why not install the current FS and try it out? You don't have to delete the old one. I think it should work for visualizing older surfaces and data, but you can always fall back if you have a problem.
Thanks for the help though Sebastian. Bruce On Fri, 19 Mar 2010, 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]: >> >>> 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 -------------- >>> An HTML attachment was scrubbed... >>> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20100319/c7f42cb8/attachment.html >>> >>> ------------------------------ >> >> > _______________________________________________ Freesurfer mailing list [email protected] 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. 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