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FreeSurfer uses the recon-all command to semi-automatically generate its statistics. This tool implies a certain directory structure in which the files with the images for the samples should be organized into. In FreeSurfer tutorial they call this specific directory structure the FSFAST structure.

I need to analyse images that were previously worked on in SPM, and it has the following directory structure for the patients:

/experiment/patients/A.o/

and for controls:

/experiment/controls/A.o/

Within each directory there are .hdr, .img, .mat and .mask files for each observation, which was obtained in two different times. So the naming of the files have the following order:

experiment_subjectnumber_time1.img

and for the second acquisition reads:

experiment_subjectnumber_time2.img

The same with all the before mentioned extensions (hdr, mat, mask).

It seems that in the FreeSurfer workflow the command unpacksdcmdir is used to extract data from the nii and dicon types and organize them in the FSFAST structure. Can it be used on directory structures like the one I have?

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I found help at the FreeSurfer mailing list regarding this question. The answer is that for the structural analysis, there is no need to run the recon-all command in a specific directory structure.

It is just a matter of running

recon-all -s SUBJECTNAME -all -i IMAGE.IMG

Note that I am feeding an img file, which is what I am using now, however the creators of the software suggest the use of the DICON filetype.

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