Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
It did, I removed 2 of them and it's running fine now. Thanks! Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2016 5:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error Check the contents of /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname It may have the subjectname repeated 3 times On 07/18/2016 05:45 PM, Hibert, Matthew Louis wrote: > Attached. I took a quick look and it seems that I wrote the subject name 3 > times, on new lines, to the subjectname file. I removed 2 of them and re-ran > selxavg3-sess and it appears to be working. > > Thanks for the help Doug. > > Matt > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2016 5:23 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error > > Can you run the command below and send me dng.log? > > register-sess -debug -s nmr00978 -d > /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 > -per-run -nolog -update |& tee dng.log > > On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote: >> Hi All, >> I'm running into an error analyzing some fMRI data with FS-FAST in >> Freesurfer version 5.3. The analysis runs fine until it gets to the >> register-sess part, which quits before actually starting to do any >> registration. The last line of the log file, attached, is "if: >> Expression syntax", but there are no other errors prior to that. The >> command I'm using, analysis, and contrasts have all worked on several >> other similar data sets. Has anyone encountered this problem before, >> or know what's causing it? >> >> Thanks, >> Matt >> >> Clinical Research Coordinator >> Stufflebeam Lab >> Athinoula A. Martinos Center >> Massachusetts General Hospital >> 149 13th Street, Room 1115S >> Charlestown, MA 02129 >> >> >> ___ >> 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/ > > ___ > 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/ ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
Check the contents of /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname It may have the subjectname repeated 3 times On 07/18/2016 05:45 PM, Hibert, Matthew Louis wrote: > Attached. I took a quick look and it seems that I wrote the subject name 3 > times, on new lines, to the subjectname file. I removed 2 of them and re-ran > selxavg3-sess and it appears to be working. > > Thanks for the help Doug. > > Matt > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2016 5:23 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error > > Can you run the command below and send me dng.log? > > register-sess -debug -s nmr00978 -d > /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 > -per-run -nolog -update |& tee dng.log > > On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote: >> Hi All, >> I'm running into an error analyzing some fMRI data with FS-FAST in >> Freesurfer version 5.3. The analysis runs fine until it gets to the >> register-sess part, which quits before actually starting to do any >> registration. The last line of the log file, attached, is "if: >> Expression syntax", but there are no other errors prior to that. The >> command I'm using, analysis, and contrasts have all worked on several >> other similar data sets. Has anyone encountered this problem before, >> or know what's causing it? >> >> Thanks, >> Matt >> >> Clinical Research Coordinator >> Stufflebeam Lab >> Athinoula A. Martinos Center >> Massachusetts General Hospital >> 149 13th Street, Room 1115S >> Charlestown, MA 02129 >> >> >> ___ >> 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/ > > ___ > 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/ ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
Attached. I took a quick look and it seems that I wrote the subject name 3 times, on new lines, to the subjectname file. I removed 2 of them and re-ran selxavg3-sess and it appears to be working. Thanks for the help Doug. Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2016 5:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error Can you run the command below and send me dng.log? register-sess -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update |& tee dng.log On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote: > Hi All, > I'm running into an error analyzing some fMRI data with FS-FAST in > Freesurfer version 5.3. The analysis runs fine until it gets to the > register-sess part, which quits before actually starting to do any > registration. The last line of the log file, attached, is "if: > Expression syntax", but there are no other errors prior to that. The > command I'm using, analysis, and contrasts have all worked on several > other similar data sets. Has anyone encountered this problem before, > or know what's causing it? > > Thanks, > Matt > > Clinical Research Coordinator > Stufflebeam Lab > Athinoula A. Martinos Center > Massachusetts General Hospital > 149 13th Street, Room 1115S > Charlestown, MA 02129 > > > ___ > 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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 11 != 0 ) set flag = $argv[1] ; shift ; set flag = -s shift switch ( $flag ) switch ( -s ) case "-sf": case -sf: case "-df": case -df: case "-d": case -d: case "-g": case -g: shift ; shift breaksw breaksw end end while ( $#argv != 0 ) while ( 9 != 0 ) set flag = $argv[1] ; shift ; set flag = -d shift switch ( $flag ) switch ( -d ) case "-g": case -g: shift ; shift breaksw breaksw end end while ( $#argv != 0 ) while ( 7 != 0 ) set flag = $argv[1] ; shift ; set flag = -fsd shift switch ( $flag ) switch ( -fsd ) if ( $#argv < 1 ) goto arg1err ; if ( 6 < 1 ) goto arg1err set fsd = $argv[1] ; shift ; set fsd = sycabs shift breaksw breaksw end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift ; set flag = -dof shift switch ( $flag ) switch ( -dof ) if ( $#argv < 1 ) goto arg1err ; if ( 4 < 1 ) goto arg1err set dof = $argv[1] ; shift ; set dof = 6 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 3 != 0 ) set flag = $argv[1] ; shift ; set flag = -per-run shift switch ( $flag ) switch ( -per-run ) case "-perrun": case -perrun: set PerRun = 1 ; set PerRun = 1 set PerSess = 0 ; set PerSess = 0 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = -nolog shift switch ( $flag ) switch ( -nolog ) set nolog = 1 ; set nolog = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 1 != 0 ) set flag = $argv[1] ; shift ; set flag = -update shift switch ( $flag ) switch ( -update ) set UpdateOnly = 1 ; set UpdateOnly = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return set SessList = `getsesspath $inputargs` ; set SessList = `getsesspath $inputargs` getsesspath -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 11 != 0 ) set flag = $argv[1] ; shift ; set flag = -s shift switch ( $flag ) switch ( -s ) if ( $#argv == 0 ) goto arg1err ; if ( 10 == 0 ) goto arg1err set SessList = ( $SessList $argv[1] ) ; shift ; set SessList = ( nmr00978 ) shift breaksw breaksw end end while ( $#argv != 0 ) while ( 9 != 0 ) set flag = $argv[1] ; shift ; set flag = -d shift switch ( $flag ) switch ( -d ) if ( $#argv == 0 ) goto arg1err ; if ( 8 == 0 ) goto arg1err if ( ! -d $argv[1] ) then if ( ! -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) then if ( ! -r $argv[1] ) then if ( ! -r /autofs/cluster/neur
Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
Can you run the command below and send me dng.log? register-sess -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update |& tee dng.log On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote: > Hi All, > I'm running into an error analyzing some fMRI data with FS-FAST in > Freesurfer version 5.3. The analysis runs fine until it gets to the > register-sess part, which quits before actually starting to do any > registration. The last line of the log file, attached, is "if: > Expression syntax", but there are no other errors prior to that. The > command I'm using, analysis, and contrasts have all worked on several > other similar data sets. Has anyone encountered this problem before, > or know what's causing it? > > Thanks, > Matt > > Clinical Research Coordinator > Stufflebeam Lab > Athinoula A. Martinos Center > Massachusetts General Hospital > 149 13th Street, Room 1115S > Charlestown, MA 02129 > > > ___ > 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/ ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FS-FAST "If: Expression Syntax" Error
Hi All, I'm running into an error analyzing some fMRI data with FS-FAST in Freesurfer version 5.3. The analysis runs fine until it gets to the register-sess part, which quits before actually starting to do any registration. The last line of the log file, attached, is "if: Expression syntax", but there are no other errors prior to that. The command I'm using, analysis, and contrasts have all worked on several other similar data sets. Has anyone encountered this problem before, or know what's causing it? Thanks, Matt Clinical Research Coordinator Stufflebeam Lab Athinoula A. Martinos Center Massachusetts General Hospital 149 13th Street, Room 1115S Charlestown, MA 02129 selxavg3-sess log file /usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess -analysis sycabs_self_lh -s nmr00978 -d /cluster/neuromind/dwakeman/tsc_pilot/subjects/ $Id: selxavg3-sess,v 1.57.2.1 2011/12/09 20:06:47 greve Exp $ uid=3882345(kz221) gid=3882345(kz221) groups=3882345(kz221),1084(megclin),1125(smsgp) /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed Jul 13 13:42:24 EDT 2016 preproc-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -a sycabs_self_lh -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ kz221 setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/ Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -a sycabs_self_lh -nolog Wed Jul 13 13:42:25 EDT 2016 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain nmr00978 Template - mktemplate-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -nolog -update Session: /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 Wed Jul 13 13:42:25 EDT 2016 Detected input format at nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz --frame 0 mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.7, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.0077173, -0.178789, 0.983857) keeping frame 0 writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz... Run: 009 Wed Jul 13 13:42:36 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz --mid-frame mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.7, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.0077173, -0.178789, 0.983857) keeping frame 238 writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz... Run: 010 Wed Jul 13 13:42:46 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/template.nii.gz --mid-frame mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.7, -0.00137983, 0.00759295) j_ras = (
