Dear All,

In this post

http://www.nitrc.org/forum/message.php?msg_id=17633

Alfonso wrote that "ICC is sign-independent (since it considers r-squared values), while global correlation is not (it averages the actual r correlation-coefficient values, considering their sign, so positive and negative correlations will cancel out)".

I`m interested in using global correlation and had a look at the formula (please see attachment) provided in the paper "Conn: a functional connectivity toolbox for correlated and anticorrelated brain networks". Now I`m confused. Doesn`t this formula use absolute values which would mean that positive and negative values are aggregated and not canceled out?

Thank you very much in advance

Dear Alfonso,

I am undertaking an analysis in which I am performing all preprocessing within conn.

1. I wondered whether there is an option to include the first order derivatives of the motion regressors calculated during realignment to the first level covariates? If not is it best to calculate these from the rp.txt file and use this newly calculated file (12 regressors in total) to replace the standard one generated by ART?

2. I also wondered what your opinion was on removing initial volumes due to the large amount of signal change. I note it is not a default - is this because ART will automatically regress out volumes where it detects a large amount of signal change?

Many thanks

Rob

Hi Alfonso and other CONN experts.

Well done on the new version. I ran a whole pipeline and it ran flawlessly until the end, including the preprocessing.
I however have a couple of queries.

1. Is there any way I can get an ALFF measure of an ROI - either based on an ICA group map or the Atlas?

2. Could you please give me the reference for the ICA temporal frequency and variability? How are these calculated? What does the variability actually mean?

4. In an ICA, temporal tab - is the time series for a component the mean of the time series within the given map or the first eigenvariate or some other method? And how is the frequency and the variablity calculated??  I would also like to calculate the amplitude of these fluctuations/ ALFF within the maps. Is it possible???


Any help would me much appreciated.. 

Cheers

Rajeev

Thanks, Alfonso!

Hi Alfonso, 

Thank you very much, I downloaded the latest version of CONN and it worked perfectly. I did a group-PCA, however, I am wondering how to do the PCA with just my group of patients. I also have a group of control scans that are loaded into the set up. Part of the analysis was comparing connectivity between the groups. The second part of the analysis is looking at within group connectivity in my patient group only and the association between 6 behavioural scores/covariates and connectivity within this patient group (by doing a PCA first). 

How can I performed a PCA within the patient group only? I am assuming this is what I would want to do, since I found many differences is rs-fc between the two groups. Now, I am only interested in the principle components within this patient group and the correlation between these principle ROIs/networks and scores.

Thank you, 

Jenna

Hello,

I have calculated group ICA Components for a set of subjects at rest, and have some behavioral/clinical score measures for each. In order to calculate the correlation of these measures within a particular component would it be correct to have the following contrasts:

Between Subjects
All Subjects, Score
[0 1]

Between Conditions
Rest
[1] 

Between Sources
Component #
[1]

Thanks, and let me know if additional information is needed.

From,

Humza Ahmed

Hey all -- 

Has anyone used data preprocessed by FSL's FEAT? I am working with a large dataset (>200 functionals) and have already done my preprocessing and QA in FEAT. They key issue I'm hitting is that of registration: I would like my files to be in subject space, and have a corresponding func2anat registration matrix. However, if I resample my functional using this matrix, the size of my files goes up to ~4GB each. Is there a way for CONN to apply a co-registration step, or is this file size something I will just have to deal with?

Thanks!
Stephen

Hi, all.

I receive the following error message when attempting 1st level processing of our data for ALFF or fALFF.  Any ideas?

ERROR DESCRIPTION:

Attempt to reference field of non-structure array.
Error in conn_process (line 2517)
options.m
Error in conn_process (line 42)
case 'analyses_gui_vv', disp(['CONN: RUNNING ANALYSIS STEP (voxel-to-voxel analyses)']); conn_process([13],varargin{:});
Error in conn (line 5801)
else conn_process('analyses_gui_vv',CONN_x.vvAnalysis); 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.b
SPM12 + DEM FieldMap LST MEEGtools bspmview cat12 decoding
Matlab v.2014a
storage: 1266.6Gb available

Thanks,
Jeff

Hello Alfonso

I have a short question. I am writing a batch script and I would like to use the first principal component of my ROI only.

In the conn_batch_help document it says:

dimensions : rois.dimensions{nroi} number of ROI dimensions - # temporal components to extract from ROI [1] (set to 1 to extract the average timeseries within ROI voxels; set to a number greater than 1 to extract additional PCA timeseries within ROI voxels; set to 0 to compute a weighted sum within ROI voxels (ROI mask values are interpreted as weights))

From the description it is unclear to me, to which number I need to set it to only get the first principal component? 

A short advice would be greatly appreciated!

Isabel

Hello,

I am planning to compare functional connectivity between two ROIs.
Is it possible to set specific coordinates such as (-28, 19, 7)?
Thank you!!

Dear Alfonso

I have an existing analysis that was run all the way, through 2nd level. I want to remove some of the ROIs that are currently included. I have removed them from the list of ROIs in the first-level tab (without re-running first level), and then when I went to 2nd level tab I was asked to choose target ROIs (I chose 'targets are selected ROIs only'). This did remove the unneeded ROIs from the list of targets, but I still have them as sources, which badly influences my FDR-corrected significance level. I want to remove these ROIs from the source level as well.
I also tried to remove them from the list in the setup tab (again, without re-running anything for the time being), but it did not change the ROI lists in the 1st and 2nd level tabs.

Could you please advise me how to remove these ROIs so that my FDR-corrected calculations will only include the ROIs which I actually need? I should note that this is an old analysis (about to be published), and so it was run on conn 15.a.  Also, ROIs are mask-based (not subject-specific).  Thank you very much in advance for any advice!!

Lee.



P.S.
Is this removal reversible? If I end up deciding that I want an ROI back in the analysis, can it be done?

[color=#000000]Dear Geon-Ho,[/color]

[color=#000000]Simple-main effects: In order to look at decreases between year1 and year3 for control subjects, for example, simply select the 'Control' group in the subject-effects list, and then select 'Year1' and 'Year3' in the conditions list and enter a [1 -1] between-conditions contrast. This will effectively perform a paired t-test comparing the connectivity values between Time1 and Time3 for the control subjects only. If you want to extend these analyses to look at potential changes between year1 and year2 as well (which may or not be associated with changes between year1 and year3) you could also select all three conditions Year1, Year2, and Year3 and then enter a between-conditions contrast [1 -1 0; 1 0 -1].[/color]

[color=#000000]Interaction effects: In order to look at temporal Time1-Time3 changes that may differ between the Patient2 and control groups, you may select both 'Controls' and 'Patients2' in the subject-effects list and enter a [1 -1] between-subjects contrast, and then select as before the Time1 and Time3 conditions and enter a [1 -1] between-conditions contrast. In the results explorer window remember to look at the two-sided results (unless you have an a priori expectation of the directionality of these differences between groups). These analyses will effectively perform a Time*Group interaction test in a repeated-measures anova with a within-subject factor (Time) and a betwen-subject factor (Groups).[/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Geon-Ho Jahng:[/i][quote]Dear CONN Experts
We scanned a resting-state fMRI in three subject groups (Control, Patient1, Patient2), 10 subjects for each group.
Each subject has scanned three times, once a year (We use the condition to set this as: Year1, Year2, Year3). After pre- and post-processing, we want to know the following issues.
However, we are not clear how to set the contrast to test several interests.
First, for each group, we want to know how much functional networks (for example, DMN and language network) decrease during the three year period.
Second, we want to find a network which more decreases in the Patient2 group during the three year period compared with the Control.
I appreciate any comments.
Geon-Ho
[/quote]

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

[color=#000000]You can do this "manually" in Matlab, for example, if you have a subjects-by-connections matrix Z of connectivity values, and a subjects-by-one vector Age of (centered) age values, you could then compute:[/color]

   X = [ones(size(Age,1),1) Age];   % design matrix (constant+slope)
   B = X\Z;                                         % regressor coefficients
   B(1,:) = 0;
   Zc = Z - X*B;                                 % Z values adjusted at 0-level of Age

Alternatively, you may also want to check the script conn_withinbetweenROItest.m which is just a simple wizard for performing this sort of within- and between- network analyses using the tests defined in CONN's second-level results GUI. 

Hope this helps
Alfonso

[i]Originally posted by Stefan Lang:[/i][quote]Hi,

I have subjects who underwent resting state fMRI and I am performing a ROI-ROI analysis using conn. I am calculating average intra- and inter-network connectivity values using the individual subject correlation matrices I obtain from the 'resultsROI_subjectx_Condition001.mat' file. However, I wish to calculate average intra and internetwork connectivity after controlling for the effect of Age on the individual correlations between ROI's. Is there a way to obtain an individual subject correlation matrix which contains the correlation values after being adjusted for the effect of Age?
Any direction would be appreciated.

Stefan[/quote]

Hello All,

I have some results from a regression from which I would like to extract beta values. I know I can import clusters as covariates and use the Tools/Calculator to extract some statistics. However I have been masking my results within the SPM display and may also be correcting for small volume. Is it possible to extract Beta/T values from these clusters after masking and correction within CONN? 

From,

Humza Ahmed

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

[color=#000000]Looks like an installation issue (potential mix-up between several conn versions on your system), simply make sure that:[/color]

[color=#000000]1) in your Matlab path (e.g. click on the the 'set path' button on the command-line Matlab gui) check that your latest conn installation folder (the folder containing the file conn.m) is listed there, ideally on the top of the list of path folders[/color]

[color=#000000]2) when starting conn (e.g. when typing 'conn' from Matlab command-line) make sure you do so from a folder that does not contain any files named conn*.m (e.g. type "ls conn*.m" without the quotes before starting conn, if there are any files listed in this command those files will interfere with your installed conn toolbox files, so make sure those are deleted or moved to a different folder before starting conn)[/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]

[i]Originally posted by dgull:[/i][quote]I recently installed Conn v17b on Ubuntu16.04 with Matlab vR2017a and SPM12 using OpenGL drivers for AMD graphics card. The very first time opening Conn everything worked fine. The second and subsequent times opening it the software would not work and the following errors were received:

[quote]ERROR DESCRIPTION:

Reference to non-existent field 'filename'.
Error in conn (line 1142)
CONN_x.isready(1)=~isempty(CONN_x.filename);
Error in conn (line 528)
conn gui_setup;
CONN v.17.b
Matlab v.2017a
Warning: art.m overloaded by version in folder /home/coded/Downloads/conn
Warning: conn.m overloaded by version in folder /home/coded/Downloads/conn
Warning: conn_ROI2dl.m overloaded by version in folder /home/coded/Downloads/conn
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[/quote]

[quote]ERROR DESCRIPTION:

Struct contents reference from a non-struct array object.
Error in conn (line 670)
if ~isfield(CONN_x.folders,'rois'), CONN_x.folders.rois=fullfile(fileparts(which(mfilename)),'rois'); end
Error in conn (line 121)
conn importrois;
CONN v.17.b
Matlab v.2017a
Warning: art.m overloaded by version in folder /home/coded/Downloads/conn
Warning: conn.m overloaded by version in folder /home/coded/Downloads/conn
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[/quote][/quote]

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

[color=#000000]The values plotted when using the 'plot values' (or extracted when using the 'import values') option are always the actual raw connectivity values (those entered into your second-level model, independent of your design). [/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Drew Sevel:[/i][quote]Hi All,

I have a brief question regarding importing values from significant clusters that were obtained in designs with covariates. For example, if a significant cluster is found in a between groups contrast controlling for the effect of covariate A, such as [1 -1 0], are the values produced though the 'Import Values' tool/REX extracted controlling for the influence of covariate A or are they the raw values?

Thank you,

Drew[/quote]

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

[color=#000000]What I would suggest just for simplicity would be to export your second-level results mask with your clusters of interest, then re-import that as a new ROI in Setup.ROIs (select the newly created file named something like [yourmaskfile].ROIs.nii) and then re-run Setup and Denoising steps (selecting the do not overwrite option) just to have those new ROIs processed. After this you will have in the conn*/results/preprocessing/ folder your new ROI_Subject*_Condition*.mat files containing the BOLD timeseries (after denoising) within each of your ROIs, including your new clusters. [/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso [/color]
[i]Originally posted by Larissa :[/i][quote]Hi Alfonso,

I have 10 subjects with two resting state conditions each. I want to plot the mean original BOLD timeseries within the significant ROI clusters I get from the 2nd-level seed-to-voxel analysis in REX for both resting state conditions separately for comparison. I understand that REX only displays the timeseries from the first-level analysis. To try this in REX, for Sources I selected 10 subject files from the 1st resting state condition in the ~/results/firstlevel/ANALYSIS_01 folder that were labeled (se_Subject001_Condition001.nii, se_Subject002_Condtion001.nii ..... se_Subject010_Condition001.nii), under ROIs I selected the significant cluster from ~/results/secondlevel/ANALYSIS_01/AllSubjects/rest_condition1(1).rest_condition2(-1)/Putamen_r/sigclusterROI.nii , and when I went to extract the data, nothing was plotted. My rationale was if this worked, I would then select the 10 subjects from Condition 2 from the first-level analysis, extract the mean time series of the significant ROI cluster and have the plots to compare. This did not work.

However, if I select my 10 subjects under Sources from the second-level analysis (irrespective of condition contrast (i.e., the subjects labeled as CON_Subject011_compA001_001.nii, CON_Subject002_compA001_001.nii etc) and keep the ROI cluster selected, hit extract mean, I get the resulting time series plotted for the significant cluster. How can I now extract the mean timeseries for this significant ROI cluster separated by condition?

Any advice?

Larissa[/quote]

[color=#000000]Hi Gol Mi[/color]

[color=#000000]Yes, that will be an F test, both 'conditions' and 'sources' are treated exactly in the same way in CONN as within-subject factors, so if you specify a matrix in either of the between-conditions or between-sources contrast the resulting analyses will be an F-test across those multiple measures (multiple conditions and/or multiple seeds/sources). For more information about the specific GLM design simply click on the 'n=*' button to see a detailed display of the second-level design for your selected analysis/contrasts.[/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by gol mi:[/i][quote]Hi all,
if in seed-to-voxel analysis, we have between-condition contrast [1] and between-source contrast , for example eye(8), should we consider  it as a simple t test or just an F- test? I know that when we have a matrix , it is an F test, however, i am not sure if it is correct when we have between-condition contrast as [1].


Thanks[/quote]

[color=#000000]Dear Snowa[/color]

[color=#000000]Thanks for reporting this, I have included the patch for this issue into the latest release (17c) just uploaded. Let me know if you still run into any issues.[/color]

[color=#000000]Alfonso[/color]
[i]Originally posted by snowa wo:[/i][quote]Dear Dr. Alfonso,(or all users)

In second level analysis, when we click on the Graph theory(with t-test option), we can see the image about my analysis.
And I know that if i right click on the image, i can select showed 3D image option.
But when i clicked 3D option, i can't see 3D node about blue node(negative vale) in 2D.
In 3D images, only red nodes are represented. But in same image, i can see the edge of blue node.
Error warning did not showing.
What should I do? please share your thoughts on these!


Best Regards.[/quote]

[color=#000000]Dear Lavinia,[/color]

[color=#000000]Thanks for reporting this, I have included a patch for this issue in the latest release (17c) just uploaded (if I am interpreting correctly this error arises because in previous releases you could not define any of the gray/white/csf mask files from a 4d nifti file, as you could with other ROIs; this has been fixed in the latest release). Let me know if you still run into any issues[/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Lavinia Carmen Uscatescu:[/i][quote]Dear all,

The error message I receive while trying to run the connectivity analysis in conn toolbox occurs at step 5/7, while importing the ROIs. It reads as follows:

ERROR DESCRIPTION:

Error using nifti/subsasgn>assigndat (line 384)
Unknown filename extension (.nii,1).
Error in nifti/subsasgn>fun (line 76)
obj = assigndat(obj,val);
Error in nifti/subsasgn (line 20)
obji = fun(obji,subs,val);
Error in spm_create_vol>create_vol (line 79)
N.dat = dat;
Error in spm_create_vol (line 13)
v = create_vol(V(i));
Error in spm_write_vol (line 83)
V = spm_create_vol(V);
Error in conn_process (line 619)
V0.fname=conn_prepend('e',CONN_x.Setup.rois.files{nsub}{nroi}{nses}{1});spm_write_vol(V0,X1);
Error in conn_process (line 15)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 1122)
else conn_process(psteps);
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.b
SPM12 + ArtRepair DEM Diffusion FieldMap LI MEEGtools TFCE Variability Volumes aal bspmview cat12 marsbar mfp rwls tsdiffana
Matlab v.2013a
storage: 342.6Gb available
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I hope someone can provide some useful advice.

Best,
Lavinia Uscatescu[/quote]