NITRC isc-toolbox: Inter-subject correlation analysis for fMRI in Matlab Forum: faq

RE: Comparison problem at x:11/91

sadiezacharek — Mon, 08 Dec 2025 21:54:10 GMT

I'm experiencing the same issue -- were you ever able to resolve this?

Trouble understanding the results folder structure for session comparison

Sumit Roy — Wed, 29 Jan 2025 13:24:22 GMT

My name is Sumit Roy, and I am a PhD student at Leibniz Institute for Working Human Factors in Dortmund. I have some questions regarding the structure of the results obtained by the ISC toolbox. I am comparing two runs from a stressful and neutral movie, from what I understood in the results folder - ISCSessionComp1Band0ZSumstat.nii contains the data. I want to plot my results in MRIcoGL according to the critvals given in the CSV file - SessionComparison1Band0ThresholdsWin0_Session_SW_MCConly_0_5000.csv I want to plot the sumZPF stats but the results file  ISCSessionComp1Band0ZSumstat.nii is in a smaller range. So, I am having a hard time wrapping my head around how we can visualize the comparison results and which crtivals correspond to these results. Sorry if it seems like a naive question but I am pretty new to MRI analysis and any help regarding the ISC analysis will be greatly appreciated.

RE: Problem with visGUI

天鹭张 — Tue, 27 Aug 2024 9:31:52 GMT

Hi，
I have met the same problem. However,I can not understand how to solve it that you say. Can you explain it clearly? Thank you very much.

Comparison problem at x:11/91

Kirill Efimov — Wed, 26 Apr 2023 5:43:08 GMT

Dear developers,

I'm having an issue with the group comparison getting stuck at x: 11/91 forever.

The thing is that the first and second halfs of my dataset taken separately work fine, but adding subjects from one half to another results in this (screenshot attached). I can't find any systematic shifts in my data judging by the headers. Also, basic ISC for the whole dataset works fine (although there are some seemingly random NaN values in a few iterations), just not the comparison .

This error has been replicated on different systems.

Is there something particular going on in this moment?

Error while evaluating UIControl Callback.

Chihhao Lien — Thu, 30 Sep 2021 15:01:30 GMT

Dear all,

I meet an error while the ISC analysis is finished and launching the GUI

When the analysis is finished, the error is:

ans =

'30-Sep-2021 16:42:28'
ans =
'30-Sep-2021 16:42:28'
Calculating critical thresholds:
Index exceeds the number of array elements (0).
Error in combineNullVals (line 98)
nullVals = nullVals(1:(1+floor(N*q)));
Error in calculateThresholds (line 66)
combineNullVals(Params,nrSession,winOn); % combine (right-tail) null-distribution data
Error in runAnalysis (line 484)
calculateThresholds(Params,nrSession,0); % across session
Error in ISCanalysis>pushbuttonRun_Callback (line 602)
runAnalysis(handles.Params);
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in ISCanalysis (line 43)
gui_mainfcn(gui_State, varargin{:});
Error in matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)ISCanalysis('pushbuttonRun_Callback',hObject,eventdata,guidata(hObject))
Error using uiwait (line 81)

In addition, when Calculating permutation distributions for each ISC map, the feedback looks weird too.

Calculating permutation distributions for each ISC map:
Started at: 30-Sep-2021, 15:45:9.681
GBW-D-W2793
: X:\fMRIprep_6Asym_20210925\ISC\results\PositiveAll\stats/vals1Session1
Realization number: 100000/10000000
Resampled ISC value: NaN
Realization number: 200000/10000000
Resampled ISC value: NaN
Realization number: 300000/10000000
Resampled ISC value: NaN
Realization number: 400000/10000000
Resampled ISC value: NaN
...

When I try to launch the GUI, there's a warning "Unexpected error while opening visu-GUI with the current parameters, use File->Open to find a correct parameter-file.

In the beginning, I thought there might have some subjects make the problem, so I try to do the same analysis with fewer subjects several times. Unfortunately, if I just include 5-6 subjects in the analysis, no one will make the error. Does anyone know how to deal with this problem?

Thanks.

Viewer for ISC maps

Chihhao Lien — Tue, 10 Aug 2021 14:33:08 GMT

Dear all,

I'm new to use ISC toolbox, and I already get some ISC maps from it.

I tried to use xjview to display the ISC maps because I want to know details of significant clusters, but it can't properly display ISC maps (ex. ISCcorrmapBand0Session1.nii). 
Could anyone recommend a proper software/viewer for ISC maps?

I'll appreciate you if someone can recommend it.

Thanks.

Error in file evaluatePvals.m

Melanni Nanni Zepeda — Tue, 13 Oct 2020 10:26:29 GMT

Hello experts,
I'm getting this error with the toolbox just after "Get thresholds for ISC maps: band 0"

Error: File: evaluatePvals.m Line: 138 Column: 5
"F" previously appeared to be used as a function or command, conflicting with its use here as the name of a variable.
A possible cause of this error is that you forgot to initialize the variable, or you have initialized it implicitly using load or
eval.

I already check the inputs and everything looks fine, I restarted matlab, but still get it.

Does someone knows what could be happening?
Thank you!

Best
Melanni

Error: File: evaluatePvals.m

Melanni Nanni Zepeda — Tue, 28 Jul 2020 9:56:18 GMT

Dear community,

I'm getting this error on the evaluatePvals file:

"F" previously appeared to be used as a function or command, conflicting with its use here as the name of a variable. A possible cause of this error is that you forgot to initialize the variable, or you have initialized it implicitly using load or eval.

I'm not defining anything with "F", I reinstalled the toolbox and it happen the same

Thanks for your help

Launch visu-GUI

Zhilin Zhang — Sat, 20 Jun 2020 6:32:00 GMT

When I click "launch visu-GUI", it suggest me to "Select directory including all nii-files of 2mm Harvard-Oxford atlas!". But I select the "templates" folder that include "HarvardOxford-cort-maxprob-thr0-2mm.nii, HarvardOxford-cort-maxprob-thr25-2mm.nii, HarvardOxford-cort-maxprob-thr50-2mm.nii, HarvardOxford-cort-prob-2mm.nii, HarvardOxford-sub-maxprob-thr0-2mm.nii, HarvardOxford-sub-maxprob-thr25-2mm.nii, HarvardOxford-sub-maxprob-thr50-2mm.nii, HarvardOxford-sub-prob-2mm.nii, MNI152_T1_2mm_brain.nii, MNI152_T1_2mm_brain_mask.nii.", it said "WRONG PATH". Can you tell me how to solve this problem?

Alignment of correlation maps

Adrian Williams — Wed, 27 May 2020 18:30:05 GMT

Hi

I'm wondering if anyone else has noticed a small mis-alignment of the ISC results? I have pre-processed my data as per the instructions and they are aligned with the MNI space. But when I overlay a correlation map on the MNI brain it seems offset by a few voxels. Its tiny, but you do notice it. When I put the underlay and overly into voxel space, the match seems good. But in world space, I'm sure there's a misalignment!

I'm using the latest version of the toolbox.

Thanks!