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RE: error msg using CONN

September 17, 2021, 7:17 pm
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I was able to fix this!

In my case i was using MriCron DCM to NIFTI converter in my macOS. I uninstalled the mricron latest version and installed MricroGL, with this CONN's error message didn't appear and i was able to complete preprocessing without any error.

This is the link to MRIcronGL download if u still need it https://www.nitrc.org/projects/mricrogl

Hope it works, see ya!
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RE: Error While Trying to Registering Preprocessed Resting State Scans to Preprocessed Structural Scans

September 19, 2021, 2:49 am
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hey ! I have a similar problem,
I tried to use freesurfer files in CONN, using the attached pipeline (we didn't use  slice timing and smoothing in our analysis)
all the data of free surfer is in the right folder (when I upload it on gui, it creates more file to use in this folder.
the error message is: 
ERROR DESCRIPTION:

Error using conn_setup_preproc (line 2709)
No FreeSurfer data found for structural file /media/neuro/LivnyLab/Research/MISTIC/analyses/Volumetric/freesurfer/V1/102_1_BD/mri/T1.nii
Error in conn (line 1105)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN19.c
SPM12 + DEM FieldMap LST MEEGtools marsbar
Matlab v.2019b
project: CONN19.c
storage: 59.5Gb available

do you have any suggestions on  what went wrong? 
thank you
Reut
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Sliding window analysis help

September 19, 2021, 10:20 am
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Hey everyone,

I'm working on setting up a sliding window analysis for my subjects but I'm not sure how to set up their windows due to a difference in scan length. My dataset consists of 162 subjects and they either require 17 windows or 34 windows (18s onset and 36s duration). To compensate for the different number of windows, my current setup maps each window condition to a session for each subject (subjects with 17 windows have 17 sessions and subjects with 34 windows have 34 sessions). Is this the correct way to go about having different scan lengths or is there something that needs to be changed? Also, if it's correct, is there any way optimize the setup to save on space because the total number of subjects and sessions requires a lot of space.

Is there something special I need to do for the first level analysis like selecting all of the sessions or something?

Finally, how do you study sliding window results in CONN?

Thank you for your help in advance!
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ALFF with REX EXTRACTION

September 19, 2021, 11:05 pm
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I would like to check that the following procedure I perform is viable - as I am only interested in whether I have a between group difference in ALFF within auditory ROIS.

At the first level I run ALFF without normalization in order to generate the raw voxel values.
At the second level of analysis I choose conditions: ALL SUBJECTS and my frequency band condition.
In the results explorer window, I select the REX tool and apply my own mask (of auditory cortical regions) under the option "other clusters of interest.." and enable the rex GUI.
In the rex GUI, I extract values at every voxel within my mask and save the output.
From the output, I then transform the values within each voxel to z-scores and then take the average over all voxels per subject in order to perform a between groups analysis.

Is this ok to do?

/Rina
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adding new and deleting old subjects

September 20, 2021, 7:38 am
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Hi,

I have analysed 9 subjects (with pre and post imaging data) previously for functional connectivity. Now, I have additional subjects I want to include to my analysis. Also, I want to exclude 2 previously analysed subjects - they only have pre imaging data so were not included in the second level analysis (post > pre). Would deleting old subjects interfere with any of the old analysis or for future analysis?

Also, for the new analysis can I do a "Save As.." version of the CONN file to work on and keep the old file as well?

I hope I explained it clearly :) Thank you so much in advance! 


Best,
Yasemin
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beta below zero but positive on surface map

September 20, 2021, 3:29 pm
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Hi CONN users,

I wanted to display a seed-to-voxel results on a surface map. The beta is below zero. however, when I displayed it on surface, the color bar shows positive value (see attached thalamus_CL.fig). I assume that the activation on surface map should be in the same direction as the beta, or did I set up anything wrong?

The result cluster locates at Thalamus, so I only displayed the sub-cortical volume. I wonder if this could be the reason why the figure looks weird.

Thank you!
Meishan
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Recurrent error during the denoising step n5 (Importing ROI data).

September 21, 2021, 5:38 am
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Dear CONN users,

I am having some trouble with the denoising step. I use the latest CONN version (20. b), SPM12, and Matlab R2021b.

I always get the following error during denoising step 5/7 (i.e., Importing ROI data). The error never happens during the same participant. It crushed once at participant 44, then at 29 and then at 41. I have a total of 86 participants.

ERROR DESCRIPTION:
Error using spm_sample_vol
Cant open image file.
Error in rex>rex_do (line 741)
temp1(i,:) = spm_sample_vol(params.VF(i),XYZ(1,:),XYZ(2,:),XYZ(3,:),0);
Error in rex (line 192)
[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 934)
else [data{nroi1},namesroi{nroi},params]=conn_rex(Vsourcethis,Vmask{nroi}{min(nses,nsesstemp)},'summary_measure','eigenvariate','dims',CONN_x.Setup.rois.dimensions{nroi},'conjunction_mask',mask,'level',level,'scaling',scalinglevel,'select_clusters',0,'covariates',entercovariates,'fsanatomical',fsanatomical,'output_type',outputtype,'output_rex',filenamerex,'output_folder',filepath);
Error in conn_process (line 16)
case 'setup', conn_disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 5743)
else conn_process(processname); ispending=false;
Error in conn_menumanager (line 121)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN20.b
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2021a
project: CONN20.b
storage: 5958.1Gb available
spm @ C:\Users\camila\Documents\MATLAB\spm12
conn @ C:\Users\camila\Documents\MATLAB\conn

Could it be an incompatibility problem between the latest versions of MATLAB, CONN and SPM?

Any help would be very much appreciated!

Thank you very much!

Camila
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RE: Missing ROI Values with Surface-Based Analyses

September 21, 2021, 7:27 am
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Errors Running in batch with multinodes & Conn20b issue

September 21, 2021, 8:16 am
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Hello,

I am unable to run distributed processing over multiple nodes in Conn. When I attempt to run preprocessing in this manner in conn19c I can see it runs for at time and then gets completely stuck at two nodes (out of 54) and fails to ever advance from there. Interestingly, the same preprocessing runs fine if I run it "locally on the server" which just takes significantly longer. Looking at the error output when I try to run it in batch on the server I can see the following error:

[i][b]/PATHTOCONN/conn_project01.qlog/210917103243256/node.0031210917103243256.sh: line 2: 55741 Aborted (core dumped) '/usr/local/MATLAB/R2019b/bin/matlab' -nodesktop -noFigureWindows -nosplash -singleCompThread -logfile '/PATHTOCONN/conn_project01.qlog/210917103243256/node.0031210917103243256.stdlog' -r "addpath '/usr/local/MATLAB/tools/spm12'; addpath '/usr/local/MATLAB/tools/conn19c/conn'; cd '/PATHTOCONN/conn_project01.qlog/210917103243256'; conn_jobmanager('rexec','/PATHTOCONN/conn_project01.qlog/210917103243256/node.0031210917103243256.mat'); exit"[/b][/i]

I do not have admin privileges to the matlab so although I can save the path locally, this does not save to the main pathdef.m file, so I wonder if this is the issue. Still weird that there is no issue when run on the same server locally?

I have Conn 20b too, but when I run it on there I cannot figure out the error because it does not give me the job manager gui of the current process. So, there is nothing showing me how the nodes are running/submitted/completed, or shows any std output or errors, nor does it then let me cancel any processes. So the only way I could figure out to stop the process is to kill matlab... Furthermore, without that job manager gui (which I do see in Conn19c) I cannot figure out how to track what the issue is. My best guess is that it is the same issue as with Conn 19c though, just based on how long I wait before it hangs, and also based on the output files that I could find. 

So, the main issues I want to figure out is:
(1) Why is it hanging there in distributed processing, and how can that be fixed.
(2) Why is Conn20b not showing the job manager that should display how the process is going? How can I get that to work too?

The server is running on red hat 7.9 (Maipo)

Thank you!
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RE: connectivity matrix

September 21, 2021, 3:52 pm
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[color=#000000]Hi Sandy,[/color]

[color=#000000]The function conn_mtx_display can be used to display an arbitrary connectivity matrix; e.g. conn_mtx_display(randn(10));[/color]
[color=#000000] See "help conn_mtx_display" for details.[/color]

Best
[color=#000000]Alfonso[/color]

[i]Originally posted by sandy11:[/i][quote]Hello,
How can I make the connectivity matrix (from ROI to ROI analysis) with a color bar that shows the negative correlations in cold tones and the positive in hot tones?
Which command should I write in MATLAB? 
thank you,
Sandy.[/quote]
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RE: how to get % of data censored/scrubbed

September 21, 2021, 3:56 pm
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[color=#000000]Hi Austin,[/color]

[color=#000000]You may simply create a new 2nd-level covariate (in the [i]Setup.Covariates.2nd-level [/i]tab) and enter in the 'values' field the formula:[/color]

[color=#000000]   QC_InvalidScans ./ (QC_ValidScans+QC_InvalidScans)[/color]

to get the percentage of scans that have been identified as potential outliers for each subject (the QC_ValidScans and QC_InvalidScans are typically automatically created by CONN's ART preprocessing step)

Best
Alfonso
[i]Originally posted by Austin Myers:[/i][quote]Hello,
I have been trying to figure out how to get a summary of the average % of data censored/scrubbed from my analysis but keep running into this error.

Error using conn_convertl12l2covariate (line 95)
Covariate does not contain the same number of dimensions across subjects/sessions

Error in conn (line 3311)
conn_convertl12l2covariate(nl1covariates);

What I have been doing is selecting my scrubbing covariate and then selecting compute summary measures from the covariate tools dropdown menu. In the popup menu for this option I am choosing average for both "summarize across time points/sessions and summarize across covariate dimensions' and then selecting my 3 conditions.

I am assuming that either I am doing something wrong within this menu or this is just not the correct way to get the information I would like in the first place. Any help would be greatly appreciated. Thank you very much

Best,
Austin[/quote]
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RE: Interaction Model in Subset of Subjects

September 21, 2021, 5:29 pm
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[color=#000000]Dear Amir,[/color]

[color=#000000]Almost exactly correct, but in GLM you would need to exclude subjects without the behavioral measure from the interaction analyses. In your example that could be done simply entering NaN for those subjects in their corresponding trait_* variables, i.e.:[/color]

group_F = [1 1 1 0 0 0]
group_M= [0 0 0 1 1 1]
covariate1 =[-2 -1 -0.5 0.5 1 2]
trait_F = [x1 x2 x3 0 0 0]
trait_M= [0 0 0 y1 NaN y2]

Regarding (2), there is no need to orthogonalize trait for this interaction analysis

And regarding (3), typically interaction effects are tested using two-tailed/sided analyses, as the sign of the interaction term only reflects whether the slopes (association between trait and connectivity within each group) are larger or smaller in one group compared to the other (i.e. the regression lines of connectivity vs. trait for each group will cross each other for both positive and negative interaction effects, in positive effects the regression line in the F group has a higher slope than in the M group, and the opposite for negative effects)

Hope this helps
Alfonso

[i]Originally posted by AmirHussein Abdolalizadeh:[/i][quote]Dear CONN users/experts,

I have two groups (group_F, group_M; n = 35), however, only 30 subjects have a behavioral measure of interest. After comparing between group differences, I am interested in the interaction model. For simplicity, I am using 6 subjects as an example (subject 5 does not have behavioral measure) and want to check whether I am doing it correctly or not.

group_F = [1 1 1 0 0 0]
group_M= [0 0 0 1 1 1]
covariate1 =[-2 -1 -0.5 0.5 1 2] #Demeaned (a.k.a., orthogonalized for all subjects)
trait_F = [x1 x2 x3 0 0 0]
trait_M= [0 0 0      y1 0 y2] #Note the fifth subject being zero in both trait_*

This is the contrast that I should use for the model below: [0 0 0 1 -1]
y ~ group_F + group_M + covariate1 + trait_F + trait_M

Three questions:
1. Am I doing all things right?
2. Do I need to also orthogonalize trait_F & trait_M? In respect to all subjects? or in respect to group_F and group_M, respectively?
3. Any [b]positive [/b]t-stat result for this contrast (trait_F > trait_M) means that there is a significant group*trait interaction in that voxels (regression lines of activity ~ trait for each group are crossing each other for that region), in which there is a positive beta for activity~trait in group_F and negative beta for activity~trait in group_M, right?


Thanks in advance!

Bests,
Amir[/quote]
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error importing bids format .tsv (regexprep)

September 21, 2021, 9:24 pm
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Could someone advise on how to address this error?
I am trying to import .tsv files for each subject. These .tsv files Arte in bids format under each subject file. I have attached an example file below incase I have formatted something wrong. There are extra columns but that should not matter. Also it should be noted that my resting task file is empty; I don't know if this is the issue.

ERROR DESCRIPTION:

Error using regexprep
The 'STRING' input must be either a char row vector, a cell array of char row vectors, or a string array.
Error in conn_importbids (line 189)
fname=conn_prepend('',regexprep(tname,'_bold\.nii(\.gz)?$','.nii'),'_events.tsv');
Error in conn_importcondition (line 176)
[ok,err,wrn]=conn_importbids('all','type','conditions','subjects',options.subjects,'sessions',options.sessions);
Error in conn (line 3538)
conn_importcondition;
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update

September 22, 2021, 3:23 am
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Hi,

I have an old data set from 2019 and I will add new subjects and repeat the analysis. Would you recommend me to download the latest update of CONN or should I work with the old one to not mess up with my previous data?

Thanks!
Best,
Yasemin
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Struct contents reference from a non-struct array object

September 22, 2021, 7:13 am
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Hi,
I got this error during the second level analysis and I don't know why. Preprocessing and denoising worked well. This error message didn't stop popping up.

ERROR DESCRIPTION:
Struct contents reference from a non-struct array object.
Error in conn (line 10863)
SPM.xX_multivariate.statsname=info.statsname;

Thanks for your time and help.
Indira
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2nd level analysis (seed to voxel) display result shows error and fails to compute connectivity maps

September 22, 2021, 11:31 am
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I'm using conn 20 and I'm trying to generate connectivity maps from 25 subjects. After following the steps toward the 2nd level analysis when pressed display results for seed to voxel analysis (seed based correlation) it shows this error.

ERROR DESCRIPTION:

Unrecognized function or variable 'cfg_branch'.
Error in cfg_getfile>reg_filter (line 1185)
dprms = {cfg_branch};
Error in cfg_getfile>mk_filter (line 1134)
sfilt.tfilt = reg_filter(typ);
Error in cfg_getfile (line 144)
filt = mk_filter(typ, filt, prms{:});
Error in spm_select (line 154)
[t, sts] = cfg_getfile(varargin{:});
Error in spm_spm (line 352)
if ~isempty(spm_select('List',SPM.swd,'^mask\..{3}$'))
Error in conn_process (line 5008)
SPM=spm_spm(SPM);
Error in conn_process (line 60)
case 'results_voxel', [varargout{1:nargout}]=conn_process(16,varargin{:});
Error in conn (line 11497)
conn_process('results_voxel','readsingle','seed-to-voxel');
Error in conn (line 10649)
if state==2, conn gui_results_wholebrain;
CONN20.b
SPM12
Matlab v.2020a
project: CONN20.b
storage: 667.1Gb available
spm @ /Users/badhon/Documents/spm12
conn @ /Users/badhon/Documents/conn
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Analysis of interaction of categorical variables

September 22, 2021, 12:05 pm
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Dear Alfonso,

Thank you for all the support offered here!
We have used CONN to investigate fALFF and SBC in four different groups: hyperphagic MDD, hypophagic MDD, euphagic MDD and healthy controls (HC). Because data were collected in four sites, we included site as covariates as well as sex (due to difference between groups for sex).
We received a request from a reviewer to explore sex in a moderation analyses given sex differences between groups, so we would like to test the interaction group*sex for fALFF and SBC in our sample using CONN.
We saw a post in which you explain this process using continuous variables (https://www.nitrc.org/forum/forum.php?thread_id=11287&forum_id=1144), but it is not very clear for us how to do that with categorial variables. We thought of adding separate 2nd-level covariates to setup including each group and each group separated by males and females (e.g., hyper females, hyper males, hypo females, hypo males, euphagic females, euphagic males, HC females, HC males) and set up the between-subject contrast in 2nd-level results to explore interaction. Would this be a way to explore this interaction? How exactly could we set up the main effect of group and group * sex interaction?

Thank you so much!

Mayron
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Using CONN in docker

September 22, 2021, 7:07 pm
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Dear Alfonso and other CONN users,

I would like to work on CONN in matlab docker. May I know how to install CONN toolbox in docker MATLAB? I tried the procedure in https://web.conn-toolbox.org/resources/installation/standalone-linux this link, but I am unable to run that standalone application. The documentation looks very old and the folders in that specific path are not the same for R2021a of MATLAB.

Can anyone please help me 

Thank you
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RE: Realign, unwarp, normalize functional runs separately in CONN

September 22, 2021, 8:42 pm
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OK, So I did this, but I cannot seem to figure out how to see the QA plots for both sessions? When I run the QA plots now for all subjects, it will only show me the functional information for Session 1, but no information for Session 2 (despite the fact that I have definitely run this). How can I create QA plots for both sessions so I can check how the realignment and then warping went for both sessions and not just session 1?

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

[color=#000000]If you want to first evaluate how well the two runs would be realigned and unwarped to the first slice of the first run, you could do that by first running the standard realign&unwarp step, and then either creating the QA plot labeled "[i]QA realignment: display center slice across multiple sessions[/i]", or similarly by using [i]spm_check_registration [/i]and selecting the first slice of the two functional runs separately for each subject.[/color]

That will often be perfectly fine, even if the different runs are really acquired in different visits/sessions, but if that is not the case in your dataset and you would like to preprocess the different runs separately, you may do that in CONN simply by running preprocessing twice, each time selecting an individual run (uncheck the option that reads 'process all sessions' and then select the session that you would like to preprocess).

Hope this helps
Alfonso
[i]Originally posted by Keith Dodd:[/i][quote]Hello,

I have resting state data split into 2 runs/sessions (with 1 structural). However, in between the two runs, the subjects have exited and then reentered the scanner. I noticed that the standard pipeline analyzes the separate sessions together (i.e. all slices from all runs are realigned and unwarped to the first slice of the first session, and then later this is segmented and normalized). I am worried that this may not be entirely accurate since the patient exits the scanner and re-enters in between as there might be different spatial distortions depending on head positioning changes?

If this is a potential issue (how much might I need to worry about this?), then I want the functional realignment and unwarping, as well normalization, to be done per session separately, instead of combined. However, I have not been able to figure out how to tell CONN to do this. Basically, I want to compare the runs and have CONN treat it as 2 runs to compare for each subject with a single structural scan (so I do not believe I want to tell CONN that these are separate subjects...), but to realign, unwarp and normalise each run separately to help keep the warping of these runs to be the more accurate.

How might I do this within the preprocessing GUI? Additionally, is there any method in CONN to check how well the two runs were realigned and unwarped to the first slice of the first run? To see how much of a factor the leaving and re-entering the scanner had?

Thank you![/quote][/quote]
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RE: MVPA analysis

September 23, 2021, 5:37 am
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Dear Alfonso or any CONN expert,

I have been using CONN to investigate  rsfMRI differences between controls and patients with mental disorders. 
 
I found interesting results with MVPA but although I read your very good 2020 handbook, it's reference on MVPA (the review Norman et al.,2006), and also browsed through CONN's help search, I still haven't found answers for crucial questions. 

Would you be so kind to clarify or point to bibliography that answers the following?

1- Which is the classifier performance from the results I get in CONN's MVPA?

2- In section 'MVPA Methods' of Norman et al.,2006 the authors divide MVPA in 4 steps (feature selection, pattern assembly, classifier training and generalizing testing). For an analysis that only inserts a Patients > Controls contrast, which are CONN's default settings regarding those 4 steps?  

3- For this Patient > Control contrast I get negative connectivity at many cerebellum's sub-areas. How does CONN compute this difference? (e.g. separate MVPA results are computed for each group and then the t-tests to find differences at each voxel's time series?)


Thank you very much for your attention.
All best
Renzo
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