Once again on this, did not get back from you after my response to this. The dicom spit out by Analyze also crashes spm5, our pacs will eat it and I can display it in pacs.

Is there a way to turn off the resampling or do I need to add a tag with the k_ras coords.

don't know what to make of WARNING: NumberOfFrames 0 != Found Count of slices 104.

I would be glad to dump the files off to you, don't know how interested you are in spending your busy day supporting Analyze software, im getting to find it more trouble than it is worth. but untill I get time to write some ITK thing to do SISCOM studies Im stuck with trying to cooregister the nuclear med hotspots generated in Analyze to FSL diffusion stats.

thankx

Greg.

-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, November 14, 2006 4:05 PM To: Kirk, Gregory Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert SC dicom

What exactly is the problem? Kirk, Gregory wrote:

Hi folks, I was trying to convert an dicom MPRAGE with a SISCOM activation( grayscale ) to nii format to use the activation for a seed for probalistic fiber tracking. The siscom is created in Analyze(program not file format) and then exported to dicom , so it is a secondary capture siscom. I know this is not really a freesurfer thing but I guess you guys when possible try to make your tools mutually usefull so I send the error in case you see a simple fix by an option I can apply. set orientation seems to be the issue notice k_ras = (nan, nan, nan) also WARNING: NumberOfFrames 0 != Found Count of slices 104. thanks if you can help Greg. reading from i170927.SCPT.1... 104 DICOM 3.0 files in list Found 104 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 104. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /home/gkirk/tillsis/dicom/i170927.SCPT.1 Date and time study date 20061114 study time 142154 series time 142014.000000 acquisition time 142014.000000 Identification patient name manufacturer SIEMENS NM Dimensions number of rows 256 number of columns 256 number of frames 104 pixel width 1 pixel height 1 slice thickness 2 field of view 256 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 4.7 repetition time 1870 inversion time 1100 echo number 0 flip angle 0.261799 bits allocated 8 Spatial information first image position -132.963 -132.808 -122.125 last image position -132.963 -132.808 -122.125 image orientation 1 -2.05103e-10 0 2.05103e-10 1 0 ------------------------------------------------- TR=1870.00, TE=4.70, TI=1100.00, flip angle=15.00 i_ras = (-1, 2.05103e-10, 0) j_ras = (-2.05103e-10, -1, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): source matrix has zero determinant; matrix is: -1.000 -0.000 nan nan; 0.000 -1.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; [gkirk@Nuit dicom]$

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