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how to decide on the right Band-pass filter?

February 26, 2018, 2:54 pm
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[color=#000000]Hello,[/color]
[color=#000000] [/color]
[color=#000000]I am working in CONNv17b to conduct functional connectivity analysis on resting state data. We acquired two resting scans (before and 1 year after surgery) in a single continuous scan with a duration of 6.35 minutes (slice thickness 2.3; TR 6270 ms and TE 32.0 ms; SIEMENS 3T Skyra).[/color]

[color=#000000]I would like to know how I should choose the correct Band-pass filter in the denoising step? How should I decide on the range of the band-pass filter? What are the factors I should take into account?[/color]

[color=#000000]I hope you can help me. Thank you in advance! [/color]
Best,
[color=#000000]H Cerit
[/color]
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RE: mat2file not compiling

February 27, 2018, 3:36 am
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I am working with spm12 (eeg data) and getting the same error , how should i handle the same problem. thank you
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How to add a session? for single group repeated measure design [baseline and follow up]

February 27, 2018, 5:39 am
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Hi Alfonso,

I have resting state for 1 group at 2 x assessment times, pre and post intervention.
I am not sure how to add in the GUI, i.e., what to click, to add baseline and follow up data separately, for each subject.
In the setup window, I can see the 'sessions', I am right clicking on the icon to add one session but it does not create any options for me.
Do you have any advice?
Thank you in advance and have a lovely day,
Vale
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RE: conn crashed after lack of storage

February 27, 2018, 9:55 am
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Hi,
If you don't mind me asking, how did you restore the project.mat file? I'm a new student trying to make this all work.

THanks so much,
Yush
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Reporting statistics from ICC findings

February 27, 2018, 12:37 pm
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Hi Alfonso and fellow CONN users, 

 I have two questions regarding reporting statistics: 

1. This may be a very simple question and I have just been looking in the wrong places. I am using a design with (within-subject; -1, 1) pre vs. post-drug administration conditions, and (between subjects; 1, -1) drug vs. placebo groups (also controlling for the site of the scan). I am hoping to report the mean and standard deviation correlation values for the two drug groups (post-pre difference) and am having trouble finding this information for my voxel-to-voxel ICC analysis in the regions that were significantly different across groups (or finding each participant's connectivity values at these significant voxels so I can manually calculate the mean and SD per group). What is the best way to find or calculate these values?

2. Also you mentioned in a previous post that the Beta Value should be reported (from the plot effects tab) in addition to the t-values. Would this also be appropriate given my design?  And what exactly do these values represent?  From the title of the graph for the plot effects tab, it seems like this effect size is only looking at the difference in average connectivity across the conditions ("-pre_IntrinsicConnectivity_1+post_IntrinsicConnectivity_1") without considering the drug vs. placebo groups, which does not seem useful to report. 

Thanks so much!
Leah
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How to skip preprocessing ?

February 27, 2018, 10:21 pm
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Hello dear conn-ers:

Thank you so much for developing this great toolbox !

I just have 2 quick questions,

1) To skip preprocessing, what structural and functional files should i choose in the set up in the gui?
2) If I want to add some more specific ROIs in the setup, does this mean that every time I change the ROI set up, I need to re-run the pre-processing again?

It would be of great help if you could help me out, any information is highly appreciated !
Thank you so much!

Best,
Zoe
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RE: conn_dynexplore

February 28, 2018, 9:02 am
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Dear experts,

 I am wondering whether anyone has an answer to the conn_dynexplore error that I have posted earlier. 

Error using ==> conn_dynexplore at 105
The specified event is not supported by the object

Error in ==> conn at 7022
conn_dynexplore;
Error in ==> conn at 6593
if ~ conn_projectmanager('ispending')&&~ispending, conn gui_results_dyn_symmarty; end

I would appreciate very much for any insights and suggestions. Thank you.


Lihong
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Preprocessing (Denoising) Error

February 28, 2018, 10:00 am
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Hi all,

I've been working to re-denoise an analyses for future dFC work. This is a CONN_x file that has been located to a different folder although path names in the conn_x structure have been updated and CONN's internal file updating process was changed as well. I've run into the following errors:

This error occurs when I load the project file:

ERROR DESCRIPTION:

Error using isfield
Too many input arguments.
Error in conn_updatefolders (line 103)
if isfield(CONN_x.vvAnalyses,'variables')&&~isfield(CONN_x.vvAnalyses.variables,'norm'), CONN_x.vvAnalyses.variables.norm=repmat({1},1,numel(CONN_x.vvAnalyses.variables.names)); end
Error in conn (line 665)
if pobj.holdsdata, conn_updatefolders; end
Error in conn (line 2798)
conn('load',filename,true);
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.16.b
SPM12 + DEM FieldMap MEEGtools wfupickatlas
Matlab v.2015a
storage: 9641.2Gb available

And this when I run denoising:

ERROR DESCRIPTION:

Incorrect number of right hand side elements in dot name assignment. Missing [] around left hand side is a likely cause.
Error in conn_process (line 1650)
CONN_x.vvAnalyses.variables=conn_v2v('measures');
Error in conn_process (line 26)
case {'preprocessing_gui','denoising_gui'}, disp(['CONN: RUNNING DENOISING STEP']); conn_process([1.5,2,6:9],varargin{:});
Error in conn (line 3474)
else conn_process('denoising_gui');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});



Does anyone have any suggestions?
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RE: Error at 1st level: incorrect # ROIs

February 28, 2018, 11:43 am
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Thanks so much for your detailed reply, Suzanne (I was not notified of a response - glad I checked back). I will re-run the analysis using an earlier version of conn, I'm thinking that will resolve this problem.

Best,
Nicole
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Applying FWE correction for ROI-to-ROI analyses in conn

February 28, 2018, 1:18 pm
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Dear Alfonso, dear experts,

apologies in advance for the probably naive question, but I was wondering if there is a way I could derive the p-FWE values (instead of the default p-FDR values) for the ROI-to-ROI analyses in the second-level results (as in the rest of my analyses, e.g. seed-to-voxel resting-state connectivity analyses, VBM analyses, etc, I have been employing FWE correction).

many thanks for your time

georgios
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ROI List (components and labeling)

March 1, 2018, 2:54 am
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Hi,

I am using the ROI List of the conn toolbox and I cannot figure out what the components DefaultModeNetwork.LP and Salience.RPFC (... prefrontal cortex?) stand for.

I would really appreciate your help!

Cheers,
Kate
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DEM FieldMap MEEG tools error

March 1, 2018, 7:18 am
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For all my subjects when I run

Preprocessing: default preprocessing pipeline for volume-based analyses (direct normalization to NMNI space), then remove slice timing correction

I get the following error.  I hit continue but I do not think that it ignores the error and continues to run.  

The following modules did not run:
Failed: Realign & Unwarp

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.17.f
SPM12 + DEM FieldMap MEEGtools
Matlab v.2017b
storage: 865.9Gb available
spm @ /Applications/Imaging/spm12
conn @ /Applications/Imaging/conn

File background and history:  Scanning on a 3T Philips, burn cd from scanner, import into Oxirix and export dicom images into a single dicom file. 
Convert images to NII using MRIcroGL/MRIcro.app.  Tried using both the dicom images and the nii images and get same error. Tried on multiple subjects (ran individually) and get the same error. Suggestions?
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Error at Outlier detection (ART-based) preprocessing step

March 1, 2018, 7:23 am
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Hello everyone,
First post for me on this forum. It's been very useful to read you all for quite some months now. Thanks to all of you.

I'm running an event functional whole-brain analysis, that's been proving to work well from beginning to the end.
I wanted to come back to the Setup step and add and Outlier detection preprocess step then re-do my analysis.
Though, when launching this step, I've got the following error:

[b]ERROR DESCRIPTION:[/b]

[b]Error using ==> disp[/b]
[b]Too many input arguments.
[/b]
[b]Error in ==> art>art_OpeningFcn at 401[/b]
[b]disp('warning: unable to write to ',output_dir,' folder. Writing output files to ',pwd,' instead.');
[/b]
[b]Error in ==> gui_mainfcn at 221[/b]
[b]feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
[/b]
[b]Error in ==> art at 143[/b]
[b][varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
[/b]
[b]Error in ==> conn_art at 8[/b]
[b][varargout{1:nargout}]=art(varargin{:});
[/b]
[b]Error in ==> conn_setup_preproc at 1695[/b]
[b]else h=conn_art('sess_file',matlabbatch{n}.art,'visible','off');
[/b]
[b]Error in ==> conn at 895[/b]
[b]ok=conn_setup_preproc('',varargin{2:end});
[/b]
[b]Error in ==> conn_menumanager at 120[/b]
[b]feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
[/b]
[b]CONN v.17.e[/b]
[b]SPM12 + DEM FieldMap MEEGtools[/b]
[b]Matlab v.2010a[/b]
[b]storage: 3691.8Gb available[/b]

I've got an event design with 39 subjects, each performing 3 sessions. Each subject has 368 scans, each has the same amount of onsets and no onset times beyond the end of the scanning session.
Besides the setup was constructed from the import function that loaded 39 spm.mat.
What do I get wrong ?

Cheers
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Within subject, multi-study design

March 1, 2018, 8:56 am
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Hello CONN experts!

I am pooling together data from 3 studies. In 2 of the studies there is data from two time points, although not every subject has data from T1 and T2. In the third study, there is only data from 1 time point. In addition, in two of the studies there are 2 sessions of data for pre and 2 session for post, while in the third study there is only 1 session of data at the pre- time point.
Can I use the strategy below?

In CONDITIONS: define two conditions ('pre' and 'post'), for subjects with pre- AND post data. In subjects with 2 sessions for each pre- and post, there would be two 4D files each for 'pre" and "post." Otherwise, there could be one or two sessions for either pre- alone, post-alone or both pre and post. For subjects with only one time point, they would only have one condition.

Thank you so much (in advance) for your input!!!

Tamara Sussman
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Custom networks and subject specific stats

March 1, 2018, 10:00 am
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Hi Conn experts!

i am running analysis of my resting state data and I want to use custom made ROI's but I need them to be treated as networks
I have 19 ROI's for DMN (.nii files) and similar number for ECN and SN.

Is it possible to add them to my analysis as networks and get (Fisher corrected?) averaged connectivity values for each network for each of my subjects?
How do I do that?

I have been able to get connectivity values for individual roi pairs but this is only halfway to where i need to get.

I would really appreciate any help in that regard
Best
Janek
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HCP Denoising Error

March 1, 2018, 2:09 pm
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Hello, 

I am processing data in CONN in a supercomputer. I have successfully set up parallel processing in the tool and all works well in the preprocessing step - with great performance. Once that is finished and saved, I click done and it takes me to the denoting tab with all looking great. After choosing my parameters and clicking done, it asks me to to select either parallel or local, and an error comes up once I try to parallel the jobs. It sends the jobs; it displays a running message, and returns an error per job.

I have then cancelled (several times) and tried to run without paralleling jobs. It gives the error box (the one that suggests the forum) at the "Denoising functional data" step. 

Any experience with that cycle? 

Thank you for all your help!
Tatiana
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dentate nucleus connectivity

March 2, 2018, 6:08 am
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hey alfonso,

while following the default preprocessing pipeline in conn, i preprocessed my data for both healthy controls and patients taking the Dentate nucleus as a custom roi. in the second level analysis, i saw that there was a good whole brain ROI-ROI connectivity( of dentate nucleus in patients) but for healthy controls the connectivity was limited to 3-4 ROI within the cerebellum(no connecitivity with SMA, frontal cortex,).
would you be able to guide me regarding the resting fMRI pipeline for custom ROI.
PS: i made the Dentate nucleus ROI via FSL maths and it is a spherical sphere with radius of 4mm and also should i make a ROI with bigger radius i.e more than 4mm.
Thanks for your reply.
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external normalization

March 2, 2018, 10:55 am
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Dear Conn developers,
  First of all, thanks for this great tool!

 I am preprocessing a 200 subjects sample of resting. The standard normalization procedure in conn (direct normalization) left a significant part of the brain outside the MNI boundaries in my sample. Thus, I am considering using ANTs to normalize the functional realigned and unwarped (au) images and then re-enter the images and continue with the preprocessing steps  and analysis using conn. A priori, it seems feasible using batch conn, however, I would like to ask:

1. Am I missing any important issue that may mess up everything? If I re-enter the nomralized images in each subject folder with the same name (eg: wau_image), then I guess the smoothing process and all the following steps could be resumed using batch.

2. If so, do I really need to preprocess the structural data? Or is it just for visualization purposes as I've read in previos posts. This is because waving this step would save a considerable amount of time.

Thanks in advance
And thanks again for your tool!
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SPM website nor responding

March 4, 2018, 10:11 am
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Hello,

The readme.txt of conn says that "This software requires SPM" followed by the website url. However, the url is not responding. Does anybody know what is happening? Is there anywhere else I can download SPM? Thanks.
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batch scripting with user defined roi

March 5, 2018, 1:10 am
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Dear experts,

My batch script was successfully done with all parts except the Analysis phase. It went in to trouble and gave me this error message:

Cell contents reference from a non-cell array object.

Error in conn_process (line 1757)
idx=strmatch(initial{n1},CONN_x.Analyses(ianalysis).variables.names,'exact');
Error in conn_process (line 37)
case 'analyses_seedandroi', disp(['CONN: RUNNING ANALYSIS STEP (seed-to-voxel and roi-to-roi
analyses)']); conn_process([9.1,10,11,15],varargin{:});
Error in conn_batch (line 1101)
else conn_process('Analyses_seedandroi',batch.Analysis.analysis_number);
Error in conn_48hcp (line 271)
%batch.Analysis.analysis_number = 0;

Does any one see this error before? or does anyone know the probable source of this error?
Thanks in advance for all your kind help.

best regards,
Boshra
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