I am attempting to run resting state analysis using example 11 in the afni_proc_py page. Since I am new to this analysis and not well versed in Freesurfer (please bear with me), I am having a trouble in creating Freesurfer output. I have created folders for each subject and each folder has two folders, one for anat DICOMS and the other for EPI DICOMS. I have tried to run the commands below but didn’t work.
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
recon-all -all -subject FT -i FT.nii
I am not sure what does FT indicate and how to get FT.nii to run recon-all. Could you please advise me on this?
Thank you in advance for your help!
I’ll take a stab at helping here, though I am not an expert. First do you have freesurfer installed? It is an entirely separate program from AFNI. AFNI just uses some of the output for some things, as in the example you’ve chosen. To install freesurfer you will need to go here[/url]and for questions related to freesurfer you may be better served to go [url=https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport]here for support.
I can answer the other questions, but I think starting with the links above may be useful as well. There are also videos on youtube that offer some details about freesurfer as well.
Regarding your question:
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
recon-all -all -subject FT -i FT.nii
I am not sure what does FT indicate and how to get FT.nii to run recon-all. Could you please advise me on this?
The first line says where your freesurfer was installed, set up during the installation procedure (details in links above) and the second is a set up script provided by freesurfer.
recon-all is the main function of freesurfer. the -all means do everything, or run. I think. I’ve never been clear on the exact meaning.
-subject is the unique identifies for the subject that will be used in the future. So, in this case, FT is the subjects name, or ID.
-i FT.nii is the MPRAGE for the subject, in nifti format.
The freesurfer website has details of how to start with dicoms, I have never done that. Hopefully this gives you enough information to start.
You might also check what SUBJECTS_DIR is set to be. By default, it will be /Applications/freesurfer/subjects. It’s possible than recon-all ran successfully, and just hid your output where it thinks it should go in /Applications/freesurfer/subjects/FT.
FWIW yes, -all does mean “run it all,” or more specifically, “start from the beginning.” If you were to go back and do manual edits to the surface (which is almost certainly unnecessary for the application at hand), then you’d use a different flag there to have recon-all start part-way through, incorporating the changes you made.
Hope that helps.