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RE: How to use mask on CONN

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Hi all,

Any luck on using masks in CONN? I've found one post on the forum which mentioned editing the TPM.nii file, but I am unsure how to do so: https://www.nitrc.org/forum/message.php?msg_id=26112

Thanks,

Matthew

RE: first level threshold

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Hi all,

Alfonso, you mentioned needing to do something more complex in order to compare results from a single subject across multiple conditions or sessions. Unfortunately this is exactly what I would like to accomplish. Has anyone had success computing effects across sessions with one subject?

Thanks,
Matthew

RE: ICC and Global Correlation Differences

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Hi Folks,
I'm bumping this year-old message from Maria to the top to see if anyone has any thoughts. I have the same issue and wondering if anyone who understands the math better can help illuminate under what conditions these two measures of centrality would get such different results. I don't want to choose a centrality measure based on the results, so wondering if there is some sort of a priori reason to pick one measure over the other.
Thanks,
Emily

RE: Preprocessing failure, problem writing header

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I revive this thread because I meet the same error. 
I'm working on a SLURM HPC. Up to now I had no issue at all. 
The msg I get is:[quote]Done functional Direct Segmentation & Normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)
Importing results to CONN project. Please wait...
saved /gpfs/ysm/project/oad4/connRuns/subject1253.0001190123131636073.dmat
Preparing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label). Please wait...
Performing functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label). Please wait...
Done functional Label current functional files as part of list of Secondary Datasets ("mni-space data" label)
Importing results to CONN project. Please wait...
saved /gpfs/ysm/project/oad4/connRuns/subject1253.0001190123131636073.dmat
Preparing structural Center to (0,0,0) coordinates (translation). Please wait...
Performing structural Center to (0,0,0) coordinates (translation). Please wait...
Done structural Center to (0,0,0) coordinates (translation)
Importing results to CONN project. Please wait...
Structural centering translation x/y/z = [1.03630065917969 -22.6367492675781 -0.917098999023438] (Subject 1)
Structural centering translation x/y/z = [1.58317565917969 -22.5089416503906 -2.84763336181641] (Subject 1)
Error: Permission denied
There was a problem writing to the header of
"/gpfs/ysm/home/oad4/project/PTSD_KPE/Converted/kpe1253/kpe1253_scan2_pb1164_harpaz-rotem/MPRAGE/ckpe1253_t1_Sag_3D_MPRAGE.nii"
/gpfs/ysm/project/oad4/connRuns/subject1253.qlog/190123131636073/node.0001190123131636073.sh error
_NODE END_[/quote]

Denoising "Setup Error"

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Hi,

I keep running into an error at the Denoising step. After I preprocess the data, make sure all the ROIs, covariates, and conditions are set up and hit done, it finishes importing all of that data, but will not let me go onto denoising saying in the GUI,

"Not ready to start Denoising step. Please complete the Setup step first (fill any required information and press "Done" in the Setup tab)"

I've checked the setup many times and don't think I'm missing anything. I've never encountered this problem before and have even tried re running a few subjects from scratch, but I am still getting the error. How can I bypass this?

Thanks,
Hanna

How to use 'age' as a covariate

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Hi Alfonso, 

I am a little confused about setting up age as a covariate in analyses. 

For example, if I have a 2 group comparison (treatment, control) on some outcome and I want to control for age, I can enter [1 -1 0], and this controls for age overall (effectively like a covariate/control variable in regression)?

If I wanted to control for age and any age-by-group interactions, I would create separate variables for each group, with ages entered for the subjects in that group, and zeros for the rest e.g. for groups of n=5: treatment_age  35 45 55 61 78 0 0 0 0 0   control_age 0 0 0 0 0 21 33 44 55 43
And then enter a contrast of [1 -1 0 0], wth the zeroes reflecting the treatment_age and control_age groups.

However, if I wanted to control for the effect of age overall AND the potential age-by-group interaction would I need to enter age, treatment_age, and control_age into the model i.e. [1 -1 0 0 0]? Or does entering the age-by-group interaction also control for age overall and this would be redundant, and I should just use [1 -1 0 0]. 

Finally, would this controlling of age-by-group be considered a standard approach (e.g. for research looking at ageing and dementia), or just included one overall age control variable be sufficient i.e. the [1 -1 0] model?

Many thanks, 
Andrew

How to obtain voxel to voxel matrix and graph for each subject ?

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Dear experts, 

I'm doing both ROI analysis and voxel to voxel analysis for two groups of subjects (patients vs. control). 

When I ran local correlation, I obtained activation map per group. Is there a way to generate local correlation map for each subject? In addition, is there a way to extract some kind of voxel to voxel matrix per subject? 

In graph theory under ROI analysis, I was able to export a spreadsheet for global efficiency/local efficiency/etc organized by each subject. Is there any way to extract a data summary / spreadsheet/ matrix like that to show connectivity values at voxel level or ROI level for each subject?

Thank you so much! 

Luie

RE: Coding Main Effect/Interactions for Symptom Covariates of Multiple Groups

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Thank you so much once again for your detailed feedback Alfonso. It is really appreciated!!

Using Conn for ASL preprocessing and MVPA

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Dear Conn Experts:

I have resting-state ASL data and would like to perform MVPA on them using CONN. I read a couple of recent papers that used CONN to run MVPA on ASL data. However they first preprocessed the ASL data in different SPM extension software and then transferred the preprocessed data to CONN for the MVPA analysis.

My question is: Is it possible to use CONN software to preprocess ASL and then continue with MVPA? This will eliminates transfer of preprocessed data from different software to CONN for MVPA.  

Any one has an experience with it? And if so, what parameters I need to change in CONN to run preprocessing for ASL.

Thank you!

Question on order of subjects/conditions in network measures output

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Dear experts,

I have run an analysis with 39 subjects and 4 conditions. In the output files of the graph measures (global efficiency, etc.), I obtain 156 rows, which correspond to the 39*4 subjects. However, I can't find the description of each row. My question is how should I interpret the rows: row 1 = Subj1 condition1, row 2 = Subj1 condition2, etc., or row 1 = Subj1 condition1, row 2 = Subj2 condition1, etc.?

Thank you!
Rebecca

RE: Bugfix: dynamic connectivity with custom rois

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Hi,

My query is not related to your bugfix, but to your custom ROIs and how they were defined? I am starting a project looking a functional connectivity between certain broadmann areas and prefer to use an atlas to define these. How did you define these custom ROIs?

Thanks,

Zoe

Atlas with Broadmann's Areas

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Hi All,

I'm starting a new study looking at functional connectivity between certain broadmann areas, however, these areas aren't well defined in the standard atlas provided with conn. I am wondering if anyone has any suggestions for an atlas that has these areas defined?

RE: Multi-session pre-post design QC_ValidScans for each separate session

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Sorry for the slow followup. Worked out great, thank you!

REX gui problem - manually selecting BETA images

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Dear Conn users,

I am using the conn18b standalone version.
When I use the REX gui, I am sometimes asked to select the BETA images for all subjects/conditions as Sources manually, as the program cannot select the images itself.
For example, in the case of an Intrinsic connectivity contrast analysis, I need to add the BETA_subject001_Condition001_Measure001_Component001.nii for all subjects and conditions manually. I found those images in the results/firstlevel/V2V/ directory, but of course this is very time consuming.
Other times it just works perfectly fine and the source images are selected automatically.

Anyone has an idea what could cause the problem?

Thanks in advance.

Best,
Steven

One patient vs Group Seed-based analyses, accounting for the patient's lesion

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Hi all,


I am going to perform a whole brain FC seed-based analysis comparing one patient vs a group of twenty-three controls. Patient presents a huge lesion and I wanted to account for it in the analyses (maybe as suggested in https://journals.sagepub.com/doi/abs/10.1177/0271678X17709198)


At which level of the analysis should I account for the lesion mask (preprocessing, first-level analyses) and how can I practically implement that in CONN?

Thank you in advance for your kind support,

Gianluca

Dynamic Connectivity Interpretation

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Hi there,
I was wondering if you could explain the Dyn ICA output for spatial and temporal properties. I assume the spatial properties are a representation of spatially connected regions throughout the scan? But is each dynamic factor (circuit/state?) a representation of several pairs of regions connected through time? I am running an analysis where I am correlating a behavioral variable (answers on a questionnaire) with these temporal factors, but I am unsure of how to interpret the results. For example, the attached spatial component is positively correlated with my behavioral measurement. Does it mean that this entire "state" should be considered as correlated, or just the pairs of regions? Any help would be appreciated, thank you!

Preprocessing and co-registering ROI to subject space

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Hi Alfonso, 

I want to do an analysis with various ROIs in CONN. I picked the ROIs using WFU picks atlas. I am in the first preprocessing steps and I have an anatomical and functional for a single subject and the ROIs selected from WFUpicks. Could you please let me know what the next steps are for preprocessing and coregistering my ROIs to the subject space with CONN?

Thanks in advance for any advice!

Realign and Unwarp Flipping part of the bold files?

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Hi All,

I'm running into a strange error. I recently decided to reprocess some of the data (180 volume bold files). I used orientLAS and 3dretroicor and then loaded the files into CONN where I ran functional Realign and Unwarp, functional center to (0,0,0) coordinates, and functional outlier detection. The resulting files (with the u* prefix) have the first volume normal, but volumes 2 - 180 are AP flipped. 

Any suggestions? I could probably just flip the last 179 volumes, but I'm concerned about why this is happening and the implications it has on the preprocessing. 

Best,
- Harris

Interaction between continuous variables

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Hi Conn experts,
thank you for this amazing software and for listening to the growing community needs and questions. 
I have a beginner's doubt regarding interactions effects between two continuous variables.

This is my study design (simplified with just 8 subjects):

All_subjects<span style="white-space: pre;"> </span>[1 1 1 1 1 1 1 1]
Age_covariate<span style="white-space: pre;"> </span>[45 50 54 49 47 42 43 52]
Scale_A<span style="white-space: pre;"> </span>[29 15 18 30 27 16 21 27]
Scale_B<span style="white-space: pre;"> </span>[8 9 12 6 6 5 7 3]

Scale_A and Scale_B are the scores in two different behavioural scales

1) I would like to see the effects of interaction of Scale_A and Scale_B on functional connectivity, and use age as a covariate of no interest. How should I set my contrast? [0 0 1 0; 0 0 0 1]? or maybe [0 0 1 -1; 0 0 -1 1]? or just [0 0 1 -1] and [0 0 -1 1] separately?

2) If the interaction is significant, then would it be ok to explore the relationship between the two variables by splitting the subjects in two groups (e.g. Scale_A high score; Scale_A low score) and then comparing the effect of Scale_B between them?

Many thanks for your kind help and support,
Davide

Error while doing seed-to-voxel analysis

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Hello, I am doing a seed-to-voxel analysis for 2 seeds and I am getting the following error message at the 2nd level analysis. Can someone let me know what I need to do to correct this error? Thank you so much!

[i]Cell contents reference from a non-cell array object.[/i]

[i]Error in conn_process (line 3888)[/i]
[i]if isdir(fullfile(filepathresults2,foldername_back{nfolderbak})), foldername=foldername_back{nfolderbak}; break; end % backwards-compatibility with existing results[/i]
[i]Error in conn_process (line 52)[/i]
[i]case 'results_voxel', [varargout{1:nargout}]=conn_process(16,varargin{:});[/i]
[i]Error in conn (line 8594)[/i]
[i]conn_process('results_voxel','readsingle','seed-to-voxel');[/i]
[i]Error in conn_menumanager (line 120)[/i]
[i]feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});[/i]
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