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NBS statistics: view non-significant results in table

March 5, 2018, 4:47 am
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Dear Alfonso, 

I am running a 2nd level ROI-to-ROI analysis (p-FDR seed-level correction at 0.05 and NBS intensity seed thresholding at 0.05). 
The results table shows me the significant ROIs and connections; however, I would like to view/extract the [b]nonsignificant[/b] results as well, so I can plot them in another software (p-values and F-values for subthreshold edges and ROIs). 

Is this possible, and, if so, how?

As always,
Thank you very much for your help,

Best wishes,
Charlotte
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RE: How to skip preprocessing ?

March 5, 2018, 5:00 am
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Hi Zoe, 

I'm not an author of this fantastic toolbox, but maybe I can help you. To answer your first question: this really depends on which steps you have run/would have run in Conn. You can load your individual structural and functional files (as preprocessed as they are) and, when you get to the preprocessing step, select any preprocessing steps you would still like to run/or de-select those you'd like to skip. During preprocessing and denoising, the program will automatically add first and second level covariates (such as realignment and scrubbing parameters, or quality assurance), which you'll need to add manually if you skip those steps in conn. 
To answer your second question: if I remember correctly, in my analyses, I usually didn't have to run the preprocessing again, but the first and second level analyses. You can speed this up a bit by selecting "skip already processed subjects/seeds ..." in the window that will appear once you have changed your ROIs. 

I hope this helps, 
Best wishes, 

Charlotte
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RE: CONN analysis: group comparision after intervention

March 5, 2018, 5:12 am
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Hi Meike, 

Maybe I can help you. If you have two groups, and two sessions, you can specify your contrasts as described in the CONN manual. 
For instance, if you are interested in the effect of drug across your groups, you can select 
group1, group2 (0.5 0.5) and placebo, agent (-1 1).

If you are interested in the between-group difference after the agent, you could select
group1, group2 (1 -1) and agent (1);

typically, however, you'd want to investigate possible group (group1, group2) x drug (placebo, agent) interactions first, by selecting the contrast
1 -1, -1 1, 

then test for main effects (of group and of drug, e.g. as the drug effect specified above ), and then test for further post hoc tests (e.g. as the second contrast specified above). 

Hope this helps!
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error in ROI file during setup

March 5, 2018, 7:42 am
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Hello CONN experts.

I have received an error during Setup.I have an experiment with one subject and 9 sessions. I am trying to extract the resting state functional connectivity of subject under only resting condition.
I got this following error and I do not know what is its source?

Error using conn_process (line 660)
No suprathreshold voxels in ROI file

Error in conn_process (line 16)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);

Error in conn (line 4439)
else conn_process('setup'); ispending=false;

Any insights would be greatly appreciated!
Regards,
Sona
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Hi, I have questions about setting my data for rsfMRI analysis in CONN

March 5, 2018, 7:50 am
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Hi!
I have had problems for setting my MRI data in CONN.
 
I have two groups; sham stimulation group, real stimulation group.
I have two conditions within subjects; pre-stimulation, post-stimulation.
I wanna compare the functional connectivity between groups and between conditions.
How can I set up my data in CONN?
 
Sincerely yours.
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ICA connectivity values

March 6, 2018, 12:23 am
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Greetings,

When going to the results explorer and importing values for the clusters in my IC, it says these are connectivity values that are then displayed during 2nd-level covariates in the "setup" bar.

Does this represent the connectivity between the clusters in that IC?

Thanks so much for clarification!

Best,

Emma
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CompCor Methode, denoising, Conn

March 6, 2018, 2:07 am
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Hi everyone!
I am a beginner in fMRI preprocessing. I am currently analyzing fMRI data using SPM12. I already run all the preprocessing steps with SPM12. I would like to denoise my images using the compcor methode in order to boost my signal within my GM. I was wondering if I could use the conn toolbox for that.

For the moment what I have done, is to extract time serie from my WM and CSF and then apply a denoising on my images. To do that I use only WM CSF and rest in the confound parameters (using 5 component per ROI).
Then I will use the images obtained after this denoising step (niftiDATA_Subject00X_Condition000.nii in the results forlder) in SPM12 in order to run the first level GLM.
For the moment I don't want to perform connectivity analysis.

My question is the following: is that a correct methode for compcor denoising method?

Thank you in advance.

Rémi J
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RE: ROI List (components and labeling)

March 6, 2018, 8:37 am
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Hi,

.LP is left parietal cortex
.RPFC i right prefrontal cortex

Good luck
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Implicit masking

March 7, 2018, 10:29 am
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Dear CONN users,

I am using CONN version 17f to do second level ROI-to-ROI connectivity analysis on fmri data using implicit masking. I did the first level analysis on SPM12, and then imported the SPM.mat files for each subject into CONN.

I had a couple of questions, as follows:

1) How can I get the implicit masks for individual subjects that CONN generates. I have found several niftiNORMS_Subject00X_Session00X.nii files in "project_folder\results\preprocessing". Are these the subject specific implicit masks?

2) Are subject specific implicit masks used in the second level ROI-to-ROI analysis, or does CONN compute a combined or 'group mask' for second level analysis?


Thank you,
Tanweer
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Single subject fMRI analysis

March 8, 2018, 5:48 pm
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Dear CONN experts,

I would like to ask if i am able to perform the following analysis in CONN, and then if i can perform it in a single subject.

I have used CONN several times for rsfMRI analysis, so i am familiar with it, but i have never used it for the following.

I have a flickering light that pulses at different frequencies and the participant is looking at it. what i want to see is which area in the brain is responsible for the rhythm in said pulsation.

The participant doesn't push any buttons or anything, just looks at the light (pulsating at different but defined frequencies) and we record his brain activity. That is all.

Is it possible to check which areas in the brain respond to the rhythm of such pulsations, and can we check (as pilot) that in one individual subject?

Thank you
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publications using Conn

March 9, 2018, 2:08 am
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Hi,

I had great experiences with the CONN toolbox and will continue to use it in future work. How can I add my publications using CONN to the website? Please see citations below - I acknowledged Alfonso Castañón for his technical assistance in the projects. I had attempted to email info@conn-toolbox.org but received an error so thought it might reach the correct person if I post here.

[b]King M, Rauch LHG, Brooks SJ et al (2017) Methylphenidate enhances grip force and alters brain connectivity. Med Sci Sports Exerc 49:1443–1451. https://doi.org/10.1249/MSS.0000000000001252[/b]

[b]King, M. et al. Methylphenidate alters brain connectivity after enhanced physical performance. Brain Research 1679, 26–32 (2018). DOI: 10.1016/j.brainres.2017.10.026[/b]



Michael

Michael King, PhD
Postdoctoral Fellow
Marine Institute, Memorial University, Canada
michael.king@mun.ca
(709) 693 0242
–––––––––––––––––––––––––––
Honorary Research Associate
University of Cape Town, South Africa
Michael.King@uct.ac.za
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RE: missing BATCH.Setup.preprocessing.sliceorder in conn_batch_humanconnectomeproject.m?

March 9, 2018, 9:30 am
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Dear Alfonso,

I have a related question, but for data that I [i]do[/i] want to fully preprocess via a CONN batch script.  Like the HCP dataset, my data were acquired with a multiband sequence and short TR, so I wish to skip the slice timing correction step but otherwise apply batch.Setup.preprocessing.steps='default_mni'.

Can you advise what code to include in a batch script file to directly set the batch.Setup.preprocessing.sliceorder field to 'do not know (skip slice timing correction)'?

I have tried [code]batch.Setup.preprocessing.sliceorder={}[/code]but that causes the GUI dialog box to pop up.

I have also tried[code]batch.Setup.preprocessing.sliceorder='do not know (skip slice timing correction)'[/code]but that prompts a "Warning: incorrect sliceorder name" error, and then causes the GUI dialog box to pop up.<span id="_plain_text_marker"> </span>

<span>Thank you,</span>
<span>Kristin
</span>
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Using CONN results explorer with "external" SPM.mat

March 10, 2018, 5:57 am
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Dear CONN experts,

as I like the CONN results explorer and the multiple thresholding options very much, I would like to be able to use this tool with external SPM analyses, e.g. some FDG PET or VBM analyses I did not perform in CONN.

I also do like the visualizing options, e.g. quickly be able to generate a 4-view-mosaic surface image of some results for a quick presentation etc.

Is there a way to use the results explorer as a kind of standalone tool?

Thanks a lot!

Best wishes

Julian
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Running standard fMRI analysis in SPM using CONN images

March 11, 2018, 2:23 pm
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Hi All,

I have a simple fMRI task with three conditions (faces and shapes, alternated by rest) and I have preprocessed my images with CONN to perform some gPPI analysis. Now I would like to perform some additional standard fMRI analysis in SPM, basically I would like to compare the BOLD signal in the faces vs shape conditions including some additional regressors of interests (behavioural covariates).

I thought I had two option (but please me correct me if I am mistaken):
- use the swau.nii images and include motion regressor parameters and run first level again in SPM - but that would not produce the denoised images that I used in CONN;
- use the images resulting from the denoising step.
As I wanted to use the most comparable images, I decided for the latter. Following previous suggestions, I converted the DATA_Subject*_Condition*.matc in a nifti file using conn_matc2nii. However, if I understood right, this file contains all the conditions collapsed together. I run spm_file_split('niftiDATA_Subject001_Condition000.nii') but this command splits the file according to the number of session - not conditions, and I am interested in the different conditions.

Therefore my questions are:
- how do I generate separate nifti files for each condition?
- the denoising step computes the effect of each task condition controlling for all other confounding effects - including the other task conditions - so would it be conceptually "wrong" to try setting up a second level GLM in SPM including my condition 1 images vs condition 2 (i.e. setting up a contrast 1 -1) using images where I previously controlled for these effects? If so, should I re-run the denoising step not including the effect of the different conditions (perhaps just rest - which I am not interested into) or is there an alternative? 

Hope that my message is clear enough - thank you so much in advance for your help!
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conn preprocessing history

March 12, 2018, 11:36 am
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Hi,
I've inherited a dataset that was processed in CONN. Is there any document in the subject folder that provides the preprocessing options that were chosen (e.g., selections for slice timing correction?  ART percentile threshold used for outlier detection? re-sampling of data?  smoothing kernel applied?)...that is, something similar to FSL's report.html file that lists the specifics of each preprocessing step that was implemented.  Of course, I can tell from the filenames which preprocessing steps were implemented, but I'm looking for more specific info (e.g., parameters chosen for each of those preprocessing steps).
Thanks,
Scott
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second-level longitudinal analysis

March 12, 2018, 12:30 pm
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Hi there,

I'm running a longitudinal ROI-ROI analysis to examine change in connectivity while co-varying out age. For my second-level analysis, I entered the matrix [-1 1 0]. The beta value is 0.16 and I'm not sure if this is high enough to be reported.

In addition, if I just look at one group, what would a beta value of 0.1 represent? 

Thanks in advance! 

-J
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RE: Average within / between network connectivity

March 13, 2018, 4:38 am
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Hi Alfonso,

I am expecting your response on my query dated Feb 16, 2018 given below.
Kindly consider it as a gentle reminder to comment on it...

Thankyou for this wonderful script (conn_withinbetweenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.

Thanks and Regards
Himanshu Joshi
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QA variables in 2nd level MVPA analyis

March 13, 2018, 7:58 am
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Hi,

I am analyzing a dataset of 292 subjects, scanned twice, under identical conditions.
I have followed the default preprocessing settings in Conn 17.f (no field maps)
I am interested in the influence of a subject variable (Xa during scan a, Xb during scan b), so I have set up the analysis as 292 subjects, 2 conditions per subject, and I entered Xa and Xb as 2nd level covariates.
Following Gabrielli 2015 (Brain connectomics predict response to treatment in social anxiety disorder) I did a MVPA (10 factors) and then perform a contrast on all 10 MVPA groups (eye 10), where I include Subjects, Xa, and Xb as subject effects, and the two scans as conditions. I then perform the between subject contrast 0 1 -1 (i.e. Xa – Xb), and the between conditions contrast 1 -1 (i.e. scan a – scan b). My understanding is that this will identify any brain regions where there is a correlation between the change in Xa vs Xb, to the change in rsFC metrics between condition a and condition b.
I will then use the resulting clusters as seeds in a post-hoc analysis.

The problem I have is that I find a cluster that looks like a CSF artifact (illustrated below at p=0.05) , and I was wondering what QA variables are suitable to include. Or if there is another way to get rid of this artifact.
Also, any comments on the approach, or suggestions on how many MVPA groups to use in the first level analysis, would be much appreciated!
Best
Clas
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MATLAB 2016

March 14, 2018, 4:26 am
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Hi all

I am using MATLAB 2016B (and SPM8).

So far there is no way to select any functional data (I tried conn 16b - 17f, as the following error measage appears:



ERROR DESCRIPTION:

Undefined variable "matlab" or class "matlab.internal.webwindowmanager.instance.findAllWebwindows".
Error in matlab.ui.internal.dialog.DialogUtils.disableAllWindowsSafely
Error in questdlg (line 406)
c = matlab.ui.internal.dialog.DialogUtils.disableAllWindowsSafely();
Error in conn (line 3022)
Answ=questdlg({'Proceeding will close the current project and loose any unsaved progress',' ','Do you want to proceed with creating a new project?'},'New project','Proceed','Cancel','Proceed');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.17.a
SPM8 + Beamforming DEM FieldMap MEEGtools fmrigrocer fmripower marsbar masking rest vbct vbm8 xjview
Matlab v.2016b

I only have Matlab v.2016b available right now (it was working with MATLAB 2013b but the licence expired)

Best wishes
Lars
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ICC and negative values: suggestion to clarify in the doc

March 14, 2018, 9:50 am
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Dear Alfonso,

During an ICC analysis, I stumbled on negative values, and at first I was puzzled, because as I read the conn manual, I expected ICC to be the "root mean square of the correlation coefficient values", so in other words I here got a root value of a necessarily positive value that was negative!

By digging on the original article by (Martuzzi et al. 2011), it's specified that "For statistical purposes, the values in the map are normalized to fit a Gaussian distribution with zero mean and unitary variance by subtracting the ICC-dth obtained at each voxel by the average value across all the voxels and dividing this by the standard deviation of the whole-brain map". I guess you implemented ICC in CONN in a similar fashion.

If that is true, the meaning of ICC is not simply "how much any voxel is central", but rather "which voxels are more central than the average voxel centrality".

If this is correct, I would suggest to rewrite the description of ICC in the documentation, here is my suggestion:

"ICC is a measure of network centrality at each voxel compared to the average. It characterizes the strength of the connectivity pattern between each voxel and the rest of the brain, then standardize to 0 mean by subtracting the average ICC and to a Z-score of variability 1 by dividing by standard deviation of whole brain (standardized root mean square of the correlation coefficient values)."

Thank you very much for confirming if this is the correct explanation for the negative values :-)

Best regards!
Stephen
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