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Masking out the cerebellum?

May 4, 2021, 9:14 pm
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Hi,

I have preprocessed 64 subjects using the CONN default preprocessing pipeline. 
The lower part of cerebellum has been cut off in the QA normalisation with MNI boundary. (see attached)
When I checked each subject, it seems like the areas were not obtained during the scan.

Should I mask this part out? or leaving as it is shouldn't be an issue? 
If I need to mask this out, what steps should I follow to do this properly?

Any suggestions would be much appreciated.

Kind Regards,

Julia Yang
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RE: Error message - Reference to non-existent field 'X1'.

May 5, 2021, 12:08 am
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Hi Alfonso,

Thanks a lot for your response!

When I checked the logfile.txt, I found Step 4/7 of Setup pipeline was skipped. Hence, I am wondering the possible issue is that the seed-to-voxel analysis was cancelled at the Setup.Options. When I chose the seed-to-voxel at the Setup.Options, there is no any error.

Thanks!

Best,
Gucy
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Realignment & Unwarping fails for some subjects

May 5, 2021, 1:35 am
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Hi Alfonso and everyone,


I am having a problem with the Realignment and Unwarping preprocessing step when fieldmaps are available.

To keep it short, in some subjects, this step fails and produces bad realignments... In fact for some subjects, it's quite bad, with the upper part of the brain being completely cut (see attached file, top realigned, bottom original). Once I re-run the preprocessing, without actually changing anything (from the same starting files), it can produce different results, and in fact work properly...

I don't know if this is a known problem with this particular step. Should we always check and repeat the step if it fails?

Cheers,
Herberto

More details:
I have 20 subjects, over five sessions. They do two very different tasks, and pre and post resting-state (the three processed separately, same structural always, but fieldmaps for each day).
Interestingly, the "fail" in the realignment doesn't always happen for the same subjects. For example task 1, initially it produced bad results for subjects, 2, 3, 8, and 10. Whereas for task 2, for 5 and 15.... Moreover, I already confirmed that repeating this, from the beginning for subjects 5 and 15, worked normally (as in Realign&unwarp produced good results).
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How to use "QA_InvalidScans" as covariate in second-level analysis

May 5, 2021, 4:38 am
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Dear CONN experts,

I am using CONN version 20.b and have read in the manual that it is possible to use "QA_InvalidScans" as a covariate in the second-level analysis. Unfortunately, it is not clear to me how to do this. How can I add this covariate to the second-level analysis ? It does not appear under my manually entered covariates (age and sex).

I would be grateful for any help on how to do this.

Thanks in advance.

Katja
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Denoising doubt

May 5, 2021, 9:53 am
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Hello Alfonso.

I am currently working with a sample of stroke patients. Reviewing the literature I have seen a method to regress the lesion-linked signal (https://doi.org/10.1016/j.nicl.2017.10.027). My intention is to do the preprocessing and denoising steps using CONN, then regress the lesion-linked signal through the ICA method (to identify the lesion-linked components) and the FSL command fsl_regfilt (to regress those components). Consequently, I need to know which are the outputs resulting from the denoising given by CONN to perform, on them, the regression of the signal explained by the lesion. In other forum posts you point out that these outputs can be found in the conn*/results/preprocessing/ folder with the name "niftiDATA_Subject#_Condition#.nii", but I have not been able to find them (I am using version 19c).

Thank you very much for your implication and for this fantastic toolbox. Any advice will be very appreciated

Best regards.


Benxa.
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Scrubbing / Denoising Issue

May 5, 2021, 10:18 am
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Hi Everyone,

I am conducting my second project with the CONN toolbox. I am working with a cross-sectional group (n = 105; 1 MRI session) of older adults with MCI. For context, I am using version 20.b of CONN and data was imported after being pre-processed in fMRIPRep. 

I have reached the Denoising stage. My scrubbing parameters are (I THINK) quite high (229p). I have also reviewed the QC-FC associations via the QA plots and see that Mean GS change, Mean Motion, and valid scans % match with NH DECREASE after the current denoising stagey. My questions are as follows: 

1) How concerning is this DECREASE? As per Alfonso's handbook, > or = 95% is considered the "goal" (https://www.researchgate.net/publication/339460691_Handbook_of_functional_connectivity_Magnetic_Resonance_Imaging_methods_in_CONN)

2) A select # of participants are quite troublesome (i.e., scrubbing over half the volumes). Is there a way to exclude/ignore a single participant at the denoising level to evaluate its impact on the overall QA plots

3) As a follow-up to #2, I recognize there is no gold-standard for denoising but was wondering if there is a "guideline" on how many volumes should be scrubbed before a participant is removed entirely. It was briefly discussed in this thread: https://www.nitrc.org/forum/forum.php?thread_id=6528&forum_id=1144

Thank you in advance.

Cheers,

Nick
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Denoising step disrupts the image with diagonal lines

May 6, 2021, 4:51 am
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Hey Alfonso!

I would love for your help. I am currently running pre-processing with the steps bellow, and outputting the denoising image (the previous step was realignment).
I did this for previous cohorts and the result was excellent, but now on a new cohort I get these diagonal lines on all my deonising.nii outputs! what can be the reason?

Thank you so much! 
Inbar
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QA information for multiple sessions

May 6, 2021, 9:30 am
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Hi,

How can I obtain QA plots and images to check registration and normalization of functional and anats for multiple sessions?

I am only able to create and view the plots for my session 1 data.

Best,
Omar
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MVPA Contrast Stats

May 6, 2021, 1:29 pm
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Hi Alfonso, 

I hope this finds you well. 

What is going on "behind-the-scenes" in my MVPA voxel-to-voxel analysis when I set: 

Subject effects - "All Subjects," "Age," "Sex," "MeanMotion," "Group," "Effect of Drug"
Between-subjects contrast - [0 0 0 0 0 1] Effect of Drug 
Conditions - "Pre-Intervention" and "Post-Intervention"
Between-conditions contrast - [-1 1] Difference between post>pre 
10 MPVA components that explain ~80% of the variance 

The new version of CONN says "Does the correlation between connectivity and Effect of Drug differ from zero after controlling for Sex, Age, MeanMotion, and Group?"

Is CONN creating a change score for between conditions and doing a simple correlation?
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RE: Cluster computing - SLURM jobmanager test fails

May 6, 2021, 2:38 pm
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Hi Alfonso, 

You are correct that the test does not progress, or show the second line 'Waiting for grid/cluster jobs to finish'.

As for the suggested tests:

>> conn_jobmanager options cmd_submit
sbatch --job-name=conntest --qos=blanca-ics

** so this is missing the --error and --output you showed in your example.

>> conn_jobmanager options cmd_submitoptions
-t 12:00:00 --mem=8Gb

>>conn_jobmanager options cmd_submitoptions_infile
** empty

Also, I did double check sbatch is not aliased and points to /usr/bin/sbatch.


Thanks again!
Amy
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RE: ROI-to-ROI Connectivity Line Color / Ball Mismatch?

May 7, 2021, 9:09 am
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Thanks, Alfonso.  This helped for the 2D visualization, but the issue still persists for the "display 3D" option.  

Is there code that can be altered to make the display 3D also reflect Allsubjects and Allconditions for this type of regression model?

Warm regards,
Jeff
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RE: Graph theory in conn

May 9, 2021, 9:15 am
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Hi Alfonso
Can I add my own correlation matrices to the toolbox for graph analysis?
Thanks
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RE: FC analysis of already preprocessed data

May 9, 2021, 10:04 am
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Hello Maximilian,

Were you able to solve this issue? I'm having the same problema and not finding any answers! How did you work around this?

Thanks in advance,
Miguel
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Dynamic connectivity Error

May 10, 2021, 9:19 am
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Hello!

I am trying to run a dynamic connectivity analysis, however, when selecting the first level dyn-ica tab in conn, nothing populates and I receive the following error:

Index exceeds the number of array elements (0).
Error in conn (line 7428)
for n=1:3, set(CONN_h.menus.m_analyses_00{8+n},'value',CONN_x.dynAnalyses(CONN_x.dynAnalysis).output(n)); end
Error in conn_menumanager (line 134)
feval(CONN_MM.MENU{n0}.callback2{n1}{1},CONN_MM.MENU{n0}.callback2{n1}{2:end});
CONN19.b
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2019b
project: CONN20.b
storage: 627574.6Gb available

spm @ /scratch/user/tmaldonado1821/apps/spm12
conn @ /scratch/user/tmaldonado1821/apps/conn


I preprocessed the data in FSL, I have motion and scrubbing parameters, and everything seemed to run fine during setup and denoising (i.e. I cannot find any errors). Does anyone have any idea on why I am getting this error, and solutions to fix it?

Thanks,
Ted
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Potentially Corrupted File

May 10, 2021, 12:12 pm
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Hello,

I recently added new ROIs to an already existing project, and have been trying to process all subjects through first-level for those new ROIs so that I may extract RRC matrices. When I get to first-level, four subject (318, 320, 322 and 326 out of 1084, perhaps it is informative that they are so close together) had errors and I was unable to get through first-level. I stopped the job, and tried to go back and denoise those 4 subjects again. That worked fine, but now when I try to merge the denoised jobs, it crashes when I get to subject 318. Here is the error:

Error using load
Unable to read MAT-file /project2/skeedy/BSNIP2_2020/BSNIP2_2020_conn.0318210430161424709.dmat. File might be corrupt.
Error in conn_merge (line 46)
temp=load(deblank(filenames{n1a}),'CONN_x','-mat');
Error in conn_merge (line 30)
value = conn_merge(char(filenames(nbatch:min(numel(filenames),nbatch+MAXMEM-1))));
Error in conn_projectmanager (line 125)
conn_merge(allfiles);
Error in conn (line 850)
conn_projectmanager('updateproject',fromgui);
Error in conn_jobmanager (line 357)
conn('load',filename);
Error in conn (line 1093)
conn_jobmanager;
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});

Now I am unable to get through merging even of denoising, so I always have a pending job dialogue and I cannot move forward. We were hoping to exclude those four subjects from the analysis, but I need to finish first-level and merge that with the project in order to extract RRC matrices, which I am unable to do if I can't merge. 

Do you have any ideas as to why these 4 subjects may have caused errors in first-level, and why they are now causing crashes when I attempt to merge denoising results? In previous analyses with this dataset we had no problems with these subjects.

Thank you,
Mikey
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RE: Scrubbing / Denoising Issue

May 11, 2021, 5:08 pm
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For anyone interested, I figured this out: 

1) I exported second level covariates (i.e., max motion, mean motion, etc.) to SPSS and identified extreme outliers via boxplots 
2) I did the same thing with MRIQC's data for DVARS and FD 
3) Cross-referenced the list to confirm the same participants were (more or less) listed in both 
4) Excluded participants in the second level covariate tab via the same we do it for the second-level analysis (*facepalm*) using NaN
5) Reviewed QA-plots and saw a significant improvement (i.e., almost all >95%)

Cheers, 

Nick
[i]Originally posted by Nick Bray:[/i][quote]Hi Everyone,

I am conducting my second project with the CONN toolbox. I am working with a cross-sectional group (n = 105; 1 MRI session) of older adults with MCI. For context, I am using version 20.b of CONN and data was imported after being pre-processed in fMRIPRep. 

I have reached the Denoising stage. My scrubbing parameters are (I THINK) quite high (229p). I have also reviewed the QC-FC associations via the QA plots and see that Mean GS change, Mean Motion, and valid scans % match with NH DECREASE after the current denoising stagey. My questions are as follows: 

1) How concerning is this DECREASE? As per Alfonso's handbook, > or = 95% is considered the "goal" (https://www.researchgate.net/publication/339460691_Handbook_of_functional_connectivity_Magnetic_Resonance_Imaging_methods_in_CONN)

2) A select # of participants are quite troublesome (i.e., scrubbing over half the volumes). Is there a way to exclude/ignore a single participant at the denoising level to evaluate its impact on the overall QA plots

3) As a follow-up to #2, I recognize there is no gold-standard for denoising but was wondering if there is a "guideline" on how many volumes should be scrubbed before a participant is removed entirely. It was briefly discussed in this thread: https://www.nitrc.org/forum/forum.php?thread_id=6528&forum_id=1144

Thank you in advance.

Cheers,

Nick[/quote]
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Problem using CONN: single group rsfMRI & 2*2 within-subjects behavioural measures

May 11, 2021, 7:00 pm
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Dear CONN experts,

Hi. I am a beginner in this field. And I encountered a problem.

I have one group subjects who completed rsfMRI and behavioural experiment separately. Behavioural experiment included 60 trials with two conditions (30/30) and two stimuli (30/30). And I am trying to find if there is a significant correlation between the functional connectivity and the behavioural performance.

1) Importing connectivity values into other statistical software (e.g., SPSS). Then, calculating the correlation between  the values and behavioural measures.

2) Importing behavioural measures into CONN, but I have no idea how to import... (conditions?)

Do you have any suggestion? Thanks in advance.

Cheers,
Lucas
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Failed merging after parallel jobs - can't visualise results

May 12, 2021, 12:36 am
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Dear Conn experts,

I tried running 6 parallel jobs for preprocessing pipeline. It worked for 4 of them, and 2 failed. I clicked on the restart button for the 2 failed jobs and they successfully completed. Now, in the job history I can see that the 6 jobs are finished, but on the project the results don't appear. I can only visualise the results for the subjects treated by the 2 nodes which last finished. I think the problem might be caused by a failed merging attempt. I tried running "conn_process(9)" from the Matlab command window, and this message show up :

"Error using conn_process (line 2019)
Some conditions have not been processed yet. Re-run previous step"

I also tried renaming the info.mat file as I saw in a previous post it could fix the issue, but it didn't work either.

I would much appreciate some help !

For your knowledge, I'm using the CONN version 20b.

Thank you!
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how to change the reference brain for display?

May 12, 2021, 9:16 am
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Hi!

Under ROI second level main results (ring or matriix) display, the results are automatically overlaid on a reference brain/glassbrain (pic attached), which I would like to switch for another image, like I am able to do so within the Glass display/conn 3d display/Surfaces/User defined surface. I was trying to find it in the code where this reference brain image is specified but could not find it on my own. Coul you point me in the right direction, please? (conn_20b)

Thanks in advance!
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Error in conn_slice_display

May 12, 2021, 12:08 pm
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Hi,

first time conn user here. this is the Error I received when trying to load slice display for both anat and func .nii files. appreciate your help.

ERROR DESCRIPTION:

Unrecognized field name "Vrange".
Error in conn_slice_display/conn_slice_display_refresh (line 919)
if state.Vrange(1)==0, tactthr_pos=tactthr; tactthr_neg=inf;
Error in conn_slice_display (line 466)
conn_slice_display_refresh([],[],'init');
Error in conn (line 1835)
if val==2, fh=conn_slice_display([],char(temp),[],[],sprintf('dataset %d',nset)); fh('background',[0 0 0]);
CONN20.a
SPM12 + DAiSS DEM FieldMap MEEGtools
Matlab v.2021a
project: CONN20.a
storage: 201.3Gb available
spm @ /Users/xxxx/Documents/spm12
conn @ /Users/xxxx/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/CONN
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