Dear Dr. McLaren,

Regarding the recent addition to the gPPI-toolbox, the FSFAST-wrapper:
What kind of 'region files' would you suggest to use when investigating the surface models (.lh / .rh)? I am interested in using individual Freesurfer-defined hippocampi as seeds.

And, by the way, I had to comment out line 171 in FSFAST2SPM.m

fileline=strtrim(fileline);

and change line 178

SPM.Sess(jj).U(kk).name{1})=fileline(~isspace(fileline));

to something like

SPM.Sess(jj).U(kk).name{1}=['condition' num2str(kk)];

to get the wrapper to run.


Thank you for a great toolbox!
Markus

Thanks for the feedback. I'll have to look at these lines as they have worked locally and for other groups.

If you want to use hippocampal seeds, then you need your seed regions to be defined in the mni305 volume space. You can still use separate regions for all subjects though. In the FSFAST PPI pipeline, there is an option for providing the source files for PPI (FSFAST_source). This will tell the program which FSFAST model (lh, rh, mni305) to use to extract the seed region data. In this way, you can use subcortical or cortical seeds to do the analysis.

models={'.lh' '.rh' '.mni305'};
P.FSFAST_source=[Study_Dir filesep Subjects{ii} filesep config.Subject_Subdirectory filesep 'SPMana' filesep config.Model models{3} filesep 'SPM.mat'];


Let me know if you have any questions.