CSPM gives the option to setup FIRST analyses with T1 files. Before proceeding, make sure the LinuxVM is running.
In the analysis GUI, keep the FSL_FIRST option selected , and run Setup All.
(See 1 right)
Each study's T1 will be copied to a "T1FIRST" subfolder of an FSL study folder (example: W:\LinuxShare\subjects4FSL\OSA205\T1FIRST), and the FIRST processing will be run, resulting in multiple files created.
(See 2 right)
After all subjects are processed, CSPM will create a set subfolder under ...\LinuxShare\FSL_FIRST (example W:\LinuxShare\FSL_FIRST\ID71N6G2), with multiple subfolders.
(See 3 right)
Each structure folder has a complied file containing all studies' structures as a concatenated bvars file. Subfolders for different shape analysis contain text files with commands to be run once designs are created.
The "designs" subfolder is empty, but is intended for the design type subfolders to be created for saving each type of design.
The "slicesdir_T1toMNI" is for error checking registrations.
The "slicesdir_segmentatations" is for error checking the segmentations; subjects that did not register correctly will not segment correctly.
The "varfiles" folder contains files for copying variables when creating design matrices.
1) FIRST option
2) Files created by FIRST setup for each study
3) Folders created for set by CSPM Setup All
