Margaret, The specified output filename needs to have .mgz at the end. In your case, it would be:
$SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002.mgz I noticed that $SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002 is a directory, which might be the source of the segfault (which, of course, shouldn't happen, and I will investigate this). So adding .mgz to your output file should work (I just tried it myself with your specified dicom file and it worked). Nick On Fri, 2005-08-19 at 12:42 -0400, Margaret Duff wrote: > Hi, Is mri_convert setup yet to convert to mgz format? I have been > trying it in both the std and dev environment from dicom format and spm > format and i keep getting a segmentation fault. it still converts to cor > format fine but i thought we were trying to get away from that. i dont > know exactly whats > causing it, but here is my command line and the running information. > > troy:mduff[84] mri_convert -ot mgz -it dicom 33749275 > $SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002 > mri_convert -ot mgz -it dicom 33749275 > /space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002 > reading from 33749275... > Getting Series No > Scanning Directory > INFO: Found 131 files in > /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028 > INFO: Scanning for Series Number 28 > INFO: found 128 files in series > INFO: loading series header info. > > INFO: sorting. > RunNo = 27 > INFO: (256 256 128), nframes = 1, ismosaic=0 > FileName > /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925 > Identification > NumarisVer syngo MR 2004V 4VB11D > ScannerModel Avanto > PatientName sm2c1 > Date and time > StudyDate 20041118 > StudyTime 180537.015000 > SeriesTime 190942.968000 > AcqTime 190056.292500 > Acquisition parameters > PulseSeq tfl3d1_ns > Protocol T1_MPRAGE_sag > PhEncDir ROW > EchoNo 0 > FlipAngle 7 > EchoTime 3.31 > InversionTime 1000 > RepetitionTime 2730 > PhEncFOV 256 > ReadoutFOV 256 > Image information > RunNo 27 > SeriesNo 28 > ImageNo 1 > NImageRows 256 > NImageCols 256 > NFrames 1 > SliceArraylSize 1 > IsMosaic 0 > ImgPos 71.7733 130.0894 131.5385 > VolRes 1.0000 1.0000 1.3300 > VolDim 256 256 128 > Vc 0.1238 -0.9687 -0.2150 > Vr -0.0454 0.2110 -0.9764 > Vs -0.9913 -0.1306 0.0178 > VolCenter -2.5670 21.9742 -19.4516 > TransferSyntaxUID 1.2.840.10008.1.2.1 > INFO: no Siemens slice order reversal detected (good!). > 128 DICOM 3.0 files in list > Found 128 DICOM Files > WARNING: NumberOfFrames 0 != Found Count of slices 128. > reading DICOM image... > ------------------------------------------------- > DICOM meta-header > > file name > /autofs/space/troy_002/users/fmridata/sm2c1_041118/3danat/dicom/028/33747925 > Date and time > study date 20041118 > study time 180537.015000 > series time 190942.968000 > acquisition time 190942.968000 > Identification > patient name sm2c1 > manufacturer SIEMENS > Dimensions > number of rows 256 > number of columns 256 > number of frames 128 > pixel width 1 > pixel height 1 > slice thickness 1.33 > field of view 256 > image number 1 (might be not reliable) > transfer syntax UID 1.2.840.10008.1.2.1 > Acquisition parameters > echo time 3.31 > repetition time 2730 > inversion time 1000 > echo number 0 > flip angle 0.122173 > bits allocated 16 > Spatial information > first image position -71.7733 -130.089 131.539 > last image position 95.662 -108.024 134.554 > image orientation -0.123794 0.968728 -0.215038 0.0453834 > -0.210951 -0.976442 > ------------------------------------------------- > > TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 > i_ras = (0.123794, -0.968728, -0.215038) > j_ras = (-0.0453834, 0.210951, -0.976442) > k_ras = (-0.99127, -0.130637, 0.0178497) > writing to > /space/troy/1/users/FREESURFER/SM2C1_autoreconall/mri/orig/002... > Segmentation fault > > i saw a couple other problems on the list but nothing exactly like this. > thanks for the help. margaret > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
