Looks like the machine I was running it on before was still running a
dev version from February, but I just tried it again with the latest
stable version (see below) and got the same thing.
I've uploaded a tar file with all of the dicom files. It also includes a
script of how afni does the conversion and the nifti output from it.
Thanks,
-Adam
PS. I like your filedrop utility. Is it freeware or something you wrote
in house?
[adamt@master ~]$ mri_convert --all-info
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion:
$Name: stable3 $ TimeStamp: 06/07/06-17:12:35-GMT CVS: $Id:
mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: adamt
Machine: master Platform: Linux PlatformVersion:
2.6.12-1.1387_FC4.rootsmp CompilerName: GCC CompilerVersion: 30400
-----Original Message-----
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu]
Sent: Thursday, July 06, 2006 12:41 PM
To: Thomas, Adam (NIH/NIMH) [E]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert: dicom to nifti 4D
I'm not sure what's going on with this -- I don't have too much
experience with GE functionals. Can you tar it up and put it somewhere I
can get or send it thru our file drop system? The file drop is at:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html.
Also, what version of mri_convert are you using? You can check with
mri_convet --all-info
doug
Thomas, Adam (NIH/NIMH) [E] wrote:
I seem to be having some trouble converting a 4D time series from dicom
to nifti format using mri_convert. Rather than outputting 144 frames of
38 slices each, it creates a volume with a single frame of 5472 slices
(see below). Is there an argument I should be using to specify number
of
frames?
I think there was a post on this back in April
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02656.ht
m
l), but I can't seem to find an answer in the archives.
Thanks,
-Adam
[adamt@master 004]$ mri_convert axialepi-00001.dcm test.nii
mri_convert axialepi-00001.dcm test.nii
reading from axialepi-00001.dcm...
5472 DICOM 3.0 files in list
Found 5472 DICOM Files
WARNING: NumberOfFrames 0 != Found Count of slices 5472.
reading DICOM image...
-------------------------------------------------
DICOM meta-header
file name
/misc/radium0/adamt/mirrorTracking/XX/2006-02-11-S2/XXXXXXXX/2006_02_11
-
15667/004/axialepi-00001.dcm
Date and time
study date 20060211
study time 170403
series time 172558
acquisition time 172558
Identification
patient name XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
manufacturer GE MEDICAL SYSTEMS
Dimensions
number of rows 64
number of columns 64
number of frames 5472
pixel width 3.28125
pixel height 3.28125
slice thickness 3.2
field of view 210
image number 1 (might be not reliable)
transfer syntax UID 1.2.840.10008.1.2.1
Acquisition parameters
echo time 30
repetition time 2500
inversion time 0
echo number 1
flip angle 1.5708
bits allocated 16
Spatial information
first image position -103.359 -132.14 75.59
last image position -103.359 -132.14 -42.81
image orientation 1 -0 0 -0 1 0
-------------------------------------------------
TR=2500.00, TE=30.00, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, -1)
writing to test.nii...
[adamt@master 004]$
---
Adam Thomas adamt@nih.gov
Functional MRI Facility, NIMH/NIH/DHHS
10 Center Dr, Room B1D708A
Bethesda MD. 20892-1148
Phone:301-402-6351 Fax: 301-402-1370
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