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
Are they straight off of the scanner or did you anonymize them? Can you send me one of the dicom files? doug
On 11/09/2012 11:39 AM, Yangmei LUO wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Yangmei LUO