I have no idea. That's pretty old code that we are not really maintaining anymore. Why are you using analyze? doug
Mohana Ramaratnam wrote: > Hello, > > I am using mri_convert to convert dicom image into analyze format using: > > mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.img > > The problem is: > > The hdr.hist.orient in the output file is set to 0, but the pixels in > the analyze image are saggital. > > Does anybody have any suggestions as to what could be wrong? > > Regards > Mohana Ramaratnam > > DIAGNOSTICS: > > mri_info on the dicom reports: > > Orientation : PIL > Primary Slice Direction: sagittal > > and that on the analyze image reports: > > Orientation : LAS > Primary Slice Direction: axial > > OUTPUT of mri_convert: > > INFO: Scanning for Series Number 4 > INFO: found 176 files in series > INFO: loading series header info. > > INFO: sorting. > RunNo = 3 > INFO: (256 256 176), nframes = 1, ismosaic=0 > PE Dir ROW ROW > AutoAlign matrix detected > AutoAlign Matrix --------------------- > 0.998 0.038 -0.051 -2.542; > -0.051 0.954 -0.294 -15.875; > 0.038 0.296 0.954 -2.910; > 0.000 0.000 0.000 1.000; > > FileName FILE_NAME_HERE > > Identification > NumarisVer syngo MR B17 > ScannerModel TrioTim > PatientName 65433 > Date and time > StudyDate 20110708 > StudyTime 110252.125000 > SeriesTime 111446.078000 > AcqTime 110635.592500 > Acquisition parameters > PulseSeq tfl3d1_ns > Protocol t1_mpr_1mm_p2_pos50 > PhEncDir ROW > EchoNo 1 > FlipAngle 8 > EchoTime 3.16 > InversionTime 1000 > RepetitionTime 2400 > PhEncFOV 256 > ReadoutFOV 256 > Image information > RunNo 3 > SeriesNo 4 > ImageNo 1 > NImageRows 256 > NImageCols 256 > NFrames 1 > SliceArraylSize 1 > IsMosaic 0 > ImgPos 104.6950 154.3827 112.3121 > VolRes 1.0000 1.0000 1.0000 > VolDim 256 256 176 > Vc -0.0493 -0.9976 0.0480 > Vr -0.0403 -0.0460 -0.9981 > Vs -0.9980 0.0511 0.0379 > VolCenter 5.4129 25.2910 -5.9690 > TransferSyntaxUID 1.2.840.10008.1.2.1 > INFO: no Siemens slice order reversal detected (good!). > TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 > i_ras = (-0.0492738, -0.997631, 0.0480037) > j_ras = (-0.0402601, -0.0460391, -0.998128) > k_ras = (-0.997974, 0.0511142, 0.0378956) > writing to 110708_TC33875.img... > Analyze Output Matrix > -0.049 -0.040 -0.998 105.782; > -0.998 -0.046 0.051 155.375; > 0.048 -0.998 0.038 113.224; > 0.000 0.000 0.000 1.000; > -------------------- > No such orientation specified in Analyze7.5. Set orient to 0 > Direction cosines for FILE_NAME_HERE > are: > x_r = -0.0493, y_r = -0.0403, z_r = -0.9980, c_r = 5.4129 > x_a = -0.9976, y_a = -0.0460, z_a = 0.0511, c_a = 25.2910 > x_s = 0.0480, y_s = -0.9981, z_s = 0.0379, c_s = -5.9690 > INFO: set hdr.hist.orient to 'transverse unflipped' > _______________________________________________ > 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.
