Hi there,
I am a newbie and I used data collected from SIEMENS 3T to practice. It works well when I tried to preprocess structural data using freesurfer. However, there is a problem when I tried to convert the functional data in DICOM into NII using freesurfer. The problem I can not solve, so I turn to you. Could you give me some advice on how to solve this problem? Any help is appreciated!
The command I run: * export FREESURFER_HOME=/usr/local/freesurfer /usr/local/freesurfer/bin/mri_convert --in_type dicom --out_type nii I0001.dcm s105.run1.nii*
and the result in terminal is */usr/local/freesurfer/bin/mri_convert --in_type dicom --out_type nii I0001.dcm ..nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from I0001.dcm... Starting DICOMRead2() dcmfile = /home/fsl/data/emotion/s105/run1/I0001.dcm dcmdir = /home/fsl/data/emotion/s105/run1 Ref Series No = 3 Found 231 files, checking for dicoms Found 228 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 228 nslices = 1 ndcmfiles = 228 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=2000.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.999945, 0.0104718) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -3.000 -0.000 nan nan; -0.000 -3.000 nan nan; 0.000 0.031 -nan -nan; 0.000 0.000 0.000 1.000;*
Thank you very much!
Best wishes,
Yangmei