anders@debian:~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon$ mri_convert 001.dcm deleteme.mgh
mri_convert 001.dcm deleteme.mgh
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 001.dcm...
Getting Series No
Scanning Directory
INFO: Found 132 files in /home/anders/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon
INFO: Scanning for Series Number 14
INFO: found 128 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 13
INFO: (256 256 128), nframes = 1, ismosaic=0
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix ---------------------
 0.993  -0.117   0.033   1.187;
 0.122   0.973  -0.197  -0.637;
-0.009   0.200   0.980   5.207;
 0.000   0.000   0.000   1.000;
FileName                /home/anders/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm
Identification
        NumarisVer        syngo MR 2004V 4VB11A
        ScannerModel      Avanto
        PatientName       anon
Date and time
        StudyDate         00000000
        StudyTime         000000
        SeriesTime        000000
        AcqTime           000000
Acquisition parameters
        PulseSeq          *tfl3d1_ns
        Protocol          anon
        PhEncDir          ROW
        EchoNo            0
        FlipAngle         7
        EchoTime          3.26
        InversionTime     1000
        RepetitionTime    2730
        PhEncFOV          256
        ReadoutFOV        256
Image information
        RunNo             13
        SeriesNo          14
        ImageNo           1
        NImageRows        256
        NImageCols        256
        NFrames           1
        SliceArraylSize   1
        IsMosaic          0
        ImgPos             68.8536 138.9441 135.4929
        VolRes              1.0000   1.0000   1.3300
        VolDim            256      256      128
        Vc                  0.1217  -0.9924  -0.0169
        Vr                  0.0065   0.0178  -0.9998
        Vs                 -0.9925  -0.1216  -0.0086
        VolCenter           0.7783   3.8396   4.6268
        TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).
TR=2730.00, TE=3.26, TI=1000.00, flip angle=7.00
i_ras = (0.121728, -0.99242, -0.0168585)
j_ras = (0.00647436, 0.0177783, -0.999821)
k_ras = (-0.992542, -0.121597, -0.008589)
writing to deleteme.mgh...
Not sure. Try running

mri_convert 001.dcm deleteme.mgh

if it fails, capture the screen output and send it to the list

doug

On 01/06/2014 06:31 PM, Anders Olsen wrote:

Hello FreeSurfer team.

I am currently trying to learn the general usage of FreeSurfer and 
have run into problems with unpacking DICOM files.

When I run:
unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info

It completes and gives me the following output:
14                        anon ok 256 256 128 001.dcm

I then try to unpack slice number 14 by running:
unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii

And it gives me the message:
ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30

I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the 
hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in 
ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt

Am I doing something wrong or is there a problem with the dcm files in 
the test data?
-- 

Venlig hilsen | Kind regards
Anders Dreisig Olsen
anders.d.olsen@gmail.com <mailto:anders.d.olsen@gmail.com>

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