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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
