That looks good. Run these commands
cd AC30_1319/Bold1/001 mri_label2vol --aparc+aseg --temp template.nii.gz --reg register.dof6.dat --o aparc+aseg.nii.gz mri_binarize --i aparc+aseg.nii.gz --match 4 --match 5 --match 43 --match 44 --match 31 --match 63 --count countfile.dat
then send me the contents of countfile.dat
doug
On 08/19/2013 02:27 PM, Omar Singleton wrote:
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) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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