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 > > > ------------------------------------------------------------------------ > > The material in this message is private and may contain Protected > Healthcare Information (PHI). If you are not the intended recipient, > be advised that any unauthorized use, disclosure, copying or the > taking of any action in reliance on the contents of this information > is strictly prohibited. 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