Hi all, I am just starting to learn to analyse neuroimaging data. So these are my first steps with FreeSurfer. I apologize if the question is too basic to the mail list.
I set myself the goal of finding volumes for several areas in a dataset from the lab I am working on, but I got stuck very early on the exercise. As far as I understood by reading the Tutorials, all the magic happens with the recon-all command, right? But it seems that it requires a specific directory structure to run properly (the FSFAST structure <http://freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct>). The problem is that the dataset for my exercise is organized in a different structure. It was previously analysed in SPM. The structure is as follows. For 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 <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData> 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? Or is there anyway of automating the conversion from this structure into the FSFAST’s? Thank you, luis
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