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Does CONN provide means for Event Related analysis?

April 15, 2021, 12:15 am
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Dear all,
I would like to analyse functional connectivity around a time locked event during scanning. Would anyone have an idea if\how this is possible with CONN?
Best wishes and stay safe
Renzo
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Slice-timing correction error

April 15, 2021, 7:21 am
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Dear CONN experts, 

I downloaded the version of CONN  (20.b) in Linux, and performed functional analysis. I used the default preprocessing pipeline. 
I choose slice-timing: interleave phillips
When slice-timing correction started , an error ocurred: "item 'reference slice', field 'val': item must be an array of natural numbers."

I tried several times, and also choose: slice-timing interleave bottom-up and I also tried entering my own values, but the same error appears.

I would very much appreciate any help with this. 

thank you in advance,

Best regards, 

Carmen
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CONN batch scripting: How to skip already-done things?

April 15, 2021, 10:20 am
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Hi Alfonso et al. I am working on using a script to maintain a fairly large CONN project, using v 20b. I only have one preprocessing step specified: Setup.preprocessing.steps={'functional_art'}; (functional data is otherwise already preprocessed). The processing got pretty far, but errored out because of a small mistake in my Results second-level specifications. I fixed this (I think) and switched Setup.isnew, Setup.overwrite, and Denoising.overwrite to 0 thinking that it would skip the preprocessing etc. that it already did and move right to the Analysis and results, but it appears to be starting over and doing all that again. What is the correct way to skip the things it already did? Should I also set Setup.done and Denoising.done to 0? Also if I add just one or two new subjects, I want it to start at the beginning for only the new subjects. I seem to remember in the GUI this worked pretty intuitively with a pull-down that just said "Do not overwrite already-processed subjects/ROIs" or something to that effect. Thanks, 

Karl
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CONN std space MNI or TLRC as reported by AFNI 3dinfo

April 16, 2021, 9:38 am
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Hi There,

I have some rest data, processed with CONN defaults.  I thought the CONN outputs were in MNI space, and I do a lot of post-processing outside of CONN with MNI atlases.

However, when I run:
3dinfo -space -av_space -prefix *.HEAD *.nii*,   3dinfo reports the CONN outputs are in TLRC space.

The 3dinfo output, for example, are:
TLRC +tlrc NUC001_Concat_Preproc_REST1_REST2.nii   (my CONN preprocessed resting state data)
TLRC +tlrc NUC001_MNI_Fused_T1w.nii                        (subj T1, warped to std space during CONN preprocessing. I labeled it MNI, now I'm not sure it is)
ORIG +orig NUC001_raw_Fused_T1w.nii                        (native T1)
MNI +tlrc NUC001_GM_Masked_REST_TS_ROIselected_Conn.nii   (file from post-processing that needs to be in same space as my preprocessed rest data)

A few questions:
1) Is this a header issue, or are the CONN default outputs really in TLRC space?
2) Can I choose which std space CONN will warp to including MNI, TLRC or freesurfer average?  I looked but didn't see where to set that option.

Thanks in advance for your help,
Sherri
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CONN v20.b beta and t values

April 17, 2021, 7:37 am
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Hello,
Could you tell me how to find the beta and T values in CONN V20.b when conducting a second-level analysis. Can we found them in any specific file?
Best,
Fred
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RE: seed to voxel and roi to roi analysis, networks

April 18, 2021, 2:34 am
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Dear Alfonso,

Thank you very much for your answer.

I did the seed to voxel analysis with the four seeds from the dorsal attention network and the rest of the brain, obtaining a significant cluster in the inferior temporal gyrus. I clicked on the plot effects button to see better the results, as suggested. Results showed that the bars of the time1 (pre) were lower than the bars of time2 (post) in all seeds of the dorsal attention network. Does this mean that the connectivity between the inferior temporal gyrus and all the seeds of the dorsal attention network was greater in the post than in the pre? But is this significant in all the seeds of the network? Is there any way to interpret whether this is significant in all areas of the network?

And on the other hand, when I clicked on plot effects, I got F(4 9) = 8.91 p(FDR) = 0.003. What do these values mean? They are different from the ones that appear in the first window before clicking on plot effects.

Thank you very much.

Kind regards,

Agurne
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the same seed, different results

April 19, 2021, 7:59 am
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Hello everyone,

I am using seed-based rs-fMRI analysis in CONN. I chose the cluster showing significant correlation of fALFF map with behavioral score as the seed. However, every time when I run the seed-based functional connectivity analysis, the results would be a little bit different. The main differences are the coordinates, but the areas are exactly  the same areas. I followed the manual to do the analysis, and chose the same threshold. Does someone have happen to meet the same situation? How should I solve this problem?

By the way, I also extract the beta image generated in the first-level analysis to run the second level-analysis in SPM. I found the significant areas would be the same but the coordinates and cluster size are a little bit different. So a little bit confused.

Thanks

Hua
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gPPI and session

April 20, 2021, 6:10 am
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Good morning:
I am using the CONN toolbox in order to perform some gPPI analyses. I have data from a longitudinal study and I would like to assess whether connectivity analyses change as a function of time. Each subject undergoes a fMRI task with 5 different conditions in two different scanning sessions (which take place two months apart). I would like to perform a gPPI analysis for each scanning session and then compare whether connecitivity maps changed across the different scanning sessions. So my question is: How should I introduce the data from the second scanning session? If I introduce it in a different session for each subject, I cannot differentiate between them in the gPPI analysis. On the other hand, if I create a new subject introducing the data from the second scanning session, I am afraid that this analysis won't take into account that this is a repeated-measure design. Could you help me to solve this issue please?
I highly appreciate your help.
Thanks and best regards,
Maite
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Error in second-level results

April 21, 2021, 7:56 am
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Dear Alfonso,

I am analysing a dataset of 6 participants (2 young adults, 2 old adults, 2 with Alzheimer's disease). The analysis is in native-space thus has used subject-specific ROIs. I just tried computing the second-level results and received an error, but I'm not quite sure what it means:

ERROR DESCRIPTION:

Error using spm_check_orientations (line 65)
The orientations etc must be identical for this procedure.

Error in spm_spm (line 323)
spm_check_orientations(VY);

Error in conn_process (line 5008)
SPM=spm_spm(SPM);

Error in conn_process (line 60)
case 'results_voxel', [varargout{1:nargout}]=conn_process(16,varargin{:});

Error in conn (line 11497)
conn_process('results_voxel','readsingle','seed-to-voxel');

Error in conn (line 10649)
if state==2, conn gui_results_wholebrain;
CONN20.b
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2020b
project: CONN20.b
storage: 3822.3Gb available

Any help would be greatly appreciated.

Kind Regards,
Pavan
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Coherence calculation

April 21, 2021, 10:17 am
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Hi,


I preprocessed and analyzed resting-state data within CONN and am now trying to figure out a method of determining the coherence (magnitude-squared coherence) of several of my ROIs. Is there a way of analyzing this within CONN? 

Thanks!
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RE: 2nd level error: dot indexing not supported for this variable type

April 21, 2021, 5:13 pm
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Hi Alfonso, 
I am having the same error: 
ERROR DESCRIPTION:

Struct contents reference from a non-struct array object.
Error in conn (line 10863)
SPM.xX_multivariate.statsname=info.statsname;
CONN20.b
SPM12 + DEM FieldMap MEEGtools vbm8
Matlab v.2017b
project: CONN20.b
storage: 209.8Gb available

Could you help me?
Thanks
Indira
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RE: Error message - Reference to non-existent field 'X1'.

April 23, 2021, 7:58 pm
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[color=#000000]Hi Alfonso,[/color]

[color=#000000]You are right! The Denoising Step didn't finish, and 3/6 Step (Denoising functional data) was skipped. I have imported AAL90 template in Setup, which might be related to this error. Could you kindly give me some suggestions? Thank you so much![/color]

[color=#000000]Best,[/color]
[color=#000000]Gucy[/color]
[i]Originally posted by Alfonso Nieto-Castanon:[/i][quote][color=#000000]Hi Nikolov,[/color]

[color=#000000]I believe this error indicates that the Denoising step has not really finished correctly yet. Please check in your project conn_*/results/preprocessing folder whether files named ROI_Subject*_Condition*.mat exist there, and if not, please try re-running the denoising step (and let me know if any error/warning messages occur during denoising)[/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by nikolov:[/i][quote]+1 - also getting this error consistently when attempting to do rsfmri connectivity analyses with a imported atlas - any insight would be appreciated! 

ERROR DESCRIPTION:

Reference to non-existent field 'X1'.
Error in conn (line 7347)
[CONN_h.menus.m_analyses.X,CONN_h.menus.m_analyses.select,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,CONN_h.menus.m_analyses.X1,[],{nregressors,nview});
Error in conn (line 6401)
conn gui_analyses;
Error in conn (line 6639)
conn('gui_analysesgo',1);
CONN20.b
SPM12 + DEM FieldMap MEEGtools
Matlab v.2020b
project: CONN20.b
storage: 939.2Gb available[/quote][/quote]
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how to add realignment parameters in denoising part in conn

April 24, 2021, 7:25 am
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I 've just start using conn and have tried my best to find a solution to this question, and I was wondering if someone could help me figure out.
I am analysising the task fmri data. I have done the preprocessing in SPM and import the 1st level analysis results in conn.But when doing the denoising,i found the confound list didn't contain realignment,and i wonder how to add realignment parameters in denoising part.
Thank you very much for a reply!
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MVPA: does CONN inform the classifier performance, which subjects were used as test and which as training?

April 26, 2021, 11:50 pm
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Dear CONN expert,
I ran CONN´s MVPA in a big cohort of rsfMRI, >100, and got an interesting result.
I read the Norman et al.,2006 review and I am still facing 2 important questions:
1- I set a constrast of patients vs controls, how do I know which subjects of the cohort were used for training and whish for testing? 
2- What was the classifier performance?

Looking forward for your answer!
All best
Renzo
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CONN ICA maps

April 27, 2021, 3:58 am
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Hi,

Does anyone knows where I can get more info about the step-by-step procedure for ICA based denoising in CONN using the last version released? I've read the manual and watched the tutorials on the website but I'm still not sure about the settings.

Thank you.
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QA information for multiple sessions

April 27, 2021, 9:12 am
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Hi,

Does anyone know how to obtain QA plots and images to check registration and normalization of functional and anats for multiple sessions? I am only able to create and view the plots for my session 1 data.

Best,
Omar
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RE: CONN batch scripting: How to skip already-done things?

April 27, 2021, 9:54 am
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Could I bump this? My question is basically just how to skip already-processed subjects/ROIs in a CONN batch script. Thanks,

Karl
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data already in mni space

April 27, 2021, 11:23 am
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I'm new to conn. I was given some fMRI data in mni space already. How can I input these data in conn20b version without structural data? or do I have to put in the structural data to finish the "setup" part? Even I input the T1 data and normalized & in mni space with preprocessing step; when I clicked done it gave me an error with wcT1 file after erosion. What did I do wrong?
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problem with import from fmriprep - ICA aroma cleaned files not imported

April 28, 2021, 10:04 am
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Hi,

I have a relatively large dataset (108 participants, 4 tasks) that I preprocessed with fmriprep including ICA aroma, and I want to import it to CONN for further denoising and first-level analyses.
However, when using "new (import) from fmriprep dataset", the functional files that are imported are the ~desc-preproc_bold.nii.gz files
and not the ~desc-smoothAROMAnonaggr_bold.nii.gz ones (i.e. the files after aroma non-aggressive cleaning).

Is there a way to import the ~desc-smoothAROMAnonaggr_bold.nii.gz files when importing the dataset?

Thanks!
Rotem
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RE: Average within / between network connectivity

April 28, 2021, 10:39 am
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[color=#000000]Hi,[/color]

[color=#000000]I had the same issue, but ended up using version 19c and it worked just fine.[/color]

[color=#000000]Best,[/color]
[color=#000000]Omar[/color]
[i]Originally posted by Nadine Smith:[/i][quote]Dear experts,

I am facing a similar issue with version 20b (I have run the script without any problems in version 18b before).

I get the following error when I try to run [u]conn_withinbetweenROItest [/u]although I have properly set up the model in the main GUI on the ROI-to-ROI tab:

[i]"Reference to non-existent field 'roiselected2'.[/i]

[i]Error in conn_withinbetweenROItest (line 16)[/i]
[i]ntargets=CONN_x.Results.xX.roiselected2; % selected target ROIs (indexes[/i]
[i]to names below)"[/i]

Any help on this is greatly appreciated!

Best,
Nadine[i]
[/i]

[i]
[/i][/quote]
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