I am new to using afni and have tried to familiarize myself with different applications by reading and attempting to complete the provided tutorials. Unfortunately I have had some trouble loading the raw data into afni with the to3d command. When I searched the message board I came across one posting that seemed relevant to my work, but this is a little more advanced than I can understand presently.

to3d: moscaic order problem Beate 03-19-08 12:24

The dicom files I obtained from the scanner are not separated by type (ie anatomical and functional files are combined). I was wondering if there are any scripts available that can read in the header information to accurately import these files to AFNI datasets. I was able to move the anatomical images to a separate folder (based on file size) but when the to3d command was used, the sagital images are shuffled. I tried manipulating the commands both with the gui and at the command line but have been unsuccessful. Without being able to identify a pattern in the naming sequence myself, this makes the organization of the functional data even more troubling to me.


My work primarily deals with intramuscular signal analysis, but for one particular study my advisor and I were looking at FMRI of finger/thumb movements in stroke survivors.

Datasets were collected by my predecessor and it is my responsibility to progress with the analysis portion.

I would appreciate any assistance or guidance you can offer to me.

Many thanks,

Kristen