help > RE: Problem displaying surface-level analyses
Oct 8, 2020  08:10 PM | Alfonso Nieto-Castanon - Boston University
RE: Problem displaying surface-level analyses
Hi Andrew,

Sorry for the cryptic error message, I believe that simply indicates that CONN is not finding the .../surf/lh.sphere.reg and .../surf/rh.sphere.reg files associated with that subject (it needs these in order to convert between subject-specific coordinates and fsaverage space). In general the function conn_annot2nii should find those automatically when you select the subject-specific annotation files stored in .../label/lh.BN_Atlas.annot, so I am thinking perhaps you copied those annot files to a different folder before importing them to CONN (or something along those lines which may be causing CONN not to find the associated .sphere.reg files?)

Best
Alfonso
Originally posted by Andrew Lynn:
Hi Alfonso,

I've tried the patch so that I can load individual subject-specific *.annot ROI files. The annotation files were created by annotating individual subjects surface with the Brainnetome map. This resulted in ?h.BN_Atlas.annot files for each subject. I would like to use these ROI maps for analysis at the subject-level in surface space.

However after implementing this patch you provided Amy, I've received the error below. Are you able to help?

Andrew





ERROR DESCRIPTION:

Unrecognized function or variable 'data'.
Error in conn_annot2nii (line 93)
else mismatchedsize=numel(data);
Error in conn_getinfo (line 17)
filename=conn_annot2nii(filename);
Error in conn_file (line 11)
[nV,str,icon,filename]=conn_getinfo(filename,doconvert);
Error in conn (line 2569)
fileinfo=conn_file(deblank(filename(n1,:)));
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
CONN19.c
SPM12 + DAiSS DEM FieldMap MEEGtools TFCE cat12
Matlab v.2019b
project: CONN19.c
storage: 1460.5Gb available
spm @ /Users/andrewlynn/Documents/MATLAB/spm12
conn @ /Users/andrewlynn/Documents/MATLAB/conn



Originally posted by Alfonso Nieto-Castanon:
Hi Amy,

No problem, just try the attached patch, that should let you load into CONN subject-specific annotation files as well (so you should be able to simply load the same DKTatlas annotation files that you were trying originally, a separate file for each subject, and located in each subject "label" folder). This patch is for release 19b, to install it simply copy the attached file to the conn distribution folder overwriting the file with the same name there

Let me know if you run into any issues
Alfonso

Originally posted by Amy Bouchard:
Hi again Alfonso,

I was able to find the ?h.aparc.annot and ?h.aparc.a2009a.annot files (left and right hemispheres), but not the ?h.aparc.DKTatlas.annot files.

Could this still work?

Thanks,
Amy

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TitleAuthorDate
Amy Bouchard Jan 22, 2020
Alfonso Nieto-Castanon Jan 27, 2020
Amy Bouchard Jan 27, 2020
Alfonso Nieto-Castanon Feb 6, 2020
Amy Bouchard Feb 12, 2020
Alfonso Nieto-Castanon Feb 14, 2020
Amy Bouchard Feb 15, 2020
Amy Bouchard Feb 16, 2020
Alfonso Nieto-Castanon Feb 16, 2020
Amy Bouchard Feb 16, 2020
Alfonso Nieto-Castanon Feb 16, 2020
Amy Bouchard Feb 16, 2020
Alfonso Nieto-Castanon Feb 16, 2020
Amy Bouchard Feb 16, 2020
Alfonso Nieto-Castanon Feb 16, 2020
Amy Bouchard Feb 16, 2020
Alfonso Nieto-Castanon Feb 17, 2020
Andrew Lynn Oct 8, 2020
RE: Problem displaying surface-level analyses
Alfonso Nieto-Castanon Oct 8, 2020
Andrew Lynn Oct 8, 2020
Amy Bouchard Feb 18, 2020
Alfonso Nieto-Castanon Feb 19, 2020
Amy Bouchard Feb 19, 2020
Amy Bouchard Feb 17, 2020
Amy Bouchard Feb 16, 2020
Alfonso Nieto-Castanon Feb 16, 2020
Amy Bouchard Feb 6, 2020
Amy Bouchard Feb 5, 2020