-
Notifications
You must be signed in to change notification settings - Fork 0
Module 3 FreeSurfer on HiPerGator
The video will walk you through setting up and processing the sample data. If you follow along, you should have everything completed for the homework assignment other than uploading the requested files. Remember that subject names, paths, directories, and more might be different. Make changes as appropriate.
Also, this video requests 6 CPU cores. Some students ran out of memory requesting 6 cores and 24GB of RAM. You can request 2-4 cores and keep the amount of RAM (just change the recon-all command to mirror the number of cores: recon-all .... --openmp 4). Or, you can request more RAM. 36GB should be fine but at least one student ran out of RAM with that much, so maybe 48GB. The easiest fix is to cut the number of requested cores down.
NIfTI, BIDS, and FreeSurferLinks to an external site.
NOTE: You can load older versions of FreeSurfer. We won't get into why you might but you can do it by specifying a particular version.
The example script you copy (please don't move or delete it!) is in the Module3 directory on the class share.
Use the ADNI_T1_dicom directory in the Module3 directory.
- Format the T1 files into a simple BIDS format.
- Process a set of 2 brains using FreeSurfer.
- screenshot of your BIDS directory.
- The recon-all.log files for the brains
Please verify that the jobs completed. The end of the log file should have something like this: recon-all -s sub-011S6303 finished without error
If you don't see that, the job did not complete appropriately, even if you did not receive an error message. I recommend deleting all files created by the script (the .nii or .nii.gz input files and the output directory for the subject) and trying again. You might need to give the script more RAM (try 4 to 6 GB) or time.