[Freesurfer] problems on converting images from the GE scanner

Hi FreeSurfer users,

I have the anatomical MR images from the GE scanner, and want to convert the images into the mgz file.

These images's file name looks as follows:

IM1 IM2 . . IM176

I use the function "mri_convert" to converting the file:

% mri_convert -it dicom IM1 $SUBJECTS_DIR/15/mri/orig/001.mgz

The problem is that the image in the output file (001.mgz) looks like "white noise". I have posted the logs regarding to this function at the end.

I have tried several ways, such as converting the files into *.ima files or a nii file before running "mri_convert", and still have the same problem.

Would someone have ideas about what to do?

Thanks!

Chun-Hsien Hsu

mri_convert -it dicom IM1 /Users/kevin/Subjects/15/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from IM1... Starting DICOMRead2() dcmfile = /Users/kevin/Subjects/15/mri/IM1 dcmdir = /Users/kevin/Subjects/15/mri Ref Series No = 3 Found 179 files, checking for dicoms Found 176 dicom files in series. First Sorting Computing Slice Direction Vs: 0.007 -0.168 0.9856 Vs: 0.00700112 -0.168027 0.985758 Second Sorting Counting frames nframes = 1 nslices = 176 ndcmfiles = 176 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=3.06, TE=0.82, TI=1100.00, flip angle=7.00 i_ras = (-0.999935, -0.00973536, -0.00592059) j_ras = (0.00860625, -0.985602, 0.16886) k_ras = (-0.00700112, 0.168027, 0.985758) writing to /Users/kevin/Subjects/15/mri/orig/001.mgz...