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
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
yes, this worked. thanks so much, margaret
On Fri, 19 Aug 2005, Nick Schmansky wrote:
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
you need to specify a file with the extension .mgz as the output name
On Fri, 19 Aug 2005, 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Margaret Duff -
Nick Schmansky