We only have a few examples of the multi frame dicom, and they’re all of humans. We can anonymize one and email it to you directly.
Flavin
On Oct 23, 2014, at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
I doubt that it will work. I've never actually seen a multi-frame dicom myself. Can you upload one to me? It should be of a phantom, not a human, so we can avoid privacy issues. doug
On 10/23/2014 01:07 PM, Flavin, John wrote:
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 /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 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 -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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