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ICC Technical Question RE: Step Function?

May 24, 2016, 5:48 am
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Our group submitted a manuscript examining the relationship between ICC change pre/post and cognitive change pre/post.  We provided information about the ICC technique as noted in the original CONN manuscript, but received the following reviewer query about whether CONN ICC uses a threshold / step function:
 
"The authors described ICC in the supplementary material.  However, a threshold (or step function u(x)) did not specify in the evaluation of ICC.  Without a threshold, both positive and negative connectivity were included in the computation of ICC.  However, according to R. Martuzzi et al. (2011), which developed a measure of ICC for the first time, the connectivity strength was binarized by a step function.  In general, researchers compute degree (including ICC) by using the positive connectivity only."
 
So, does CONN ICC use a step function (positive connectivity only)?  If not, are there other papers/references for ICC being used without one?  Justification for not including it? 

Any recommendations on how best to address this would be most appreciated.
 
Warm regards to all,
Jeff
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Error when running voxel-to-voxel analyses

May 24, 2016, 7:06 am
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Hi everyone,
I am trying to run voxel-to-voxel analyses in conn and keep receiving an error message (see attached screen shot). Do you know what leads to this error message and how I can fix it?
When I try to start second level analyses despite the error message, conn seems not to be able to access the results directory. When opening the results folder via Windows Explorer, I noticed that the MVPA-folder can not be opened. Also its name appears to be very long... 
Please let me know if you need any further information about the analyses I was trying to run.
Thanks a lot!
Best
Antonie
 
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RE: need help with dynamic FC between conditions

May 26, 2016, 3:19 pm
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So I tried to do dynamic FC for two datasets:

* One with 8 subjects in one group with two sessions/conditions each (that I call the "intra-subject dataset").
* One with 16 subjects with one session/condition each but in two different groups (the "inter-subjects dataset").

For the intra-subject dataset, I had to make a new third condition "AllSessions" that includes all subjects and both 2 previous conditions. This indeed allowed the backprojection technic to work, and dynamic FC was correctly computed with no error.

For the inter-subjects dataset, I made a new group (second level covariate) named "AllSubjects" that was a vector full of 1, so that it includes all subjects of all groups. This also allowed the backprojection technic to work, and Dynamic FC too. However, contrary to what Alfonso said, it was necessary to create this additional "AllSubjects" group, else the backprojection technic would not work (the group is not implicitly created). But this may be because I use conn_batch to define my conn projects. Note: initially I added the "AllSubjects" group manually from the GUI, but it's also possible programmatically using conn_batch but not by using batch.Setup.subjects.groups but batch.Setup.subjects.effects instead (it doesn't matter if the "AllSubjects" group is the last in the list of 2nd-level covariates, it will work just the same thank's to the smart backprojection).

Next step is to try to do both intra and inter subjects datasets in one conn project. I guess I will have to create one "allsessions" condition and one "allsubjects" group so that the backprojection technic works for both cases at the same time. I'll report here if it works.
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Define second level covariates in conn_batch

May 26, 2016, 3:26 pm
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Hi there,

I'm trying to define second level covariates using conn_batch (like age, or just to create overlapping groups of subjects), but I can't find anything about it in the conn_batch header comments documentation.

How should I do that? Should I try to modify directly the generated CONN_x?
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subjects specific exclusion masks

May 27, 2016, 1:13 am
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Hi everybody,

For my analysis I would like to use an explicit mask (i.e. an image), but one that is specific for each subject (it is a mask that has been calculated excluding the voxels with unreliable signal).
I see that in the CONN option one can chose to use an explicit mask, groupwise, or using a single subject mask, that is an implicit one (I guess in a similar fashion that the same option in SPM).
Is there a way to use a subject specific [i]explicit[/i] mask ?

Thank in advance for any help

Alain
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Clarifying contrast interpretation

May 27, 2016, 8:14 am
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Hi all,

First, thank you for developing such a user-friendly toolbox! I have a few questions regarding interpretation of contrasts. I am interested in the effect of patient symptoms on default mode connectivity. I have selected my group 'Patients' and covariate 'Symptom Score' and entered contrast [0, 1] to test for simple main effect of symptoms. I then selected two DMN seeds (MPFC, RLP) and ran two contrasts: [0.5 0.5] and [1 -1] in a seed-voxel analysis.

1) For the [0.5 0.5] contrast, a cluster in the middle frontal gyrus was significant. Am I correct in saying that symptom score is correlated with connectivity between MPFC, RLP, and middle frontal gyrus?

2) For the [1 -1] contrast, a cluster in the lateral occipital cortex was significant. Is it correct to say that symptom score is correlated with increased connectivity between MPFC-occipital cortex and/or decreased connectivity between RLP-occipital cortex?

Thanks very much for your help,
Tessa
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number of frames replaced by despiking?

May 27, 2016, 10:06 am
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Hi, 

Is there a way to quantify the number of frames replaced per subject in the despiking procedure within CONN?

Thank you,
Hilary
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RE: Lesion Masks

May 28, 2016, 12:49 pm
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[color=#000000]Hi Cole,[/color]

[color=#000000]The procedure in SPM12 to include lesion masks is to modify the file TPM.nii (tissue probability maps) by adding a new tissue class indicating the spatial distribution of the lesions. You may either modify SPM's TPM.nii file directly (located in spm12/tpm/TPM.nii), or define your own TPM.nii file and let CONN know that you would like to use that alternative tpm file instead (e.g. if using batch scripts in CONN you would do this using the fields batch.Setup.preprocessing.tpm_template and batch.Setup.preprocessing.tpm_ngauss)  [/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[color=#000000] 
[/color][i]Originally posted by Cole Sugden:[/i][quote]Hello!
Some of my participants have very large lesions due to arterial stroke and the segmentation process has incorrectly classified the lesion as grey and white matter rather than CSF. To try to adjust for this and to help with normalisation, I would like to use  Cost Function masking to individually fix the issue.  

My question is, at which point in preprocessing can I enter the lesion mask image? It does not seem to be an option in SPM12 and I prefer to use CONN. Is there a way I would be able to manually enter them somewhere?

Thanks! 

Cole[/quote]
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RE: Error in preprocessing (realign)

May 28, 2016, 12:53 pm
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[color=#000000]Hi Olaia,[/color]

[color=#000000]If I am interpreting correctly the error message, the realign&unwarp step may have finished correctly for the first subject but run into an issue for the second subject, so I would probably suggest to check that you have entered the correct functional files for all subjects in [i]Setup.Functional[/i] as well.[/color]

Hope this helps
Alfonso

[i]Originally posted by Olaia Lucas:[/i][quote]Hello,

I have tried to preprocess my data in the toolbox and this message appears:

ERROR DESCRIPTION:

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
------------------
Running job #1
------------------
CONN v.15.h
SPM12 + DEM FieldMap MEEGtools
Matlab v.2015b
storage: 106.5Gb available


========================================================================
Computing mask... : ...done
Reslicing images... : ...done
Writing mean image... : ...done
Completed : 09:41:04 - 21/05/2016
Done 'Realign & Unwarp'
The following modules did not run:
Failed: Realign & Unwarp

http://www.nitrc.org/forum/forum.php?forum_id=1144



Any idea?

Thank you in advance,
Best regards,

Olaia[/quote]
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CCA

May 29, 2016, 11:50 pm
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Hello!
Which algorithm is used to find voxel connectivity? Is CCA somehow used?

Many thanks,
Michal
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RE: Removing task-effects

May 30, 2016, 3:22 am
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Dear Alfonso,

Thank you! That is exactly what I need. Could you explain a little bit more how to appropriately use those beta maps to explore the result of the task-effect removal regression?

Karolina
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Preprocessing

May 30, 2016, 7:31 am
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Hello CONN experts,

I am trying to use the CONN toolbox to analyze Task-BOLD functional connectivity analysis.

I have 12 patients, scanned under 3 conditions A, B and C; (before and after three month of treatment); and I have 12 Controls also scanned under 3 condition A, B and C.

Please tell me if I am setting up the analysis is correctly:

FOR Basic: Number of session 6 for the first 12 subjects and 3 sessions for the second 12 subjects.

Condition: I want to compare one condition versus another, So I define 9 conditions. ('Befor-treatment-CondA, Befor-treatment-CondB, Befor-treatment-CondAC'; After-Treatment-CondA, ..' and 'Control-CondA, Control-CondB, Control-CondC, ).

I'm nut sure how, if it's ok?

Thanks in advance,
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Masks resolution and skipping CONN steps

May 30, 2016, 7:58 pm
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Hi,
I have two sets of questions that relate to two different studies that I am running:

1. I am running 7T MRI data, the fMRI data is 1.25mm isotropic, the T1 is 0.7mm isotropic and I have a mask in MNI space of 0.5mm isotropic. Is this a problem or should I first warp the mask to each subject's space?

2. For the second study, I am using 3T data where the preprocessing has been done by in-house and SPM methods. I figured out that I can skip the preprocessing steps, by simply not running them. In the denoting them, I then put all the physiological regressors back to the left side of the panel, but how can I be sure that no denoising is being done again?
Related to this, I have been looking at differences between the CONN procedure and the in-house pipeline and I do see differences, but not sure how to compare exactly. I do see that the white matter PCA in CONN has no declining standard deviation. Is this to be expected? What happens when I regress out the rest condition? In SPM, it is possible to use tissue probability maps for white matter, is this also being used in CONN? And a final question: what is the ROI.objects?

Many thanks!!
Heidi
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RE: ART Repair Settings Prompt Question

May 31, 2016, 6:54 am
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Hi Alfonso, 

Thank you for your response. I have not used the "New (wizard)" option to preprocess. Once I have my basic info set up in the setup tab and files are loaded, I press the preprocessing button and add all preprocessing steps. The art repair prompt had always come up, only recently stopped appearing, but since I started using a different copied conn software folder I have not had the issue (still strange, as it should have been an exact copy of the software folder I originally used that had this issue).

Best,
Nicole
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Error importing SPM.mat

May 31, 2016, 1:28 pm
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I'm setting up a new project and trying to import SPM.mat for all my subjects. I get the following error: 
Only my first subject's conditions import - all others are empty. I've checked that the conditions have identical names in all subject's SPM.mat and that there are the same number of conditions in each case. 

ERROR DESCRIPTION:

Error using cell/strmatch (line 20)
Requires character array or cell array of strings as inputs.
Error in conn_importspm (line 147)
idx=strmatch(name,CONN_x.Setup.conditions.names,'exact');
Error in conn (line 2761)
conn_importspm;
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.g
SPM12 + DEM FieldMap MEEGtools
Matlab v.2013b
storage: 327.4Gb available
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Seeing an error while importing SPM.mat

May 31, 2016, 1:29 pm
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I'm setting up a new project and trying to import SPM.mat for all my subjects. I get the following error: 
Only my first subject's conditions import - all others are empty. I've checked that the conditions have identical names in all subject's SPM.mat and that there are the same number of conditions in each case. 

ERROR DESCRIPTION:

Error using cell/strmatch (line 20)
Requires character array or cell array of strings as inputs.
Error in conn_importspm (line 147)
idx=strmatch(name,CONN_x.Setup.conditions.names,'exact');
Error in conn (line 2761)
conn_importspm;
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.g
SPM12 + DEM FieldMap MEEGtools
Matlab v.2013b
storage: 327.4Gb available
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Connectivity values of each subject in PPI

June 1, 2016, 12:56 am
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Dear CONN experts,

I want to extract the connectivity vales between each seed and target ROI for each subject after ROI-to-ROI PPI analysis was done. I found the fisher-transformed connectivity values (r-to-Z) in the following file:
conn_*/results/firstlevel/ANALYSIS_01/resultsROI_Subject###_Condition###.mat

I thought it is used when correlation measures were used in combination with PPI. Can I also use it when I selected 'regression' and 'task-modulation effects (gPPI)' in 'Analysis options' of first-level Analysis?

Thanks in advance,
Shige
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Errror in dynamic FC - again

June 1, 2016, 4:42 am
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Dear all,
 
I'm still running into following error when using the dynamic FC option - any ideas?
 
Thanks a lot,
 
Eugenio
 
ERROR DESCRIPTION:
Error using eig
Input to EIG must not contain NaN or Inf.
Error in conn_ica (line 47)
[Q,D]=eig(X*X'/(Ns-1));
Error in conn_invPPI (line 164)
[S,W]=conn_ica(reshape(B1,[Nr*Nr Nk1])',[],'dodisp',DOPLOT,'rndseed',RNDSEED);
Error in conn_process (line 2871)
[H,B,H0,B0]=conn_invPPI(Y,Ncomponents,X,Xfilter,1);
Error in conn_process (line 40)
case 'analyses_gui_dyn',disp(['CONN: RUNNING DYNAMIC CONNECTIVITY STEP']); conn_process([13.5],varargin{:});
Error in conn (line 4469)
conn_process('analyses_gui_dyn');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.15.h
SPM8 + Anatomy Beamforming DEM FieldMap LI MEEGtools Masking TFCE marsbar psc rwls vbm8 xjview
Matlab v.2014a
storage: 599.4Gb available  
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Batch prompt sliceorder

June 1, 2016, 6:43 am
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Hello everybody!

I'm using a conn batch for my resting-state analyses which is working great except for one small annoyance. Everytime the script tries to perform slice time correction a prompt pops up asking me to specify the slice order. I use the default MNI preprocessing pipeline and the "batch.Setup.preprocessing.sliceorder={'interleaved (Siemens)'}" line but the prompt keeps appearing. I read that this might be an issue of an older conn version, however, I had this problem with both v15h as well as with v16a.

Any help would be very much appreciated.

Clemens
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RE: Error in preprocessing (realign)

June 1, 2016, 8:13 am
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[color=#000000]Thank you very much for the reply.[/color]
Indeed, it was a fault with the images.

Best regards,

Olaia






[color=#000000]Hi Olaia,[/color]

[color=#000000]If I am interpreting correctly the error message, the realign&unwarp step may have finished correctly for the first subject but run into an issue for the second subject, so I would probably suggest to check that you have entered the correct functional files for all subjects in [i]Setup.Functional[/i] as well.[/color]

Hope this helps
Alfonso

[i]Originally posted by Olaia Lucas:[/i][quote]Hello,

I have tried to preprocess my data in the toolbox and this message appears:

ERROR DESCRIPTION:

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
------------------
Running job #1
------------------
CONN v.15.h
SPM12 + DEM FieldMap MEEGtools
Matlab v.2015b
storage: 106.5Gb available


========================================================================
Computing mask... : ...done
Reslicing images... : ...done
Writing mean image... : ...done
Completed : 09:41:04 - 21/05/2016
Done 'Realign & Unwarp'
The following modules did not run:
Failed: Realign & Unwarp

http://www.nitrc.org/forum/forum.php?forum_id=1144



Any idea?

Thank you in advance,
Best regards,

Olaia[/quote]
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