I am trying to do an ICA analysis using archival data from the ABCD study. My reading of the documentation is that the structural data has undergone inhomogeneity correction and been registered to an atlas while the resting state data has undergone inhomogeneity correction, and motion correction but has not been registered to the structural data. I am in the early stages of the analysis and so at this point am not picky about what atlas the data is registered to so long as it is in a common space from which I can do the ICA. With this in mind I am looking to register the preprocessed resting state date to the preprocessed structural data. To do this I chose the processing step labeled 'Functional direct coregistration to structural without reslicing (rigid body transformation)'. This selection however resulted in the following error message:

ERROR DESCRIPTION:
Error using conn_setup_preproc (line 2335)
No FreeSurfer data found for structural file asdf.nii
Error in conn_setup_wizard (line 143)
Error in conn (line 4398)
Error in conn_menumanager (line 120)
CONN18.b
SPM compiled
Matlab v.2018b
project: CONN18.b
storage: 148.0Gb available

I guess the first question is whether functional direct coregistration is the proper processing selection or if there is a better choice. If functional direct coregistration is the proper choice, what do I do about the FreeSurfer files?

My impressions is that this error messsage indicates that you may have accidentally selected the option labeled 

"functional Direct Coregistration to structural without reslicing followed by Resampling of functional data at the location of FreeSurfer subject-specific structural cortical surface (converts volume- to surface- level data)"

 (since the error message indicates CONN is looking for FreeSurfer files there). If that is the case simply select instead the option labeled:

"functional Direct Coregistration to structural without reslicing (rigid body transformation)" 

and that should work without a problem. Please let me know otherwise

Best
Alfonso

Originally posted by ythncuvgbvn:

I double checked that I selected 'Functional direct coregistration to structural without reslicing (rigid body transformation)' but the error persists.  I attached a screenshot of the data preprocessing pipeline before I hit 'start'.  In the menus after this I choose the defaults.

Hi,

When you choose one of the default pipelines CONN is going to run all those 11 steps that your screenshot is showing (not just the coregistration one that you have highlighted). The error that you are seeing is associated with the 7th step there (the one labeled "functional Resampling of functional data...", where CONN is trying to resample your data at the location of the FreeSurfer-generated cortical ribbon, and the error indicates that CONN is not finding the expected FreeSurfer-generated files.

If, as I understand, your intention was simply to run the "functional Direct coregistration to structural" step alone, you simply need to first select all of the other 10 steps in your current "data preprocessing pipeline" list and click 'Remove' (to remove those steps and leave in your list only the "functional Direct coregistration to structural" step), and then click "Start" to run that individual step (also before any of this double-check that the functional and structural data that you have in CONN's functional and structural tabs, respectively, are the proper raw files (and not the result of previous attempts at running different preprocessing steps)

Hope this helps
Alfonso
Originally posted by ythncuvgbvn:

hey ! I have a similar problem,
I tried to use freesurfer files in CONN, using the attached pipeline (we didn't use  slice timing and smoothing in our analysis)
all the data of free surfer is in the right folder (when I upload it on gui, it creates more file to use in this folder.
the error message is: 
ERROR DESCRIPTION:

Error using conn_setup_preproc (line 2709)
No FreeSurfer data found for structural file /media/neuro/LivnyLab/Research/MISTIC/analyses/Volumetric/freesurfer/V1/102_1_BD/mri/T1.nii
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 + DEM FieldMap LST MEEGtools marsbar
Matlab v.2019b
project: CONN19.c
storage: 59.5Gb available

do you have any suggestions on  what went wrong? 
thank you
Reut