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.moeller@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-request@nmr.mgh.harvard.edu wrote:

> Message: 7
> Date: Fri, 19 Mar 2010 14:37:24 -0500
> From: Paige Scalf <pscalf@gmail.com>
> Subject: [Freesurfer] trio dicom files and mri_convert
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>       <1113e70c1003191237y6f5723aeha927124dd30b593e@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;
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