tkmedit and the
labels for the ventricles showed up the same as in subjects that worked.
I
checked registration by eye and used this command from the tutorial:
tkregister-sess -s AC30_1319 -fsd Bold1 -per-run -bbr-sum
Which output:
AC30_1319  001 0.4437
I'm not sure what the problem is with these subjects. Is there another
way
I should check the data? Do you have any other suggestions?
Best,
Omar
...
Hi Omar,  it is not finding any ventricle voxels. Check the FS
segmentation to make sure that the ventricles are labeled and also
check
the registration to make sure it looks ok.
doug
On 8/14/13 12:04 PM, O S wrote:
...
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)
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Re: [Freesurfer] fcseed-sess error

Cut-and-paste the following info into your FreeSurfer problem report:

Cut-and-paste the following info into your FreeSurfer problem report: