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?
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I ran the command you suggested and it appears to run without any errors or warnings.
*OUTPUT: ---------------------------------------------------------------------------------------- *
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...
*----------------------------------------------------------------------------------------------------------------
*As far as I can tell, the Avanto is a Siemens model, which does not explain why unpacksdcmdir does not work, since unpacksdcmdir can find the slice with -scanonly but cannot unpack it.
Any other ideas?
Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.olsen@gmail.com mailto:anders.d.olsen@gmail.com
On 07-01-2014 01:09, Douglas N Greve wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Anders Olsen -
Douglas N Greve