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

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).<span id="_plain_text_marker"> </span>
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!

two open positions in neuroimaging genetics in Bari, Italy

Linda Antonucc — Mon, 17 Feb 2020 9:30:58 GMT

The Group of Psychiatric Neuroscience at the University of Bari Aldo Moro (Italy) aims to discover the biological sources of differences between individuals that make them at risk of - or resilient to -psychiatric disorders.

We are about to publish 2 calls for research fellowships in neuroimaging genetics in different projects with two PIs. Ideally, the positions are targeted at postdoctoral fellows and funding is available for several years. Outstanding predoctoral candidates will be evaluated. Expected starting dates are between May and July 2020.
Expressions of interest are welcome until positions are filled, preferably before the end of February.
The group is headed by Prof. Alessandro Bertolino and investigates the association of genetic variability with brain phenotypes, with a special focus on subjects at risk for psychiatric disorders (for recent articles from the lab, see [1], [2], [3]). Successful candidates will work in the lab of Brain Imaging, Networks, and Data mining (BIND) directed by Dr. Giulio Pergola. The department has an in-house Elekta Triux magnetoencephalography with two dedicated technicians. Two 3T MRI scanners are available in collaborating hospitals. Prof. Giuseppe Blasi and his team have access to and routinely tests patients, relatives of patients, and individuals at risk for psychosis. The environment is interdisciplinary, including psychologists, biotechnologists, and MDs, and internationally oriented, e.g., including Marie Curie awardees Dr. Pergola and Dr. Linda A. Antonucci, along with several other members trained for > 1 year in UK, USA, and Finland.
The ideal applicant is a neuroimager with international experience and a PhD in Neuroscience, Cognitive Sciences, Neuropsychology, Computational Science, or any quantitative research field. Coding experience (Matlab, R, Unix, and/or Python) is required, whereas machine learning and graph theory expertise are a plus. Successful candidates are expected to have at least one published/submitted lead author paper. We expect the successful candidate to be motivated and research-oriented. It is equally important to have a team-working attitude and a motivation to fit in the group. Proficiency in Italian is not required.
Consider applying even if you only have strong coding and analytic skills – definitely apply if you think you have smart ideas on how to analyze multimodal neuroimaging/genetic/neuropsychological data from hundreds of subjects.
The University of Bari Aldo Moro is one the largest Italian universities (50.000 students, 1500 permanent professors and researchers, 1500 units of technicians and administrative staff). Bari is a sunny city located by the sea, and the third largest Italian city south of Rome. The cost of living is low relative to Italian standards.
Please contact Dr. Giulio Pergola sending a CV and the contact details of at least two references if you would like to have more information on the positions and on the ongoing projects (giulio.pergola@uniba.it).

Frequency bands without visGUI

ndamestani — Fri, 07 Feb 2020 13:43:09 GMT

Hello,

Is it possible to derive the frequency bands (range in Hz) used to generate the ICC band maps without using the visGUI?

Thanks!

Subject Source File

Nobody — Wed, 24 Apr 2019 13:27:12 GMT

Hi,

We want to select the data files to work with but the GUI doesn't allow to select data files. I attached a screenshot from what my GUI looks like, and it looks different from the screenshots presented in the manuals. We have tried various Matlab versions and various computers but get the same GUI screen. Does anyone know the data files can be added so we can run the analysis?

Thanks in advance!
Sophie