---------- Forwarded message ----------
From: Luc Amdahl <luc.amdahl@gmail.com>
Date: Mon, Jun 17, 2013 at 3:45 PM
Subject: Re: [Freesurfer] DICOM unpacking error
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>

Hi Bruce,

Thanks for responding.

Here is the command line and screen output:

[Sheinberg-Lab-MRI-iMac:~/MRI/Solar_System] lab% unpacksdcmdir -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii

$Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $

/Users/lab/MRI/Solar_System

-src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii

Fri Jun 14 09:47:20 EDT 2013

mri_convert -all-info

ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/14-13:47:20-GMT BuildTimeStamp: May 13 2013 16:45:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: lab Machine: Sheinberg-Lab-MRI-iMac.local Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000

Sheinberg-Lab-MRI-iMac.local

Darwin Sheinberg-Lab-MRI-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386

Fri Jun 14 09:47:20 EDT 2013

Log File is subj_4/unpack.log

INFO: Logfile is subj_4/unpack.log

SkipMoCo 0

Scanning source directory ...

INFO: summary file is subj_4/dicomdir.sumfile

INFO: status file is subj_4/parse.status

Scanning directory Fri Jun 14 09:47:20 EDT 2013

mri_parse_sdcmdir --sortbyrun --d DICOM --o subj_4/dicomdir.sumfile --status subj_4/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 Fri Jun 14 09:48:46 EDT 2013

------------------------------------------

1 localizer ok 512 512 3 1 59198979

2 T1_MEMPRAGE_freesurfer ok 256 256 176 4 59199008

3 T1_MEMPRAGE_freesurfer ok 256 256 176 4 59187534

4 T1_MEMPRAGE_freesurfer ok 256 256 176 1 59175542

5 ep_TR2500_128 ok 64 64 42 128 59175096

6 ep_TR2500_128 ok 64 64 42 128 59170659

7 ep_TR2500_128 ok 64 64 42 128 59169456

8 ep_TR2500_128 ok 64 64 42 128 59168253

9 ep_TR2500_128 ok 64 64 42 128 59167050

10 ep_TR2500_128 ok 64 64 42 128 59162613

11 ep_TR2500_113 ok 64 64 42 113 59299072

12 t2_3DFLAIR ok 256 240 176 1 59297629

unpacking config ------------------

{5 bold nii f.nii} {6 bold nii f.nii} {7 bold nii f.nii} {8 bold nii f.nii} {9 bold nii f.nii} {10 bold nii f.nii}

-----------------------------------

---------------------------------------------------------

Run 5 -----------------------------------------

Fri Jun 14 09:48:46 EDT 2013

5 bold nii f.nii

ERROR: reading DICOM/59175096 tag 28 30

Here is the version of FS I'm using: freesurfer-i386-apple-darwin10.8.0-stable5-20130513

What exactly do you mean when you ask where the DICOM's are from? I receive them from Brown's MRF facility, and we've been successful in converting them on other iMac's using the same version of FS.

Thanks,

Luc

On Mon, Jun 17, 2013 at 2:36 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

can you send the complete command line and screen output, and tell us what version of FS you are using and where the dicoms are from?

On Mon, 17 Jun 2013, Luc Amdahl wrote:

Hi Freesurfers,
I am trying to use Freesurfer to convert DICOM files to nii f.nii files.
Freesurfer is able to find all the DICOM files but always gives me an error:
"ERROR: reading DICOM/59175096 tag 28 30".

Can anyone help?

Thanks,

Luc

--
Luc Amdahl
Brown University '14
Sc.B. Neuroscience
69 Brown St., #6137
Providence, RI 02912
603.252.4441

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