Resting State Analysis with Downsampled Subject Cortex

Dear CONN community,

I have a downsampled subject specific cortex file (15002 vertices) produced from the MEG/EEG software Brainstorm. I would like to use this specific cortex to do fMRI functional connectivity with. I have a few questions and ran into some errors in trying to attempt this.

I could export the cortex and white matter as .gii files, which I then transformed into .pial and .white files using Freesurfer's mris_convert, which I then used to replace the original .pial and .white files produced by Freesurfer in the subject's folder. I then imported this cortex folder into CONN, and a few things happened.

One, the cortex looks appropriately downsampled, but is upside down; is this detrimental to the analysis?

Secondly, I tried doing a single subject preprocessing of the fMRI data using this cortex folder, and ran into the following error:

Preparing functional Resampling of functional data at the location of FreeSurfer subject-specific structural cortical surface (converts volume- to surface- level data)
Please wait...
ERROR DESCRIPTION:

Index in position 2 exceeds array bounds (must not exceed 7501).
Error in conn_surf_extract (line 199)
data_ref=data_ref(:,refinfo{hem}.ref2sphere);
Error in conn_surf_resample (line 10)
[nill,tfileout{n},nill,refinfo]=conn_surf_extract(tfilename{n},[],FS_folder,0,false,true,refinfo);
Error in conn_setup_preproc (line 2710)
outputfiles{isubject}{nses}=conn_surf_resample(filename,filestruct);
Error in conn (line 1105)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});

CONN19.c
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2018b
project: CONN19.c
storage: 387.2Gb available

Can anyone please suggest how I could go about doing such an analysis and addressing these errors?

Best,
Paul