Hello Dr. Spielberg and colleagues,
I was running into an error with bsxfun (which might perhaps be a
matlab version issue?).
Here is my matlab output... Any thoughts?
###
>> GTG
Error using bsxfun
Mixed integer class inputs are not supported.
Error in cov (line 154)
xc = bsxfun(@minus,x,sum(x,1)/m); % Remove mean
Error in corrcoef>correl (line 206)
r = cov(x);
Error in corrcoef (line 131)
[r, n] = correl(x);
Error in Rest2GNI_edit>mycorrcoef (line 131)
[CC,P]=corrcoef(TC);
Error in Rest2GNI_edit>MyCorrcoefSmallLarge (line 105)
[r,p]=mycorrcoef(TC_Small,TC_Large(:,1+(iSection-1)*nTC_OneSection:iSection*nTC_OneSection));
Error in Rest2GNI_edit (line 74)
[R,P]=MyCorrcoefSmallLarge(GSTC.',WBTC.',nVoxelPerSectionMax);
Error in GTG_preprocess_GUI>preprocess_for_graph (line 1752)
GNI = Rest2GNI_edit(func_filename,funcmask_filename,100);
Error in GTG_preprocess_GUI>Start_pushbutton_Callback (line
1385)
[out.ts{currsub,1},out.num_censored_vols(currsub,1),out.num_censored_vols_FD(currsub,1),out.num_censored_vols_DVARS(currsub,1),out.GCOR(currsub,1),out.mean_FD(currsub,1),out.mean_DVARS(currsub,1)]
=
preprocess_for_graph(out,sub,logfile_fid,img_ext,func_filename,parc_filename,funcmask_filename,WM_filename,vent_filename,parc_warp_filename,WM_warp_filename,vent_warp_filename,par_filename);
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in GTG_preprocess_GUI (line 134)
gui_mainfcn(gui_State, varargin{:});
Error in
@(hObject,eventdata)GTG_preprocess_GUI('Start_pushbutton_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback
>>
###
For potential insights into the issues, I was interested in
using GTG to (partially) preprocess my data...
Outside of GTG, I thought I could mcflirt my EPI data for motion correction (and output the .par file), FNIRT this functional data to MNI space, and segment the corresponding T1w structural to get a white matter and csf mask (which I could use in GTG). The motivation was that I could do all this on a cluster to move the data along quickly (Matlab has some issues running on said cluster...).
I then thought I could include this warped, motion
corrected functional volume as my functional volume in GTG, uses an
MNI mask as the brain mask and ROI masks, select the subject white
matter and csf masks and then output the intermediate
functional volumes. Do you think that is possible/reasonable
?
Again, any thoughts or suggestions are greatly
appreciated!
And apologies for the multiple
emails/issues!
Thanks much!
Jamie.
RE your error, try using the attached script (replace your current version in GTG/dependencies).
As for your data analysis path, that all sounds good. I'm guessing you know this, but just in case, if your functional data is in MNI space, you will also need the vent/WM masks to be in MNI space...
Best,
Jeff
And yes, I warped all my segments to MNI space also. Do you recommend using unsmoothed segments?
Or should I use a small kernel to smooth?
Thanks again!