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I think Benny Liberg mentioned MRIConvert already, but I'll mention it again. It will take a directory full of files and sort them into the appropriate volumes automatically. It does use the DICOM image orientation information to correctly align the slices. If you find it does not sort your data correctly, let me know and I will be happy to fix it. It includes a command line utility (for Windows or linux) so it is scriptable. You can get it at lcni.uoregon.edu/~jolinda/MRIConvert. I also have a little command-line utility (DicomSorter) that reads a directory of dicom files and sorts it into subject, study, and series. You might find that useful. Benny says it has some problems with his mprage images, but we certainly haven't observed this at our site. I'm still waiting for him to provide me with some example data so I can investigate. Jolinda -- Jolinda Smith MR Physicist Lewis Center for Neuroimaging University of Oregon Eugene, OR 97403 [log in to unmask] On Tue, 15 May 2007 15:25:46 +0100, Alle Meije Wink <[log in to unmask]> wrote: > Hi Ged, > > Thanks for that info! > > > Going from DICOM to NIfTI via Analyze like this loses the orientation > > information in the DICOM fields (e.g. ImagePatientPosition, etc) > > [snip] > > Some of the direct DICOM->NIfTI programs set the NiFTI qform from the > > DICOM fields (although, when I checked this, a couple of them were > > inconsistent, so do take care!) I think these programs try this: > > - dcm2nii > > - SPM5 DICOM import > > - dinifti > > - possibly LONI Debabaler and others > > Links to all these are at the bottom of Chris Rorden's dcm2nii page: > > http://www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html > > I have tried a few of these, but most of them seem to expect volume/4D > files to begin with or simply didn't work. In the DICOMDIR setting, > scripting it together and having medcon make the volumes, was the best > way I could convert whole batches of files from a CD. > > Plus, are you sure that these programs estimate the position of a volume > using the positions of individual slices? > > I tried the links, but none of them actually gave useful information in > terms of: this is your DICOM cd, and this is how you rip your volumes > off it... > > Any advice is still much appreciated, and if those programs really come > up with Q-forms from slice data, I'm very impressed! > > bw > Alle Meije >