Well, I have retinotopy data (analyzed using FSL) that is flatmapped and registered (painfully by hand) using 3.0.3. I need the data for my current study, and I'm not sure how well it would survive transformation to the more recent version. If someone can tell me that the data I processed using 3.0.3 will still be usable/play nicely after an upgrade, I can do that. If that's not possible, I'd prefer to transplant files; multiple operational versions of software does get confusing, but that would also work as a last resort.
Thanks, Paige On Fri, Mar 19, 2010 at 3:10 PM, Sebastian Moeller < sebastian.moel...@lur.rwth-aachen.de> wrote: > Hi Paige, > > I ran into a similar problem a few months ago. Freesurfer 3.0.5 could not > read data from a TIM trio with numaris B17. I solved this by transplanting > (copying) a number of files from freesurfer 4.4.0 (the recent one at the > time) into 3.0.5. unpacsdcmdir, mri_convert and a few more, that worked > okay, but I since switched to freesurfer 4.5.0 for good. If you have to > stick to 3.0.3 I can try to look up which files I had to replace in 3.0.5. > Or alternatively you can install v4.5.0 parallel to 3.0.3 and only use it to > import the DICOM data... > > best regards > Sebastian > > On Mar 19, 2010, at 12:37 PM, freesurfer-requ...@nmr.mgh.harvard.eduwrote: > > > Message: 7 > > Date: Fri, 19 Mar 2010 14:37:24 -0500 > > From: Paige Scalf <psc...@gmail.com> > > Subject: [Freesurfer] trio dicom files and mri_convert > > To: freesurfer@nmr.mgh.harvard.edu > > Message-ID: > > <1113e70c1003191237y6f5723aeha927124dd30b5...@mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello, > > > > I've been trying to use mri_convert > > (freesurfer-Darwin-tiger-stable-pub-v3.0.3) to reconstruct images from > our > > Siemens Magnetom Trio. When I type: > > > > mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_ > > A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > Block1.img > > > > > > DB*.IMA and Block1.img are the input and output files respectively, I get > > the output detailed below (the salient error seems to be that > mri_convert > > can't find a useful transformation matrix). > > > > Can you tell me what I can do to correct this problem? > > Many thanks in advance, > > > > Paige Scalf > > > > > > mri_convert -it siemens_dicom -ot analyze4d > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > > Block1.img > > reading from > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... > > Getting Series No > > Scanning Directory > > INFO: Found 111 files in > /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 > > INFO: Scanning for Series Number 3 > > INFO: found 107 files in series > > INFO: loading series header info. > > > > INFO: sorting. > > RunNo = 2 > > INFO: (120 110 50), nframes = 107, ismosaic=1 > > ERROR: incorreclty formatted version string syngo MR B17 > > found in dicom tag 18,1020 (len = 3 != 6) > > Numaris Version: syngo MR B17 Maj = 0, Min=-1073775504, MinMin = 0 > > mojo:/Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 paige$ mri_convert > > -it dicom -ot analyze4d > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > > Block1.img > > mri_convert -it dicom -ot analyze4d > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > > Block1.img > > reading from > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... > > Getting Series No > > Scanning Directory > > INFO: Found 111 files in > /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 > > INFO: Scanning for Series Number 3 > > INFO: found 107 files in series > > INFO: loading series header info. > > > > INFO: sorting. > > RunNo = 2 > > INFO: (120 110 50), nframes = 107, ismosaic=1 > > ERROR: incorreclty formatted version string syngo MR B17 > > found in dicom tag 18,1020 (len = 3 != 6) > > Numaris Version: syngo MR B17 Maj = -1073770984, Min=22021328, MinMin = > > -1610546680 > > 107 DICOM 3.0 files in list > > Found 107 DICOM Files > > WARNING: NumberOfFrames 0 != Found Count of slices 107. > > reading DICOM image... > > ------------------------------------------------- > > DICOM meta-header > > > > file name > > > /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1/DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA > > Date and time > > study date 20100318 > > study time 160300.312000 > > series time 162802.453000 > > acquisition time 162802.453000 > > Identification > > patient name DB_A0A1_318 > > manufacturer SIEMENS > > Dimensions > > number of rows 880 > > number of columns 960 > > number of frames 107 > > pixel width 2.13333 > > pixel height 2.13333 > > slice thickness 2.1 > > field of view 1877.33 > > image number 1 (might be not reliable) > > transfer syntax UID 1.2.840.10008.1.2.1 > > Acquisition parameters > > echo time 25 > > repetition time 3000 > > inversion time not found > > echo number 1 > > flip angle 1.5708 > > bits allocated 16 > > Spatial information > > first image position -1027.46 -12.1727 952.833 > > last image position -1027.46 -12.1727 952.833 > > image orientation 1 0 0 0 -0.00174528 -0.999998 > > ------------------------------------------------- > > > > TR=3000.00, TE=25.00, TI=0.00, flip angle=90.00 > > i_ras = (-1, -0, 0) > > j_ras = (-0, 0.00174528, -0.999999) > > k_ras = (nan, nan, nan) > > Reslicing using trilinear interpolation > > MRIresample(): error inverting matrix; determinant is nan, matrix is: > > -2.133 -0.000 nan nan; > > -0.000 0.004 nan nan; > > 0.000 -2.133 nan nan; > > 0.000 0.000 0.000 1.000; > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20100319/c7f42cb8/attachment.html > > > > ------------------------------ > >
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