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.htm 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