I'm not sure what to tell you. You can try dcm2nii or MRIconvert (different package than mri_convert). You can also try an mri_convert from an older version of FS, which you can get from here
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ On 03/15/2017 03:18 PM, Mark Lescroart wrote: > Hello, > > I'm trying to create a nifti file from some older (2006-2009) dicom > files using mri_convert, and I'm having some difficulty. Part of this > is uncertainty about the dicom files in question. The files were > collected on Siemens scanner between 2006 and 2009, and I *believe* > they should be in Siemens dicom format. They came off the magnet > without a .dcm extension, if I recall correctly, but I used Brain > Voyager to rename the dicom files (I believe all it does is re-title > them to reflect the acquisition order, but I'm not 100% sure about > that - that could be part of the problem). Running mri_convert to > create a nifti file from the first file in each of the sequences I > have yields the error I have copied below. > > <redacted> bits are there for anonymity, I don't think those fields > relate to the problem. The main problem with this call seems to be > that some fields regarding the image position are not read correctly, > so the affine transform has nans in it. > > I also tried calling mri_convert -it dicom, which succeeded, but > created an image that was of shape (384, 384, 1, 202). I don't know > why that call to mri_convert doesn't correctly recognize that the > images in the dicoms are, in fact, mosaic images (in the first call, > there was an "IsMosaic" field that was set to 0, but I'm pretty sure > it should be 1 or True or whatever); the resulting 4D array should be > (64, 64, 32, 202). > > However, the image that the second call created may have had a correct > affine transform (at least there were no nans) - to check on it in > python, I called: > > nii = nibabel.load(file_name) > nii.affine > > ... and got: > > array([[ -3.5 , -0. , -0. , 672.67797852], > [ -0. , -3.5 , -0. , 690.59564209], > [ 0. , 0. , 3. , -52.07869339], > [ 0. , 0. , 0. , 1. ]]) > > > ... So, now I'm a little stuck. -it seimens did not help, gave me the > same error as below (same for -it siemens_dicom). I don't fully > understand how to possibly override the bad info, or how to tell > mri_convert where to find the correct info, or how to tell if I'm just > out of luck with this whole endeavor. > > mri_convert --version spits out "stable5", which might be a slightly > older version. > > Any help will be much appreciated. > > Cheers, > Mark > > > Error message: > ---- > > Getting Series No > Scanning Directory > INFO: Found 993 files in old_data/ML_Localizers/Raw_Retinotopy_05_29_09 > INFO: Scanning for Series Number 21 > INFO: found 202 files in series > INFO: loading series header info. > > # <there were lots of these error lines, one for each file in the > series; i think these are due to the space between the subject ID, > which I've redacted, and -0021-0001-00001.dcm > # > error: > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings: > > invalid decimal number in flag: -0021-0001-00001.dcm > Usage: > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings > > [-] [-a] [-o] [-t format] [-number] [-n number] [[-arch <arch_flag>] > ...] [--] [file ...] > > > WARNING: file <redacted> -0021-0001-00001.dcm does not contain a > Siemens ASCII header > has this file been anonymized? > Proceeding as best as I can ... > > INFO: (384 384 1), nframes = 202, ismosaic=0 > PE Dir COL COL > FileName <redacted>/<redacted> -0021-0001-00001.dcm > Identification > NumarisVer syngo MR B15 > ScannerModel TrioTim > PatientName <redacted> > Date and time > StudyDate <redacted> > StudyTime 105825.156000 > SeriesTime 122023.890000 > AcqTime 122021.700000 > Acquisition parameters > PulseSeq *epfid2d1_64 > Protocol <redacted> > PhEncDir COL > EchoNo 1 > FlipAngle 90 > EchoTime 30 > InversionTime -1 > RepetitionTime 2000 > PhEncFOV 0 > ReadoutFOV 0 > Image information > RunNo 20 > SeriesNo 21 > ImageNo 1 > NImageRows 384 > NImageCols 384 > NFrames 202 > SliceArraylSize 0 > IsMosaic 0 > ImgPos 672.6780 690.5956 -52.0787 > VolRes 3.5000 3.5000 3.0000 > VolDim 384 384 1 > Vc -1.0000 -0.0000 0.0000 > Vr -0.0000 -1.0000 0.0000 > Vs nan nan nan > VolCenter nan nan nan > TransferSyntaxUID 1.2.840.10008.1.2.1 > UseSliceScaleFactor 0 (slice 0: 1) > INFO: no Siemens slice order reversal detected (good!). > TR=2000.00, TE=30.00, TI=-1.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -1, 0) > k_ras = (nan, nan, nan) > Reslicing using trilinear interpolation > MRIresample(): error inverting matrix; determinant is nan, matrix is: > -3.500 -0.000 nan nan; > -0.000 -3.500 nan nan; > 0.000 0.000 nan nan; > 0.000 0.000 0.000 1.000; > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
