Hi Timothy

you should be able to. You can use the -nth <frame #> switch to convert 
each frame individually

cheers

Bruce


On Mon, 11 Jul 2011, Timothy Brown wrote:

> Hi All,
>
> Can mri_convert be used with multiframe dicom?

Is this advice still valid? I tried converting a multi frame DICOM (176 frames in one file) using the -nth flag in mri_convert in Freesurfer 5.3 and it did not work as I expected.

$ $FREESURFER_HOME/bin/mri_convert -i RAW/301/foo.dcm -o PROCESSED/subj/mri/orig/001.mgz -nth 0
/path/to/bin/mri_convert -i RAW/301/foo.dcm -o PROCESSED/subj/mri/orig/001.mgz -nth 0

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from RAW/301/foo.dcm...
Starting DICOMRead2()
dcmfile = RAW/301/foo.dcm
dcmdir = RAW/301
WARNING: tag image orientation not found in RAW/301/foo.dcm
Ref Series No = 301
Found 3 files, checking for dicoms
WARNING: tag image orientation not found in RAW/301/foo.dcm
Found 1 dicom files in series.
WARNING: tag image orientation not found in RAW/301/foo.dcm
First Sorting
Computing Slice Direction

WARNING: it appears that the image position for all slices is the same.
This is a problem with the DICOM file. Using direction cosines from col and row
to compute slice direction, but the output may be misoriented.

Vs: 0 0 0
Vs: -nan -nan -nan
Second Sorting
Counting frames
nframes = 1
nslices = 1
ndcmfiles = 1
PE Dir = UNKNOWN (dicom read)
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0, -0, 0)

j_ras = (-0, -0, 0)

k_ras = (nan, nan, -nan)

Reslicing using trilinear interpolation

/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficient by 2

MRIresample(): error inverting matrix; determinant is -nan, matrix is:

-0.000 -0.000 nan nan;

0.000 0.000 -nan -nan;

0.000 0.000 0.000 1.000;

I get the exact same output running with -nth 0 as I do not using the -nth flag at all. If I try using -nth 1 (or -nth i for any integer i > 0) I get

mri_read(): start frame (1) is out of range (1 frames in volume)

mri_convert reports nframes = 1. I can look in the DICOM headers of the file and find

(0028, 0008) Number of Frames                    IS: ‘176’
and

(2001, 1018) [Number of Slices MR]               SL: 176

Anything I can do to tell mri_convert the correct number of frames?

Flavin

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