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ROIs in CONN

July 9, 2018, 8:37 am
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Dear CONN experts,

I would like to know if we can upload a ROI file containing multiple labels (regions)? or do I need to individualize each ROI?  
I know that there used to be a 'multiple ROIs' option but it doesn't seem to be available anymore.

Thank you.

Regards,

Hugo
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Task-related conditions as confound

July 9, 2018, 11:05 am
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Hello experts and thanks in advance for your help.
My question is related to the Denoising step. Should i use my task-related conditions as confounds to be removed -regressed out?
I understand that by including them, conn will be removing task effects from the BOLD signal before computing connectivity measures to avoid task-related coactivations that can be misleading when being interpreted as region correlated activations. I am now quite confused, how can I explore task-related connectivity if i'm removing task-effects from the signal?

Thank you very much.
Santiago
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vglrun display error with standalone conn

July 10, 2018, 7:44 am
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With version 16 of standalone conn I was able to open using 'vglrun conn' but with 17 and 18 (matlab/R2017a), I can no longer open conn, getting the error: "[VGL] ERROR: Could not open display :0"

I am pretty sure my cluster isn't having VirtualGL problems because I can open other programs with vglrun, e.g., matlab, firefox. I followed the instructions here (https://sites.google.com/view/conn/resources/installation?authuser=0) and have tried using MCR installed on its own and through a matlab module.

I can get standalone conn to open without vglrun, so I'm at a loss for what the problem is. The only thing I can think of is that the folder MCR/v92/X11 doesn't exist, so XAPPLRESDIR isn't going to be set correctly. There's no X11 folder in the matlab installation either though, and that opens with vglrun. 

Here's the full command line output:
[joseph.orr@gfx ~$ vglrun conn
[VGL] NOTICE: Automatically setting VGL_CLIENT environment variable to
[VGL] 165.91.12.191, the IP address of your SSH client.
Initializing MATLAB Runtime version 9.2
Loading MCR. Please wait...
[VGL] ERROR: Could not open display :0.

My LD_LIBRARY_PATH is set to:
/fdata/scratch/joseph.orr/software/MCR/v92/runtime/glnxa64:/fdata/scratch/joseph.orr/software/MCR/v92/bin/glnxa64:/fdata/scratch/joseph.orr/software/MCR/v92/sys/os/glnxa64

My modulefile is doing:
[joseph.orr@gfx ~$ module show conn
-------------------------------------------------------------------------------------------------------------------------------------------
/apps/psyc/psyc-modules/conn/conn18a.lua:
-------------------------------------------------------------------------------------------------------------------------------------------
conflict("matlab/R2017a")
prepend_path("PATH","/apps/psyc/conn/conn18a")
setenv("MCRROOT","/fdata/scratch/joseph.orr/software/MCR/v92")
setenv("XAPPLRESDIR","/fdata/scratch/joseph.orr/software/MCR/v92/X11/app-defaults")
prepend_path("LD_LIBRARY_PATH","/fdata/scratch/joseph.orr/software/MCR/v92/sys/os/glnxa64")
prepend_path("LD_LIBRARY_PATH","/fdata/scratch/joseph.orr/software/MCR/v92/bin/glnxa64")
prepend_path("LD_LIBRARY_PATH","/fdata/scratch/joseph.orr/software/MCR/v92/runtime/glnxa64")

Any suggestions?
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Covariate of interest

July 10, 2018, 4:20 pm
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Hello,

I am working on a project with fibromyalgia patients.  We have a BOLD resting state on 15 patients pre and post hyperbaric treatment.
And we have pain scores (pre and post) ranging from 0 to 100.

- I did all the default pre-processing.
- Then, I input the pre-post difference of the pain scores.
- I used the ROI-to-ROI analysis

In Subject effects, I selected "all patients" and then "pain scores difference".
For Between-subjects contrast I wrote [1 0]  (or simple main effect of "all subjects")

For condition:
pre
post

Between con contrast: [-1 1]


The question is:

Should I input a "percentage difference" for the pain scores or simply a difference?
Because I get difference answers whether I input one or the other.


Thank you .

Julien.
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QC plots and confounding variables

July 10, 2018, 10:29 pm
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Dear CONN users

Thanks for considering my request.

Please see the attached screenshots as PDF.

1. How to interpret the graph generated by calculator tools? (AD-NC: gray dots, blue dots, and two-sided p)
2. How to interpret the QC_histogram report? 
3. As of second-level covariates (confounding variabls), what would the next step be?


Best wishes
Larry Lai
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RE: Errors when using conn 18a

July 12, 2018, 2:41 pm
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Hi,

I am receiving the exact same error message during the ROI setup. Was there a solution to this?

Thanks!
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RE: Small-world network properties & Network edges options

July 12, 2018, 2:50 pm
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[color=#000000]Hi Alfonso,[/color]

[color=#000000]Just wanted to re-circulate this. Thanks again for your time and help![/color]

[color=#000000]Best,[/color]
[color=#000000]Panos[/color]
[i]Originally posted by Panagiotis Fotiadis:[/i][quote][color=#000000]Hi Alfonso,[/color]

[color=#000000]Thank you for the detailed response and the patch! I had two follow-up questions:[/color]

[color=#000000]1) Since I am comparing two groups is there a way (or does it even make sense) to calculate a measure that reflects their small-world propensity (or their small-"worldness")? I was thinking something like the small coefficient sigma (defined as (C/C_r)/(L/L_r), where C is the clustering coeff. of my network, C_r is the clustering coeff. of an equivalent random network, L the average path length of my network, and L_r the average path length of an equivalent random network), or any other measure that you might have in mind. Even though I know how to look up the clustering coeff. and average path length parameters of each subject, I didn't know how to calculate the same measures for an equivalent random network. [/color]

[color=#000000]2) Also, am I correct to assume that the ROI.mat that is saved under the secondlevel tab of my results is the binary connectivity matrix of the ROI-to-ROI correlations of the analysis that I have specified (i.e. diseased group vs control group)? And if it is, is there a way to plot said brain connectivity matrix?[/color]

[color=#000000]Thanks again for your time and comments![/color]
[color=#000000]Panos[/color]

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

[color=#000000]Your two questions are related. You can of course always justify the choice of threshold from previous studies, but one relatively simple way to justify the choice of cost threshold from your data is to find which threshold value results in networks that seem to follow "small-world" properties (i.e. comparatively high global efficiency compared to lattices, and comparatively high local efficiency compared to random graphs). In CONN graph-theory GUI you may simply delete the threshold value in the "adjacency matrix threshold" field, and that will create a small plot that shows the network global and local efficiency for different cost threshold values (and also for reference the global and local efficiency values for the same cost threshold values for random graphs and regular graphs / lattices). Choosing a threshold value that seems to jointly maximize the difference between global efficiency of your networks (compared to lattices) as well as the local efficiency of your networks (compared to random graphs) is a common/reasonable approach (and the default cost=.15 value typically is close to this "optimal" level for medium-size networks). [/color]

[color=#000000]In case this helps, I am also attaching a patch that will create an additional plot to the above display showing you directly GE_data-GE_lattice+LE_data-LE_random for each threshold value, to perhaps more directly/intuitively justify the choice of threshold value using this approach (this patch is for 18a, to install it simply copy the attached file to your conn distribution folder overwriting the file with the same name there)[/color]
 
Hope this helps
[color=#000000]Alfonso[/color]
[i]Originally posted by Panagiotis Fotiadis:[/i][quote]Hello,

I just started using CONN (version 18.a) and wanted to thank you for designing such a user-friendly and powerful software!

I am trying to explore the resting state functional connectivity differences between two groups (one diseased group: 16 subjects, and one control group: 14 subjects), and I had a few questions:

1) Is there a way to see/define whether the brain of each subject obeys small-world network properties (for instance by looking at the average path length and clustering coefficients)? 

2) Also, I am a little confused about the 'Network edges (adjacency matrix threshold)' options in the 'graph theory results explorer' GUI: If I decide to use 'cost' (the default setting) with a value of 0.15, how would I explain to the potential reviewers why I chose that particular threshold for my analyses? Is there something in the adjacency matrix that could point me to that?


I apologize for the potential triviality of the questions, and thank you in advance for your time!

Best,
Panos[/quote][/quote][/quote]
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RE: Task-related conditions as confound

July 12, 2018, 9:11 pm
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Thank you for your answer wzhong. I don't seem to get it, how to account for task-effect if they're regressed out? I'm currently interested in task related connectivity, and connectivity difference between diferent tasks.

https://www.nitrc.org/forum/message.php?msg_id=10467
In that message, Alfonso states

"This form of task-related responses are more readily identified using standard functional task-related analyses, so when analyzing condition-specific functional connectivity it is more common to focus on the remaining functional connectivity effects (not purely driven by common main task effect)"

Conn toolbox main paper identifies BOLD signal to be processed as the residual of regression model fit.
Must remaining signal be orthogonal to confound+noise list? Should that be interpreted? I can't understand where are task-effects expressed, in both conceptual and mathematical senses.

I hope i'm making myself clear, and thanks for your patience.
Santiago
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Graph theory task-based FC difference between two conditions

July 13, 2018, 7:32 am
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Dear CONN experts, 

I would like to apply graph theory for task-based functional connectivity, i.e., connectivity related to the difference between 2 frequencies of muscle vibration (60Hz and 20 Hz). I am thus interested in connectivity during 60 Hz that "goes above" 20 Hz.
I have a network of 20 ROIs. I specified both stimulus conditions (60 Hz, 20 Hz), as well as rest blocks (no stimulus) at the first-level (onsets and durations of blocks) and included stimulus conditions as confounds during Denoising (as well as motion parameters, CSF, WM).

I would like to calculate graph theoretical measures of the contrast of 60 Hz - 20 Hz in my subject group ("patients", n=20). Therefore, I selected patients,  contrast [1] in the between-subject contrast field, and 60 Hz and 20 Hz, contrast [1 -1] in the between-conditions contrast field. After clicking Graph Theory, specifying my desired adjacency matrix threshold and clicking Export data, CONN saves a .csv file, a two .mat files (xxx.networkmeasures, xxx.stats). When opening the .csv file, I noticed I have 40 rows, with different graph theoretical measures for the network, and for each ROI. I assume that the rows 1:20 contain graph measures for my 20 patients for condition 60 Hz, and that rows 21:40 contain the same measures for condition 20Hz. Is this correct?

However, I am specifically interested in calculating graph measures on the difference in connectivity between both conditions. Can I obtain this by calculating "difference matrices" per subject, i.e., by subtracting their correlation matrix at 60 Hz and correlation matrix at 20 Hz, and apply graph theory analysis on these difference matrices?

Thank you for your help, 

Kind regards, 
Nina
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RE: Covariate of interest

July 13, 2018, 8:14 am
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[color=#000000]Hi Julien,[/color]

[color=#000000]If I am understanding correctly you are looking at differences in connectivity before- and after- treatment, while controlling for those differences that may be more simply explained by pain-score differences among the two sessions. If that is the case your analysis set up looks perfectly correct, and the choice between the two versions of your analyses (whether to represent pain scores differences in raw or percent units) should probably be based on the nature/interpretation of your pain-score measures and your a priori assumptions about the association between those pain-score differences and connectivity-differences (e.g. if you expect that a difference in pain scores S=1 before treatment and S=2 after treatment would be commensurate in terms of expected connectivity differences to a difference in pain scores S=50 before treatment and S=100 after treatment then probably a percent change measure makes most sense, while if you expect that a difference in pain scores S=1 before treatment and S=2 after treatment would be commensurate to a difference in pain scores S=50 before treatment and S=51 after treatment then probably a raw change measure makes most sense)[/color]

Hope this helps
Alfonso
[i]Originally posted by julien poublanc:[/i][quote]Hello,

I am working on a project with fibromyalgia patients.  We have a BOLD resting state on 15 patients pre and post hyperbaric treatment.
And we have pain scores (pre and post) ranging from 0 to 100.

- I did all the default pre-processing.
- Then, I input the pre-post difference of the pain scores.
- I used the ROI-to-ROI analysis

In Subject effects, I selected "all patients" and then "pain scores difference".
For Between-subjects contrast I wrote [1 0]  (or simple main effect of "all subjects")

For condition:
pre
post

Between con contrast: [-1 1]


The question is:

Should I input a "percentage difference" for the pain scores or simply a difference?
Because I get difference answers whether I input one or the other.


Thank you .

Julien.[/quote]
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Urgent Help Needed: CONN Memory Error

July 13, 2018, 7:11 pm
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Hi,

I keep running into the issue that some back in 2014-2015 have posted about where in the second-level results step trying to access the results explorer I get an error message regarding insufficient memory (or memory fragment after long Matlab sessions). I have retried selecting fewer seeds/sources, restarting matlab, trying just about everything so far. Each time to restart this process I need to go back and re-process the first level analysis step (~20-30 mins) and then it gets about 5-7 hours into processing the second-level results until it crashes. I am using the 17.f version of Conn Toolbox. This is the first project I am using CONN for and it is all a bit new for me, but this is the first real issue I have encountered. Thank you so much in advance for all your help!

Sincerely,

Samantha

Here is the error message I am receiving:

ERROR DESCRIPTION:

Error using ==> times
Out of memory. Type HELP MEMORY for your options.

Error in ==> spm_trace at 14
C = sum(sum(A'.*B));

Error in ==> spm_reml at 141
dFdh(i, 1) = -spm_trace(PQ(i},U)*N/2;

Error in ==> spm_est_non_sphericity at 269
[V,h] = spm_reml(Cy, xX.X,xVi.Vi);

Error in ==> spm_spm at 421
[xVi, am] = spm_est_non_sphericity(SPM);

Error in ==> conn_process at 4235
SPM=spm_spm(SPM);

Error in ==> conn_process at 52
case 'results_voxel', [varargout{1:nargout}]=conn_process(16,varargin{:});

Error in ==> conn at 8594
conn_process('results_voxel','readsingle','seed-to-voxel');

Error in ==> conn_menumanager at 120

feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU.callback{n1}{2:end});

CONN v.17.f
SPM12 +DEM Fieldmap LST MEEGtools TFCE cat12
Matlab v.2010b
Storage: 4749.1Gb available

spm @ /opt/spm12
Warning: Contents.m overloaded by version in folder
/opt/spm12/toolbox/cat12
conn @ opt/conn/conn17f

SUGGESTIONS:
Insufficient memory, or memory fragmentation after long Matlab sessions. Try restarting matlab and attempting this procedure again.
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CONN error during step 5 (ROI)

July 14, 2018, 9:08 am
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Hi Conn users,

I keep running in to the same error message below during my my Conn setup when clicking done. The error persists even after using already preprocessed/normalized images and removing grey matter ROI from setup. Any help on this error would be greatly appreciated!

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)
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problems saving a project

July 15, 2018, 11:32 pm
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Hello,

I have problems saving projects. I use the 'save' or 'save as' button but when I try to reload the project later (via 'load' ) I get an empty project (as if I pressed the 'new' button). Nevertheless it creates the folders for data and results when I work my way through until the 2nd level analysis. I just cannot load the project into the GUI anymore.

Any ideas what could go wrong? (I tried it several times with the same result every time. Moreover, as far as I know conn should save the project automatically if I press 'done' after one step but it seems as if this does not happen either.)

Best regards,
Eli
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CONN Version 18a error when removing initial scans

July 16, 2018, 9:38 am
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Dear Alfonso, dear all,

I ran a preprocessing pipeline in CONN 18a including the removal of the intial 5 scans on images containing 140 frames (1 session) at the beginning of the pipeline. However, afterwards it shows 18900 files per subject in the functional tab and also in the conditions tab. I cannot proceed, as the error comes up that the file number and the number of 1-level covariates (which correctly show 135 timepoints per subject) do not match. When I open the preprocessed files in any viewer they seem fine and only have 140 (135) frames. I checked again using only the "remove initial scans" step without any further preprocessing and the same thing happens.

This however doesn't occur when I preprocess the same data in CONN 17f. And when I open the project preprocessed in CONN 18a using CONN 17f everything seems to be fine as well.


Any idea what seems to be the problem here?

Thank you and best wishes

Julian
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RE: Calculate framewise displacement Jenkinson

July 16, 2018, 9:40 am
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Dear Alfonso,

thank you very much, this works great!


Best wishes

Julian
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RE: Task-related conditions as confound

July 16, 2018, 5:01 pm
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Thanks Alfonso, that was very helpful.
Best,
Ben
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m1-m1 communication

July 16, 2018, 11:25 pm
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Dear Experts 

 I am new in to CONN and I wish you help me to progress. 

I have done an experiment with fMRI. 3 tasks were there

1- Resting (R) do nothing
2- Movement 1
3- Movement 2

We believe that movement 2, causes better connectivity between Motor area 1 (m1) in both sides of the brain than the other two situations. 

with CONN, I understood that this high functional connectivity between m1-m1, is possible to be proved. Any hits on how to conduct analysis in CONN to prove that Task 3 cause higher connectivity between m1-m1, then the other two tasks (task 1, and task 2).

Any help please
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Inputting ROIs erases all data

July 17, 2018, 9:51 am
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Hello,

I'm having a problem where, after inputting even just a few ROIs for a few subjects, my file doesn't save and even erases everything I have previously input upon reopening the file. Structural and functional data saves and reopens just fine; I only have this problem with ROIs.

I get this error message each time I click on an ROI and then select it:
Warning: An error occurred when running a class's loadobj method. The object that was loaded from the MAT-file was a copy of the object before the loadobj method was run. The rest of the variables were also loaded from the MAT-file.
The encountered error was:
Error using maroi_image/loadobj (line 18)
Error using spm_slice_vol
Cant open image file.
> In read_extras (line 23)
In nifti (line 27)
In spm_vol_nifti (line 19)
In spm_vol>spm_vol_hdr (line 128)
In spm_vol (line 61)
In conn_getinfo (line 39)
In conn_file (line 4)
In conn_filesearchtool (line 189)
Warning: An error occurred when running a class's loadobj method. The object that was loaded from the MAT-file was a copy of the object before the loadobj method was run. The rest of the variables were also loaded from the MAT-file.
The encountered error was:
Error using maroi_image/loadobj (line 18)
Error using spm_slice_vol
Cant open image file.
> In read_extras (line 23)
In nifti (line 27)
In spm_vol_nifti (line 19)
In spm_vol>spm_vol_hdr (line 128)
In spm_vol (line 61)
In conn_getinfo (line 39)
In conn_file (line 4)
In conn (line 2266)
In conn_filesearchtool (line 171)

And I get this error after trying to save my file:
Saving file. Please wait...Warning: Variable 'CONN_x' was not saved. For variables larger than 2GB use MAT-file version 7.3 or later.
> In conn (line 780)
In conn (line 4083)
In conn_menumanager (line 120)
Done

And I get this error after closing my file:
Warning: Variable 'CONN_x' was not saved. For variables larger than 2GB use MAT-file version 7.3 or later.
> In conn (line 780)
In conn>conn_closerequestfcn (line 9218)
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SPM MatLab Error

July 17, 2018, 5:36 pm
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Running into MatLab error:
<span style="white-space: pre;"> </span>Error using spm_vol>subfunc (line 103)
<span style="white-space: pre;"> </span>File "T1_MNI.nii" does not exist.

<span style="white-space: pre;"> </span>Error in spm_vol>subfunc1 (line 77)
<span style="white-space: pre;"> </span>v = subfunc(P(i,:));

<span style="white-space: pre;"> </span>Error in spm_vol>subfunc2 (line 69)
<span style="white-space: pre;"> </span>V = subfunc1(P);

<span style="white-space: pre;"> </span>Error in spm_vol (line 54)
<span style="white-space: pre;"> </span>V = subfunc2(P);

<span style="white-space: pre;"> </span>Error in newest8_short>generate_slice_mosaic (line 323)
<span style="white-space: pre;"> </span>Vi = spm_vol(img_name);

<span style="white-space: pre;"> </span>Error in newest8_short (line 97)
<span style="white-space: pre;"> </span>generate_slice_mosaic( 'T1_MNI.nii' , orientation )
Any help/suggestions appreciated.
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the error when setup "done"

July 18, 2018, 6:08 am
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Hello,
       I met some problems when I achieved the setup and clicked "done",CONN reported the error description as below：

Undefined function 'eq' for input arguments of type 'struct'.
Error conn_menumanager>@(x)any(x==varargin{1}) (line 327)
idx=find(cellfun(@(x)any(x==varargin{1}),CONN_MM.onregionhandle));
Error conn_menumanager (line 327)
idx=find(cellfun(@(x)any(x==varargin{1}),CONN_MM.onregionhandle));
Error conn_menu (line 535)
conn_menumanager('onregionremove',position.h5);
Error conn (line 4872)
conn_menu('update',CONN_h.menus.m_preproc_00{3},[]);
Error conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.18.a
SPM12 + DEM FieldMap MEEGtools
Matlab v.2014a
storage: 209.2Gb available
spm @ D:\Toolbox\spm12
conn @ D:\Toolbox\conn18a\conn
        
       Do you know how to solve the problem?  I will look forward to your reply!<span style="white-space: pre;"> </span>
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