Try using a lower case nii insteadof NII.
doug
On 12/11/2012 05:45 PM, Staples, Lindsay Katharine wrote:
> 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/
>
> _______________________________________________
> 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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