Hi Paige,
so I went and copied the following files from freesurferv4.4.0/bin to
freesurferv3.0.5/bin:
mri_convert
mri_parse_sdcmdir
mri_probedicom
unpacksdcmdir
tcl_setup
unpacksdcmdir.tcl
I then edited the new unpacksdcmdir to read (you will have to put in the proper
path to your freesurfer 4 install):
#!/bin/tcsh -ef
set FREESURFER4_HOME =
/space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0-full/
source $FREESURFER_HOME/bin/tcl_setup.4.4.0
$FREESURFER4_HOME/lib/tcltktixblt/bin/tclsh8.4
$FREESURFER_HOME/bin/unpacksdcmdir.tcl.4.4.0 $argv
I hope that this will help you to get your old setup working with Numaris B17
best
sebastian
On Mar 19, 2010, at 1:23 PM, Paige Scalf wrote:
> 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
> <[email protected]> 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, [email protected] wrote:
>
> > Message: 7
> > Date: Fri, 19 Mar 2010 14:37:24 -0500
> > From: Paige Scalf <[email protected]>
> > Subject: [Freesurfer] trio dicom files and mri_convert
> > To: [email protected]
> > Message-ID:
> > <[email protected]>
> > 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 --------------
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> > URL:
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> >
> > ------------------------------
>
>
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