Thanks- the command line is
unpacksdcmdir -src
/cluster/archive/302/siemens/TrioTim-35006-20121203-151132-241000 -targ
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037
-cfg
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/cfg.file
Here is the output:
$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037
-src /cluster/archive/302/siemens/TrioTim-35006-20121203-151132-241000 -targ
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037
-cfg
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/cfg.file
Tue Dec 11 17:08:22 EST 2012
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2012/12/11-22:08:22-GMT BuildTimeStamp: Sep 27 2011
05:57:44 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
User: shin Machine: grover Platform: Linux PlatformVersion:
2.6.32-279.11.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400
grover
Linux grover 2.6.32-279.11.1.el6.x86_64 #1 SMP Tue Oct 16 15:57:10 UTC 2012
x86_64 x86_64 x86_64 GNU/Linux
Tue Dec 11 17:08:22 EST 2012
Log File is
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/unpack.log
INFO: Logfile is
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/dicomdir.sumfile
INFO: status file is
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/parse.status
Scanning directory Tue Dec 11 17:08:22 EST 2012
mri_parse_sdcmdir --sortbyrun --d
/cluster/archive/302/siemens/TrioTim-35006-20121203-151132-241000 --o
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/dicomdir.sumfile
--status
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/parse.status
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38
40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78
80 82 84 86 88 90 92 94 96 98 100
Done scanning Tue Dec 11 17:13:44 EST 2012
------------------------------------------
1 localizer_32ch ok 512 512 3 1
MR.1.3.12.2.1107.5.2.32.35006.201212031512189488415605
2 RF_spectrum_8192 ok 32 32 1 1
MR.1.3.12.2.1107.5.2.32.35006.2012120315131372885015622
3 AAScout ok 128 128 128 2
MR.1.3.12.2.1107.5.2.32.35006.2012120315134276071315665
4 MEMPRAGE_4e_1mm_iso ok 256 256 176 4
MR.1.3.12.2.1107.5.2.32.35006.2012120315210056072317298
5 MEMPRAGE_4e_1mm_iso ok 256 256 176 1
MR.1.3.12.2.1107.5.2.32.35006.2012120315210131818517338
6 field_mapping_64_3mm_habit ok 64 64 48 2
MR.1.3.12.2.1107.5.2.32.35006.2012120315231053573121267
7 field_mapping_64_3mm_habit ok 64 64 48 1
MR.1.3.12.2.1107.5.2.32.35006.2012120315231076313621362
8 ge_func_64_3mm_HABIT ok 64 64 48 64
MR.1.3.12.2.1107.5.2.32.35006.2012120315244232996221682
9 field_mapping_64_3mm_cond ok 64 64 48 2
MR.1.3.12.2.1107.5.2.32.35006.2012120315301277946634078
10 field_mapping_64_3mm_cond ok 64 64 48 1
MR.1.3.12.2.1107.5.2.32.35006.20121203153013658334173
11 ge_func_64_3mm_COND ok 64 64 48 315
MR.1.3.12.2.1107.5.2.32.35006.2012120315305614911534475
12 field_mapping_64_3mm_ext ok 64 64 48 2
MR.1.3.12.2.1107.5.2.32.35006.2012120315471467803295583
13 field_mapping_64_3mm_ext ok 64 64 48 1
MR.1.3.12.2.1107.5.2.32.35006.2012120315471490523995678
14 ge_func_64_3mm_EXT ok 64 64 48 315
MR.1.3.12.2.1107.5.2.32.35006.2012120315480029624995988
15 field_mapping_DTI ok 112 112 72 2
MR.1.3.12.2.1107.5.2.32.35006.2012120316060970677357073
16 field_mapping_DTI ok 112 112 72 1
MR.1.3.12.2.1107.5.2.32.35006.2012120316061096822157398
17 DTI_1.9mm_iso err 112 112 72 70
MR.1.3.12.2.1107.5.2.32.35006.2012120316070863798257936
18 DTI_1.9mm_iso ok 112 112 72 1
MR.1.3.12.2.1107.5.2.32.35006.201212031617379119982912
19 DTI_1.9mm_iso ok 112 112 72 1
MR.1.3.12.2.1107.5.2.32.35006.201212031617379168082913
20 DTI_1.9mm_iso ok 112 112 72 1
MR.1.3.12.2.1107.5.2.32.35006.201212031617379226382914
21 DTI_1.9mm_iso ok 112 112 72 1
MR.1.3.12.2.1107.5.2.32.35006.201212031617379260882915
22 DTI_1.9mm_iso ok 112 112 72 1
MR.1.3.12.2.1107.5.2.32.35006.201212031617379312582916
23 DTI_1.9mm_iso ok 112 112 1 72
MR.1.3.12.2.1107.5.2.32.35006.201212031617379352382917
unpacking config ------------------
{5 anat NII anat1_d1.nii} {8 BOLD NII habit.nii} {11
BOLD NII cond.nii} {14 BOLD NII ext.nii}
-----------------------------------
---------------------------------------------------------
Run 5 -----------------------------------------
Tue Dec 11 17:13:44 EST 2012
5 anat NII anat1_d1.nii
mri_convert
/cluster/archive/302/siemens/TrioTim-35006-20121203-151132-241000/MR.1.3.12.2.1107.5.2.32.35006.2012120315210131818517338
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/anat/005/anat1_d1.nii
--sdcmlist
/autofs/space/ernie_002/users/RAW_DATA_All_Subjects/Patients_and_Controls/Controls_32ch/San_Juan_TENC/SJT037/anat/005/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
---------------------------------------------------------
Run 8 -----------------------------------------
Tue Dec 11 17:14:02 EST 2012
8 BOLD NII habit.nii
while executing
"close $flfid"
("foreach" body line 149)
invoked from within
"foreach runcfg $unpackcfg {
set RunNo [lindex $runcfg 0];
set SubDir [lindex $runcfg 1];
set Fmt [lindex $runcfg 2];
set Name [lindex $r..."
(file "/usr/local/freesurfer/stable5_1_0/bin/unpacksdcmdir.tcl" line 1197)
[grover:SJT037] (nmr-stable5.1-env)
________________________________________
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: Tuesday, December 11, 2012 5:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] unpacking error
Hi Lindsay, you'll have to give us more information. Tell us what the
command line is and the full terminal output.
thanks
doug
On 12/11/2012 05:20 PM, Staples, Lindsay Katharine wrote:
> Hi-
>
> I don't know much about freesurfer other than the very basics. Can anyone
> tell me why I would be getting the following error when I run the second
> unpacking command?
>
> while executing
> "close $flfid"
> ("foreach" body line 149)
> invoked from within
> "foreach runcfg $unpackcfg {
> set RunNo [lindex $runcfg 0];
> set SubDir [lindex $runcfg 1];
> set Fmt [lindex $runcfg 2];
> set Name [lindex $r..."
> (file "/usr/local/freesurfer/stable5_1_0/bin/unpacksdcmdir.tcl" line
> 1197)
>
>
> Thanks!
> Lindsay
>
> _______________________________________________
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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