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 >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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