mri_convert in 4D - Freesurfer

11 Apr 2006


      I am viewing it with tkmedit. For the timeseries, it only displayed some of
it. I also tried viewing it with fslview. There it was a single dashed line
in the coronal view.
Here is the output:
mri_convert -it dicom -ot nii i6757552.MRDC.1 run.nii.gz
reading from i6757552.MRDC.1...
1260 DICOM 3.0 files in list
Found 1260 DICOM Files
WARNING: NumberOfFrames 0 != Found Count of slices 1260.
reading DICOM image...
-------------------------------------------------
DICOM meta-header
file name
/data/Cued_Recall/CR_ds7/s6757551/i6757552.MRDC.1
Date and time
        study date              20050601
        study time              183408
        series time             190627
        acquisition time        190627
Identification
        patient name            ds060105
        manufacturer            GE MEDICAL SYSTEMS
Dimensions
        number of rows          64
        number of columns       64
        number of frames        1260
        pixel width             3.43752
        pixel height            3.4375
        slice thickness         7
        field of view           220.001
        image number            1 (might be not reliable)
        transfer syntax UID     1.2.840.10008.1.2.1
Acquisition parameters
        echo time               30
        repetition time         720
        inversion time          0
        echo number             1
        flip angle              1.5708
        bits allocated          16
Spatial information
        first image position    -108.281 -113.295 54.3301
        last image position     -108.281 -60.2276 88.2841
        image orientation       1 -0 0 -0 0.538953 -0.842336
-------------------------------------------------
TR=720.00, TE=30.00, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -0.538953, - 0.842336)
k_ras = (0, -0.842337, 0.538951)
writing to run.nii.gz...
thanks
~julia
On 4/8/06, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
...
how are you displaying it? And can you send the entire output?
On Fri, 7 Apr
2006, Julia Hamstra wrote:
...
Hi,
I am getting two errors when creating NIFTI files from dicoms using
mri_convert.
The first is that the 4D images are being spatially contactonated. It
does
...
not seem to be treating it as a timeseries. This is the command:
mri_convert -it dicom -ot nii s6761334/i6761335.MRDC.1 run.nii.gz
Additionally it is an oblique acquizition so the coronal view is not
displaying the plane of acquizition (as intended), but an orthogonal cut
through multiple slices. Am I missing an option or additional
information? I
...
searched the options and couldn't figure out anything that helped. The
problem applies to the co-planar oblique structural scan too.
I'm guessing there is something simple that I am overlooking. What may
that
...
be?
thanks
~julia
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