Dear Alfonso,

I was trying to perform analysis on some already preprocessed data (starting with swau* preprocessed by SPM). Everything was working properly (all the way to the 2nd level GLM analysis), until today when I tried importing a Schaefer atlas, it gave me this error during the setup step:

ERROR DESCRIPTION:
 
Error using read_hdr (line 39)
Error reading header file "/work/cnelab/Camcan/CONN_proj/preprocessed_rest/waufMR10033_CC110033-0005.nii".

Error in nifti (line 26)
 vol = read_hdr(fname);

Error in conn_expandframe (line 23)
 ni = nifti(filename);

Error in conn (line 3412)
 temp1=cellstr(conn_expandframe(temp{1}));

Error in conn (line 2031)
 [varargout{1:nargout}]=conn('gui_setup',varargin{3:end});

Error in conn>conn_callbackdisplay_roiclick (line 12879)
 fh=conn('gui_setupgo',4,14,3,nroi*(1-2*erois),nsub,nses);

Error in conn_menu>conn_menubuttonmtnfcn (line 1367)
 if numel(data.buttondown.matdim.dim)>=5, feval(data.buttondown.callbackclick,xyz,1+floor((posabs(1)-1)/data.buttondown.matdim.dim(1))+data.buttondown.matdim.dim(4)*floor((posabs(2)-1)/data.buttondown.matdim.dim(2)));

Error in conn_menu>@(varargin)conn_menubuttonmtnfcn('volume',CONN_h.screen.hfig,h.h1,h.h2,h.h6a,h.h2c,varargin{:}) (line 342)
 conn_menumanager('onregion',h.h6a,1,position,h.h2,@(varargin)conn_menubuttonmtnfcn('volume',CONN_h.screen.hfig,h.h1,h.h2,h.h6a,h.h2c,varargin{:}));

Error in conn_menumanager>conn_menumanager_mousemove (line 744)
if nargin>0, feval(varargin{:}); end

Error in conn_menumanager (line 261)
 if cond, anymtn=true; conn_menumanager_mousemove(CONN_MM.onregionmotioncallback{n0},handle); end

It seems that it was trying to look for data starting with wau* but I don't have it. Any advice would be appreciated!

Thank you so much,

Meishan

First confirm that the file waufMR10033_CC110033-0005.nii exists in the specified path /work/cnelab/Camcan/CONN_proj/preprocessed_rest/. Check file permissions to ensure you have read access.

If the path or file name is incorrect, update it in your script. For MATLAB, it would be something like filePath = /correct/path/to/your/file/waufMR10033_CC110033-0005.nii;. Also, confirm the NIfTI file is not corrupted by opening it with a NIfTI viewer.

Thank you! This file actually does not exist in the first place - we started with the swau* files which were preprocessed already in SPM from the data source. Is there a way I can ask CONN to not to look for this file?

Additionally, this error has not appeared untill we imported a Schaefer atlas as ROIs (we have imported other atlas and performed 2nd level analysis multiple times). The error itself seemed to be irrelevant to Schaefer atlas, but it did appear after we imported this atlas. Everything has been performed on a computing cluster, would this have something to do with it?

Thank you so much!

Meishan

Hi Meishan,

I imagine the issue may be that the new ROI file is set to extract data from the unsmoothed volumes (so CONN is looking for the wau* files, i.e. prior to smoothing)? If so, simply go to the Setup.ROIs tab click on your new atlas ROI, and change the option that reads "extract from unsmoothed volumes" to "extract from functional data"

Hope this helps

Alfonso

Originally posted by Meishan AI:

Thank you! This file actually does not exist in the first place - we started with the swau* files which were preprocessed already in SPM from the data source. Is there a way I can ask CONN to not to look for this file?

Additionally, this error has not appeared untill we imported a Schaefer atlas as ROIs (we have imported other atlas and performed 2nd level analysis multiple times). The error itself seemed to be irrelevant to Schaefer atlas, but it did appear after we imported this atlas. Everything has been performed on a computing cluster, would this have something to do with it?

Thank you so much!

Meishan