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second-level beta extraction for repeated measures design

March 28, 2018, 11:55 pm
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Hi there, 

I have entered a 2X2 ANOVA and found a significant interaction effect but I am having trouble extracting the betas to interpret this. 

I have a group of patients and a group of controls and I am comparing drug to placebo in a repeated-measures design. I defined my patients and controls in the setup.conditions, and I have defined my sessions as session 1 is drug and session 2 is placebo. I have defined my patient/control groups within Setup.conditions. 

To interrogate my group X session interaction I have entered the contrast [-1 1; 1 -1] which refers to controls > patients; drug > placebo. To which I have found 4 significant clusters which I have extracted the betas using "import values" and then going to setup > Covariates 2nd-level > select covariate > covariate tools > export data to file. 

My question is; this is a single beta weight for each participant representing drug-placebo. I would like a beta weight for the drug and placebo sessions separately. Which makes it hard to plot the interaction for the preparation of manuscripts and post-hoc testing. 

Is there a way that for the significant clusters identified within the groupXdrug interaction I could extract beta weights for the drug and placebo sessions for each participant so that I can plot the interaction.

Thanks in advance!
Sally.
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Help with Connectivity Matrix & Nuisance regressors

March 31, 2018, 9:36 am
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Dear CONN Experts,

I would like to conduct a functional connectivity analysis (Graph Theory). My plan is to preprocess my resting state fmri data with nuisance regression and then submit the data for a ROI to ROI analysis in CONN.
 
So, just to make sure I get it right, I conduct a ROI to ROI analysis with CSF/WM/GM and use CSF/WM then as nuisance regressors in the next, atlas based ROI to ROI analysis?

I want to submit the Connectivity Matrix to Brain Connectivity Toolbox for Graph theoretical Parameter Testing, so I am not sure if
the Connectivity Matrix derived from CONN is 'cleaned'?


Kind Regards,
Pablo Reinhardt
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RE: Smoothed and unsmoothed data

March 31, 2018, 5:37 pm
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Dear Experts 

What's the rationale behind using the smoothed data as voxel time series, while the unsmoothed data as seed timeseries for statistical analyses?

Thanks!

Best
Larry

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

Seed-to-voxel analyses will look at the correlation between a "seed timeseries" and a "voxel timeseries". If you use all default settings in CONN (including the default MNI-space preprocessing pipeline, which includes spatial smoothing as the last preprocessing step) then seed-to-voxel analyses will use:

1) smoothed data at each voxel, to define each "voxel timeseries"

and 2) unsmoothed data aggregated across all voxels within each seed ROI, to define each "seed timeseries"


Just to clarify, this behavior can be modified by the user. You may enter in [i]Setup.Functional [/i](dataset 0) whichever data that you want to use to define the "voxel timeseries" above; and you may specify in [i]Setup.ROIs [/i]"from functional dataset ##" whichever data you want to use to define each "seed timeseries" above (even differently for each ROI if you want). 

Hope this helps
Alfonso


[i]Originally posted by Kaylah Curtis:[/i][quote]Hi Alfonso,

We are trying to run seed-to-voxel analysis using an unsmoothed dataset. If we run the analysis under the default setup, with ROI-level BOLD signal extraction set to use unsmoothed data, will seed-to-voxel use smoothed or unsmoothed data?


Thanks for your help![/quote][/quote]
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How to handle twin pairs that are not statisticly independent

March 31, 2018, 7:45 pm
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Dear Alfonso and CONN Community

In advance excuse me if my questions are a little bit blunt I m new to the field.

I am currently using weighted GLM correlation measures within task condition to map the ROI to ROI effects of task performance. The HCP dataset that I am using consists around 200 MZ and 200 DZ twins out of 1200 subjects and I am wondering how to control for this statistically independent subjects since they are sharing exactly the same genes.

As an approach to this problem I was wondering whether if it would be appropriate to assign a number for each twin pair and use it as a covariate:
TwinPair1 sub1       1
TwinPair1 sub2       1
TwinPair2 sub1       2
TwinPair2 sub2       2
...

whereas second level modeling would be like: 

All Subjects - Age - Gender - Education - Handedness - [b]TwinPairs[/b] - Relational Task [0 0 0 0 0 [b]0[/b] 1]

Regards
Erkam
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corrupted mat file

April 2, 2018, 8:17 am
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Somehow my mat file was corrupted, but all of my data and results are intact. I can't open the mat file in either matlab or conn. Can I import the results back into a new project?
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Task FC estimation using basis functions in CONN

April 2, 2018, 8:52 am
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Dear Alfonso and CONN experts,

I'm running an event-related FC analyses in CONN using gPPI, and would like to convolve my task regressors with a set of basis functions rather than the canonical HRF (cf. https://www.biorxiv.org/content/biorxiv/early/2018/03/30/292045.full.pdf).

Is this possible to implement using CONN, or will I need to write some house-made scripts to accomplish this?

Any advice much appreciated!

Cheers,
Jeremy
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Extract ROI-ROI connectivity measures for a subset of subjects

April 2, 2018, 4:14 pm
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Hi,
I would like to extract ROI-ROI connectivity measures for only a subset of subjects. As the results are Fishers z converted I would like to know how I can re-run the first level/second level analyses for only a subset of subjects in conn?
Thank you very much for your help in advance.
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Coordinates of V1，V2， V5 implemented in CONN

April 2, 2018, 7:37 pm
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Does anyone know the coordinates of the ROIs provided by visual regions in Conn software (V1，V2， V5)?
In one of my studies I got some significant results with these ROIs and it would be nice to know the exact coordinates of these ROIs (the related reference if it possible?).
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RE: Information on ROIs provided by CONN

April 4, 2018, 6:12 am
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Hi there,

I too would be very grateful if someone could help answer this question.

Best wishes,
Jonathan

[i]Originally posted by mm_44:[/i][quote]Hi, 

I have some questions about the atlas and networks ROIs provided by CONN:

Is it possible to confirm that when using these ROIs:

-Networks ROIS: the average signal from a 10 mm sphere around the provided coordinates

-Atlas ROIS: the average signal from all voxels in the whole anatomical region (and same for AAL or BA atlases?)

Thank you so much![/quote]
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RE: network ROI citations

April 4, 2018, 6:14 am
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Hi there,

Like Nick, it would be really useful if someone could provide a citation to find out a bit more about the network ROIs provided in Conn. I would be grateful for the assistance.

Best wishes,
Jonathan



[i]Originally posted by Nick Fallon:[/i][quote]Apologies for re-posting, but does anyone know the relevant citations for the network ROIs included in Conn v17 or where to find them.

Many thanks,

Nick[/quote]
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RE: Conn17a Networks

April 4, 2018, 6:18 am
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Hi there,

As the other users have indicated here, I too would really appreciate any additional information that can be provided about the network ROIs in Conn. It is a really useful addition to have, and I would really like to use it in my current analyses, but I wouldn't be able to use them appropriately without knowing a bit more about their origin, what they look like, and how they are used within Conn (is it a 10mm sphere in that location?)

Best wishes,
Jonathan 

[i]Originally posted by Rob McCutcheon:[/i][quote]Dear Alfonso and other users,

I was just wanting to check if there has been any more information made available regarding how the CONN networks were defined. Has anybody published using these ROIs?

Many thanks

Rob[/quote]
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CONN for Animal study

April 5, 2018, 1:08 am
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Dear conn users,

I wonder if someone has used conn toolbox for animal (esp. Monkey) studies? if so, please help me how to adjust the parameters and coordinates according to animal brain...

Thanks in advance,
Sona
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ALFF CONN Methods?

April 5, 2018, 9:42 am
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Hello,

Are there any technical materials available for what CONN is doing "under the hood" with respect to voxel-wise ALFF data?  Our group would like to use the method, but for reproducibility sake we would like more detailed methods materials for the technique as implemented in CONN.

Thanks,
Jeff
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Recurring Error in Denoising Step

April 5, 2018, 4:25 pm
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Hi all,

I'm in the midst of analyzing FC in a sample of 87 participants resting state fMRI data. Every time I come to the denoising step I run into the following error:

ERROR DESCRIPTION:

Error using /
Matrix dimensions must agree.
Error in conn_process (line 1408)
ffilter(isinf(ffilter))=1/max(CONN_x.Setup.RT)/2;
Error in conn_process (line 28)
case {'preprocessing_gui','denoising_gui'}, disp(['CONN: RUNNING DENOISING STEP']); conn_process([1.5,2,6:9],varargin{:});
Error in conn (line 5070)
else conn_process('denoising_gui'); ispending=false;
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.17.f
SPM12 + DEM FieldMap MEEGtools TFCE TOM8 cat12 conn wfupickatlas
Matlab v.2017b
storage: 65074.9Gb available
spm @ C:\Users\mvande66\Desktop\Neuroimaging_Programs\spm12
Warning: Contents.m overloaded by version in folder C:\Users\mvande66\Desktop\Neuroimaging_Programs\spm12\toolbox\cat12
conn @ C:\Users\mvande66\Desktop\Neuroimaging_Programs\spm12\toolbox\conn


Can someone please help me in figuring out this error message and how to fix it? Thank-you very much!
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ROI timeseries output is the same for all conditions???

April 6, 2018, 1:15 pm
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Hello Conn users,

I set up a project in CONN with task-based data from multiple conditions. Now I would like to obtain the subject-level confound-corrected time series for each condition in each ROI.

From what I have read, I should be able to find these in [i]/results/preprocessing/ROI_Subject#_Condition#[/i]; however, I have found that the timeseries for any given ROI is exactly the same no matter which condition I look at. In other words, when I open 'data' and select an ROI, its time course is exactly the same whether I look at [i]ROI_Subject#_Condition000, ROI_Subject#_Condition001, ROI_Subject#_Condition002,[/i] or[i] ROI_Subject#_Condition003.[/i]

Does anyone know why this would be the case and how I can obtain the condition-specific time series?

Thank you!

Jeff
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Unwarp terminated abnormally (Matlab 2017b/SPM12/conn 18.a)

April 7, 2018, 8:32 am
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Dear Experts

I got these errors while performing functional realignment and unwarp. 

Thanks for considering my request.


Best regards
Larry

------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign & Unwarp'

SPM12: spm_realign (v7141) 23:07:00 - 07/04/2018
========================================================================
Completed : 23:07:18 - 07/04/2018
SPM12: spm_uw_estimate (v6824) 23:07:18 - 07/04/2018
========================================================================
Completed : 23:09:24 - 07/04/2018
SPM12: spm_uw_apply (v6301) 23:09:24 - 07/04/2018
========================================================================
Computing mask... : ...done
Reslicing images... : ...done
Writing mean image... : ...done
Completed : 23:10:11 - 07/04/2018
Done 'Realign & Unwarp'
Running 'Realign & Unwarp'
SPM12: spm_realign (v7141) 23:10:11 - 07/04/2018
========================================================================
Completed : 23:10:30 - 07/04/2018
SPM12: spm_uw_estimate (v6824) 23:10:30 - 07/04/2018
========================================================================
Completed : 23:13:44 - 07/04/2018
SPM12: spm_uw_apply (v6301) 23:13:44 - 07/04/2018
========================================================================
Computing mask... : ...done
Reslicing images... : ...done
Writing mean image... : ...done
Completed : 23:14:31 - 07/04/2018
Done 'Realign & Unwarp'
Running 'Realign & Unwarp'
SPM12: spm_realign (v7141) 23:14:31 - 07/04/2018
========================================================================
Completed : 23:14:50 - 07/04/2018
SPM12: spm_uw_estimate (v6824) 23:14:50 - 07/04/2018
========================================================================
[color=#ff0000]Unwarp terminated abnormally.[/color]
[color=#ff0000]Failed 'Realign & Unwarp'[/color]
[color=#ff0000]Error using spm_bsplinc[/color]
[color=#ff0000]Cant open image file.[/color]
[color=#ff0000]In file "C:\spm12\spm_uw_estimate.m" (v6824), function "make_ref" at line 712.[/color]
[color=#ff0000]In file "C:\spm12\spm_uw_estimate.m" (v6824), function "spm_uw_estimate" at line 352.[/color]
[color=#ff0000]In file "C:\spm12\config\spm_run_realignunwarp.m" (v6554), function "spm_run_realignunwarp" at line 90.[/color]
Running 'Realign & Unwarp'
SPM12: spm_realign (v7141) 23:17:07 - 07/04/2018
========================================================================
Completed : 23:17:27 - 07/04/2018
SPM12: spm_uw_estimate (v6824) 23:17:27 - 07/04/2018
========================================================================
Completed : 23:20:50 - 07/04/2018
SPM12: spm_uw_apply (v6301) 23:20:51 - 07/04/2018
========================================================================
Computing mask... : ...done
Reslicing images... : ...done
Writing mean image... : ...done
Completed : 23:21:38 - 07/04/2018
Done 'Realign & Unwarp'
Running 'Realign & Unwarp'
SPM12: spm_realign (v7141) 23:21:38 - 07/04/2018
========================================================================
Completed : 23:21:58 - 07/04/2018
SPM12: spm_uw_estimate (v6824) 23:21:58 - 07/04/2018
========================================================================
Completed : 23:24:06 - 07/04/2018
SPM12: spm_uw_apply (v6301) 23:24:07 - 07/04/2018
========================================================================
Computing mask... : ...done
Reslicing images... : ...done
Writing mean image... : ...done
Completed : 23:24:54 - 07/04/2018
Done 'Realign & Unwarp'
Running 'Realign & Unwarp'
SPM12: spm_realign (v7141) 23:24:54 - 07/04/2018
========================================================================
Completed : 23:25:13 - 07/04/2018
SPM12: spm_uw_estimate (v6824) 23:25:13 - 07/04/2018
========================================================================
Completed : 23:27:18 - 07/04/2018
SPM12: spm_uw_apply (v6301) 23:27:18 - 07/04/2018
========================================================================
Computing mask... : ...done
Reslicing images... : ...done
Writing mean image... : ...done
Completed : 23:28:05 - 07/04/2018
Done 'Realign & Unwarp'
Running 'Realign & Unwarp'
SPM12: spm_realign (v7141) 23:28:05 - 07/04/2018
========================================================================
Completed : 23:28:24 - 07/04/2018
SPM12: spm_uw_estimate (v6824) 23:28:24 - 07/04/2018
========================================================================
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Errors when using conn 18a

April 8, 2018, 12:03 am
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Dear conn users,


I'm running into the following error listed below when using conn 18a that I had not met when used previous version. Can anyone give me any insight into what is causing this problem?

Error using horzcat
Dimensions of matrices being concatenated are not consistent.

Error in rex>rex_do (line 725)
cov1=[dataM,detrend(params.covariates,'constant')];
Error in rex (line 179)
[params.ROIdata,params.ROInames,params.ROIinfo.basis,params.ROIinfo.voxels,params.ROIinfo.files,params.ROIinfo.select,params.ROIinfo.trans]=rex_do(params,1);
Error in conn_rex (line 8)
[varargout{1:nargout}]=rex(varargin{:});
Error in conn_process (line 805)
[data{nroi1},namesroi{nroi},params]=conn_rex(Vsourcethis,Vmask{nroi}{min(nses,nsesstemp)},'summary_measure','eigenvariate','dims',CONN_x.Setup.rois.dimensions{nroi},'conju
Error in conn_process (line 16)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 4447)
else conn_process('setup'); ispending=false;
Error in conn_menumanager (line 120)

Thanks a lot!
Yang
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Problem feeding niftiDATA files into first level GLM in SPM

April 8, 2018, 9:56 am
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Hi All,

I want to run an SPM first level GLM using data that is denoised using Conn's CompCor. I loaded my preprocessed images into Conn 17f and ran through the denoising step, and got the resultant niftiDATA .nii files.

But when I take those denoised .nii files back to SPM and try to feed them into the GLM as if they were the smoothed, warped, realigned preprocessed data, I get an error when running spm_spm.

The error is:

Error using spm_est_non_sphericity (line 196)
Please check your data: There are no significant voxels.

I looked at the volumes in the niftiDATA files and I have the correct # that SPM is expecting, and I looked at the data with fsleyes and they all look normal - in that they are all there. But, the values in the voxels are wildly different than what would be found if I input a typical smoothed warped bold image. in the denoised data, there are a lot of negative values (as expecting based upon the way the distribution of voxel values changes after denoising), which I suppose could be causing a problem in the estimation in SPM?

Has anyone tried doing this and run into this problem?
Perhaps there are defaults I need to shut off when running the SPM GLM if I feed in the denoised data?

I have attached a screenshot showing the spm error.

Thanks for any advice!

Best,
Emily
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RE: Average within / between network connectivity

April 9, 2018, 6:47 am
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[color=#000000]Hi Alfonso,[/color]

[color=#000000]Kindly answer my query provided below
[/color]
[i]Originally posted by Himanshu Joshi:[/i][quote]Hi Alfonso,

Thankyou for this wonderful script (conn_withinbeteenROItest). 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; [i](p=0.006720)[/i].

The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= [i]0.0134[/i].

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[/quote]
[color=#000000]The two tailed value which came significant can be reported or we need to perform a post-hoc comparison in the above case.[/color]

[color=#000000]Thanks and Regards[/color]
[color=#000000]Himanshu Joshi
[/color]
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Sliding window type

April 10, 2018, 1:52 am
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Hello,

I was just wondering if the sliding windows employed in the latest versions of CONN follow,

a) a simple block nature, taking the entire chuck of the time series, OR

b) a similar type to the sliding windows with sigmoid edges (described by Dr. Calhoun), and used in dynamic functional connectivity analysis by Allen et al (2013)

I have tried to visualize the two types I have mentioned, and attached the image (Apologies for my drawing!).

I would just like to clarify this, to understand how the sliding window separation is done in the SETUP.

Thank you,
Aditya
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