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New subjects create NaN 2nd level covariates

March 23, 2017, 1:42 pm
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Hi all,

I'm relatively new to using CONN and fMRI data-analysis en masse. That said, I have been conducting preliminary analyses and everything was going fairly smoothly. I recent updated my set-up stage to include newly collected data from new research subjects; however, following pre-processing and denoising, the QA_MaxMotion, QA_InvalidScans, and QA_ValidScans second-level covariate values for all previously analyzed subjects has been replaced with "NaN" values. Can anyone explain this to me and hopefully point me in the right direction for finding these previously available values? Thanks!
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No suprathreshold voxels in ROI file

March 25, 2017, 11:57 pm
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At the end of the 'setup', after pressing 'Done', the process stops at the 21st participant and the Error is:
No suprathreshold voxels in ROI file --------- after erosion (original file contained 164 suprathreshold voxels).

What is the meaning of this error and what can I do in order to solve it?
I checked the structural file and the ROI fles and they both seem fine.
Thank you !
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RE: Batch -- Preprocessing Error

March 26, 2017, 3:04 am
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Hi!

I had the exact same error generated while running SPM12 from the [i]nipype[/i] library in python and it was simply because my inputs were [color=#808080]<font color="#000000">[b]*.nii.gz[/b] files and not[b] *.nii[/b] files...[/color]</font>

[color=#808080]<font color="#000000">Hopping SPM teams will improve that behavior in the future by throwing a more meaningful exception![/color]</font>

[color=#808080]<font color="#000000">Best,[/color]</font>

[color=#808080]<font color="#000000">GJ[/color]</font>
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CONN error

March 27, 2017, 3:58 am
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I got the following error:

ERROR DESCRIPTION:

Error using subsref
Reference to non-existent field 't'.
Error in spm_get_defaults (line 41)
varargout{1} = subsref(defaults, subs);
Error in spm_hrf (line 44)
fMRI_T = spm_get_defaults('stats.fmri.t');
Error in conn_process (line 409)
hrf=spm_hrf(rt);
Error in conn_process (line 15)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 3195)
else conn_process('setup');
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.17.a
SPM12 + Anatomy DEM FieldMap MEEGtools
Matlab v.2013b
storage: 361.8Gb available

What is the source for that error?

Thank you very much!!
Maayan
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RE: t-test paired or unpaired for two timepoints

March 27, 2017, 5:44 am
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Great that helps a lot, Alfonso! Thank you.
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RE: Preprocessed fMRI data into CONN toolbox

March 27, 2017, 11:54 am
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Hi,
I'm trying to run FreeSurfer processed data (structural and functional data using FSFAST) through CONN. Based on my readings of the manual and forum, I thought CONN might accept FreeSurfer output (.mgz files). However, when I try to select the T1.mgz in the structural set-up using the CONN GUI, I receive the message below...can CONN accept .mgz files or do I need to convert these to .nii.gz? If I don't need to convert to .nii.gz, I would appreciate any insight you might have.
Thanks,
Scott

ERROR DESCRIPTION:
Error using gunzip>gunzipwrite (line 223)
Could not open file "/2525_ARF/conn_test/SUBJ463_recon/mri/T1" for writing.
Error in gunzip>gunzipEntries (line 151)
names{k} = gunzipwrite(entries(k).file, outputDir, baseName, streamCopier);
Error in gunzip (line 87)
names = gunzipEntries(entries, outputDir);
Error in conn_mgh2nii (line 14)
filename(redo)=gunzip(filename(redo));
Error in conn_getinfo (line 7)
filename=conn_mgh2nii(filename);
Error in conn_file (line 4)
[V,str,icon,filename]=conn_getinfo(filename,doconvert);
Error in conn (line 1696)
V=conn_file(deblank(filename(n1,:)));
Error in conn_filesearchtool (line 167)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end
CONN v.17.b
SPM12 + DEM FieldMap MEEGtools
Matlab v.2017a
storage: 56531.9Gb available
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Graph results

March 27, 2017, 12:36 pm
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Dear Conn Users,

I have been using CONN for the last couple of months for applying graph analysis on subject dataset.

I was wondering if anyone had a clear definition in relation to the circular graph, with connections between different regions, that is displayed in the 'results explorer' window.

I have attached a sample of the display window.

Thank you for all the help.
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How to describe the threshold of the result

March 27, 2017, 7:24 pm
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Hi all,

I have performed the seed-to-voxel FC analysis by CONN 17a recently. I have attached the result. I want to confirm whether the threhold I described was corrected and included all the informatin it should have. It goes as "Results were thresholded at voxel level p < 0.001 (uncorrected) and at cluster level p < 0.05 (FDR corrected)". If I'm wrong what it should be?

Based on the threshold I decribed above, the reviewer said that it should be described as "Results were thresholded at voxel level p<.001 and then corrected for whole-brain comparisons by False Discovery Rate (FDR) to q<.05" and asked "Was there then also a small cluster-size threshold applied, in addition to FDR? ". Actuall, it was the cluster-level FDR correcteion not the voxel-level correction.  Does the cluster-level FDR correction should set a cluster-szie based on the voxel-level p < 0.001 uncorrected and how to do that in CONN?  Does the default cluster-size of the p < 0.001 uncorrected at voxel level is zero?  I am confused a little bit.  Any comments are greatlly appreciated. Thank you.

Best, Xiuqin
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error during functional normalization

March 27, 2017, 8:05 pm
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Dear Alfonso,

I have been using output that has been pre-cleaned in FSL (using FIX). I have removed motion correction, slice timing correction and smoothing from the default preprocessing as that was already done in FEAT. During the functional normalization, I get this error:

filtermeaned_func_data_clean.nii not found

Error in conn (line 805)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 119)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.17.a
SPM12 + DEM FieldMap MEEGtools suit
Matlab v.2015b
storage: 4126.9Gb available
Warning: Contents.m overloaded by version in folder /Users/heidi/Documents/MATLAB/CanlabCore-master/CanlabCore/External/matlab_bgl
Warning: spm_data_read.m overloaded by version in folder /Users/heidi/Documents/MATLAB/peak_nii_nitrc_v1
Warning: spm_dctmtx.m overloaded by version in folder /Users/heidi/Documents/MATLAB/CanlabCore-master/CanlabCore/OptimizeDesign11/borrowed_from_spm
Warning: spm_hrf.m overloaded by version in folder /Users/heidi/Documents/MATLAB/CanlabCore-master/CanlabCore/OptimizeDesign11/borrowed_from_spm

Apparently, it cannot find the mean functional volume. How should I solve this?
Thanks
Heidi
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Definition on graph theory(statistics)

March 27, 2017, 11:58 pm
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Dear expert.
 
When doing two-sample t-test in graph thoery,
statistical values were delicered such as beta, T and dof.
What beta and dof does it mean?
i know the beta value is the value from the regression analysis.
i do not know why the beta value appears in the t-test.
And i do not know why dof values comes out differently in each ROI (not whole network)
When I ran the t-test with 52 samples(group A=25, group B=27),
The dof value of the whole network is 50.
However, the dof value of ROI in the row below are 42, 46.. and so on.
Are ROI below the whole network not the result of t-test?
Additionally, what determines the node size and edge thickness in 3D image of graph theory?
(ex) edge thickness of 3D image reflects T value)
 
thank you!
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FDR correction only within a mask

March 28, 2017, 2:30 am
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Hi everybody and Alfonso,

I was wondering if there is a way of performing the FDR correction for a seed-to-voxels analysis only within a certain mask.

I want to observe if there are age-related changes in connectivity with seed A, but only for those voxel that show higher connectivity for seed A relative to seed B. I thought that I would calculate the seed-to-voxel connectivity contrast seed A > seed B and then use the result of this contrast as a mask for the age-related analysis. However, now I realize that I can not provide a mask in the seed-to-voxel tab in order to limit the analysis.
If i use the spm-style tab I can only calculate FWE correction or use SVC, that I think to understand is a little frown upon these days.

Any suggestion ?


Alain
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Recursive file function+vectors (Basic Qs)

March 28, 2017, 5:30 am
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Hello,

I am familiarizing myself with the toolbox, and I have a few questions I have not yet been able to answer:

1. How can I upload different condition vectors for different subjects?
2. How should I use the "Find" recursive option to read in same-type files for various subjects (and do I have to order my subject directories all in the same manner)? Also, more importantly, do I simply select all subjects to take care of the search for my whole set, rather than manually for each?
3. How can I include motion and conditions (and other not-so-straightforward covariates & parameters) in the 1st-level covariates?

I am currently unable to use the toolbox, so I cannot experiment and figure out some of the easier questions. Until the issue is resolved, any help and advice you may provide will very beneficial to me in the short term. Thanks very much.

~AYK
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Display results Volume Display

March 28, 2017, 2:37 pm
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Hello, 

I am currently doing a seed to voxel analysis in Conn.  I have been displaying all my results by using the volume display from the Conn results screen.  I have been doing this for all my previous results and everything appears to be going fine.  However, one significant voxel appears to be outside of the brain when shown in display view.  I was wondering if anyone might have an explanation as to why.  Can this be fixed?  I have attached the output for a voxel in the superior frontal gyrus.  Is this a real result?  If not, how in the word do I report it as such?  

Thanks again CONN users.  I would be lost without your help!  

Jennifer
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Remove volumes from functional images

March 28, 2017, 4:06 pm
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Hi everyone,

Does any of you have some code to remove specific volumes from functional images? Like removing the following volumes: [1:3 43:58 121:142].

Thanks a lot in advance,

Eric
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2*3 ANOVA Conn help

March 29, 2017, 7:11 am
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Hello Conn experts,

I am defining a 'reward network' at rest (using coordinates from meta-analysis.) (resting state data)

I have a 2*2*2 ANOVA: one within factor (drug – placebo/drug); 2 between factors (group – depression/healthy) (drug order – 1-2/2-1)
I am interested in:
1. Effect of drug
2. Effect of depression
3. Drug*depression interaction
For.....
1. measures of efficiency and centrality within the reward network 
2. for hubs (i.e. how connected the ventral striatum is to all the other ROIS in the network, which involves summing the absolute values of all VS-ROI correlations)

• Do you have step by step instructions of how I can set up this ANOVA in Conn
- Do you think it will be easiest to extract ROI-ROI correlation values and then do the 2*2*2 ANOVA in SPSS as opposed to setting up the 2*2*2 ANOVA in Conn?


Thank you for your help.

Selina
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problems with batch processing

March 29, 2017, 8:25 am
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Dear all,

I want to preprocess my data using batch preprocessing. This is my batch-file:[quote]clear BATCH;
Batch.New.RT=2;
Batch.New.sliceorder=[1:2:31,2:2:32];
Batch.New.FWHM=6;
Batch.New.VOX=2;BATCH.filename='/data_august/sascha/BEST/conn_best.mat';
Batch.Setup.isnew=1;
Batch.Setup.RT=2;
Batch.Setup.nsubjects=2;BATCH.New.steps={'realignment','slicetiming','coregistration','segmentation','normalization','smoothing','initialization'};
BATCH.New.functionals{1}{1}='/data_august/sascha/BEST/BEST-BN-001/rsfMRI/rsfMRI.nii';
BATCH.New.structurals{1}='/data_august/sascha/BEST/BEST-BN-001/ANAT/T1.nii';
BATCH.New.functionals{2}{1}='/data_august/sascha/BEST/BEST-BN-002/rsfMRI/rsfMRI.nii';
BATCH.New.structurals{2}='/data_august/sascha/BEST/BEST-BN-002/ANAT/T1.nii';
Batch.Preprocessing.filter=[.008 0.09];
Batch.Preprocessing.done=1;
conn_batch(BATCH);[/quote]When I execute it, conn asks me to manually enter the slice acquisition order for each subject. Why? I specified the slice order in the third line.

Thanks!

Best,
Sascha

EDIT: Nevermind everyone, I figured it out myself: Of course I have to spell out "BATCH" in all caps (instead of Batch.Setup it has to be BATCH.Setup etc.)
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realignment&unwarp

March 30, 2017, 3:01 am
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Hello,

I would like to preprocess my data using realignment&unwarp. How do I implement this in my BATCH script?

Does[quote]BATCH.New.steps={...,'realignment','unwarp',...};[/quote]do the trick?

Best,
Sascha

EDIT: Nevermind, I found it out myself. I was confused by the batch-manual which is not very exha8ustive, but the batch-description inside the matlab function answered the questions I had.
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RE: Denoising r-value "show all" function gone?

March 30, 2017, 4:43 am
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[color=#000000]Hello![/color]
[color=#000000]I cannot see the r-value distribution / Bold explained variance, also after adding the attached .mat file, and could not find the 'QA plots' button. What is the 'QA plots' button?[/color]

Thanks you so much for the help!

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

[color=#000000]Thanks for reporting this and sorry there was a GUI bug that made that change a bit less obvious! [/color]The r-value distribution plots are now offered as part of the Quality Assurance plots. In the [i]Denoising[/i] tab simply clicking on the 'QA plots' button will generate and display those same r-value distribution plots as the ones you used to get in previous CONN versions using the 'show all' button (you now have also some additional functionality like being able to display those distributions just for a few subjects/sessions and/or storing different versions of those plots, as well as of course having also access to several additional QA plots meant to visually check the quality of your data). Please use the attached patch to fix this issue and let me know if you run into any issues (this patch is for release 17b, simply copy this file to the conn distribution folder overwriting the file with the same name there). 

Best
Alfonso


[i]Originally posted by Jeff Browndyke:[/i][quote]I noticed that in CONN 17.b that the r-value distribution "show all" function under the denoising tab is no longer present in the GUI.  Is there a hidden way to get these back?  I have found these r-value distribution maps to be helpful in ferreting out additional potential outlier scans after denoising.

Warm regards,
Jeff[/quote][/quote]
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DYN-ICA circuits

March 30, 2017, 7:37 am
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Hello, 
I'm trying Dyn-ICA circuits, getting following error during the first level analysis. 
Error using save
Cannot create 'dyn_Base.mat' because
.../conn_Denoising/results/firstlevel/DYN_01' does not exist.

Can I get some solution for this error? 
Thank you
Hanadi
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RE: How to describe the threshold of the result

March 30, 2017, 1:12 pm
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[color=#000000]Hi Xiuqin,[/color]

[color=#000000]Your description is perfectly fine, the reviewer probably just wants you to be a bit more precise. Simply refer to "K.J. Friston, K.J. Worsley R.S.J. Frackowiak, J.C. Mazziotta, and A.C. Evans. Assessing the significance of focal activations using their spatial extent. Human Brain Mapping, 1:214-220, 1994" for additional information, and perhaps clarify that your voxel-level p<.001 threshold is the "height" or "cluster-defining" threshold, and that among the resulting suprathreshold clusters you are only reporting as significant those with cluster-extent FDR-corrected p-values below a p<.05 threshold (this is a multiple-comparisons correction acoss the entire brain that controls the chance of false discoveries among your reported clusters below the prescribed 5% rate). [/color]

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

[i]Originally posted by xiuqin jia:[/i][quote]Hi all,

I have performed the seed-to-voxel FC analysis by CONN 17a recently. I have attached the result. I want to confirm whether the threhold I described was corrected and included all the informatin it should have. It goes as "Results were thresholded at voxel level p < 0.001 (uncorrected) and at cluster level p < 0.05 (FDR corrected)". If I'm wrong what it should be?

Based on the threshold I decribed above, the reviewer said that it should be described as "Results were thresholded at voxel level p<.001 and then corrected for whole-brain comparisons by False Discovery Rate (FDR) to q<.05" and asked "Was there then also a small cluster-size threshold applied, in addition to FDR? ". Actuall, it was the cluster-level FDR correcteion not the voxel-level correction.  Does the cluster-level FDR correction should set a cluster-szie based on the voxel-level p < 0.001 uncorrected and how to do that in CONN?  Does the default cluster-size of the p < 0.001 uncorrected at voxel level is zero?  I am confused a little bit.  Any comments are greatlly appreciated. Thank you.

Best, Xiuqin[/quote]
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