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RE: scrubbing in setup but not denoising

April 25, 2016, 12:47 pm
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[color=#000000]Hi Alain,[/color]

[color=#000000]Not sure about that, have you tried re-running the setup step (in the [i]Setup [/i]tab click 'Done' and select the 'do not overwrite' option to avoid repeating already-computed results)? That should make sure that any changes in the [i]Setup[/i] tab are propragated to the [i]Denoising[/i] tab. [/color]

[color=#000000]Best[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Federico Nemmi:[/i][quote]Hi everybody!
I am experiencing a strange behavior with conn (14p).
In particular, I get the rp parameters and the artifact removal for all subjects. For all but two subjects the artifact matrix is empty, and it is shown as such if i look at it in the covariates -> 1st level tab. For the two subjects with volumes that have been censored, these volumes do get visualized in the same tab. However, when I got to the denoising tab, these two subjects do not have their associated scrubbing parameters, that are empty instead.
What could be happening here ?

Thanks in advance

Alain[/quote]
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Surface Based Analysis - Setup Error (??)

April 25, 2016, 7:16 pm
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Hi,

I am performing surface based analyses in CONN using precomputed FreeSurfer surface files.  I wrote a batch script to set up my analysis, however when I load the .mat file in CONN and click "Done" on Setup the analysis crashes out at my 46th subject with the following message (see below).  I'm currently dealing with the problem by excluding this subject.  Does anyone have an idea of how to diagnose this problem?

Thank you,
Shady


ERROR DESCRIPTION:[quote]
Matrix dimensions must agree.
Error in conn_surf_extract (line 129)
xyz_data=conn_bsxfun(@times,alpha,xyz1')+conn_bsxfun(@times,1-alpha,xyz2');
Error in conn_create_vol (line 68)
[data,nill,nill,refinfo]=conn_surf_extract(V1(nscan),[],V0,surfacesmooth,false,false,refinfo);
Error in conn_process (line 534)
V=conn_create_vol(filename,Vsource,[],Vref,sfile,Vmask,CONN_x.Setup.analysisunits==1,CONN_x.Setup.spatialresolution==4,CONN_x.Setup.surfacesmoothing);
Error in conn_process (line 14)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 2977)
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.15.h
SPM12 + DEM FieldMap MEEGtools
Matlab v.2015b
storage: 2984.6Gb available[/quote]
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RE: Surface display questions

April 26, 2016, 1:16 am
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Hello Alfonso,

This works now, thank you. I get the exported .nii file with the results.

Back to my initial question then: Could I open the surface view and execute a Print -> Current view from the command line?
In other words, is there an easy way to call conn_mesh_display() on the exported image above that would lead to a saved .tiff file from a certain view point?

Thanks again for your help and for saving me hours of looking into the code.

Cheers,
Sami
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RE: conn_batch how to do all 1st-level analyses

April 26, 2016, 4:29 am
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Hello Alfonso,

Thank you very much for your detailed reply (and for checking my script!). Indeed, I was aware that the conn_process API might change in the future (hence why I tried to limit that by supplying analyses names instead of the sequence of experiments ids), but indeed using conn_batch is way better! I will try this, thank you very much. Maybe this should be noted in conn_batch header comment (that BATCH can be an cell array and supplied directly to conn_batch, to define multiple experiments in one batch)?
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RE: dmn seed definition rationale?

April 26, 2016, 6:12 am
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RE: need help with dynamic FC between conditions

April 26, 2016, 7:04 am
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Hello Alfonso,

Thank you very much for your reply, I will try your advice for multiple conditions (make one rest condition that includes all subjects).

About multiple groups, would the technic you describe work with current CONN version? If I understand correctly, it means I should create a new group "AllSubjects" that would include all subjects, just like we should have at least one condition including all subjects?
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Strange second level effect

April 28, 2016, 6:40 am
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Hi everybody, 
sorry for posting two thread in such little time, but there is something really bothering me.
I am after the association of certain behavioral variables with connectivity of the reading network.
I have 5 seed regions and 5 behavioral variables. The idea is that certain variables will be associated with the connectivity of certain regions but not other and vice versa.
I was looking at my second level effect seed - to - voxel and i noticed something strange: for some reason, i have some of the variables entered as Z score and some other variable entered as row score. None of the variables entered as Z score show any significant association. On the other hand, all the variables entered as raw score show strong significant association. The funny thing is that they show association with the connectivity of all my seeds (and this is already pretty unexpected) but more strikingly, the association are almost exactly overlapping to the effect that I have when I look at the "All subjects" variable. Basically, it seems that all the variables entered as raw score are associated with exactly the connectivity network of each seeds. I have attached some picture for comparison.
At the beginning I thought it was something due to the deameaning (since Z scored variable did not show this behavior), but demeaning should not affect simple correlation (that is what is going on when you test the association of a behavioral variable with the seed to voxel connectivty, as far as I understand).

Have you got any idea about what is going on here ?

Best

A.
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Error in CONN after Denoising

April 28, 2016, 10:24 am
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Hi Alfonso,

I seem to be having an issue with voxel-to-voxel analysis I'd l like to perform using gPPI.

I set up the conditions (via SPM import), functional and structurals (T1's not surfaces) without any problems, but once I get the denoising, it will run, finish, and then give me the popup stating that the denoising needs to be set up and then hit "Done" before going to the second level, with no error message or report as to what went wrong.

This has occurred across CONN versions 15h and 16a, on our computing cluster as well as my own desktop, and with SPM12 preprocessed data as well as the CONN recommended pipeline.

The switch and popup always seems to occur at step 6 of the denoising (Updating Analysis Variables).

Would you have any recommendation about what might be causing this?
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Graphic issue on Linux with X11 forwarding

April 29, 2016, 2:57 am
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Dear experts,

I'm running into an error when I ssh to a linux machine with X11 window forwarding and try to start conn (see pics)

Is there a quick workaround for this?

Thank you very much for your support

Viv
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A couple if issues: confounds, ART, MVPA stat

April 29, 2016, 4:13 am
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Dear Alfonso, dear Colleauges

During my experience with CONN a couple of problematic issues appeared and I would be grateful to hear your advice. I really apologize if the list is somewhat long...

[b]1. Denoising step[/b]: should the list of confounds, next to White Matter, CSF, realignement and scrubbing, include also separate effects of conditions (e.g. Effect of condition A pre-intervention, Effect of condition A post-intervention, Effect of condition B pre-intervention, etc.)? As I know, CONN puts them on the list sometimes by default, sometimes not, but they are to choose manually. Which consequences does it have to have them or not on the list as confound?

[b]2. Preprocessing and ART[/b]: I would like to investigate the impact of different ART parameters on results. If I am right, the preprocessing routine has no option "skip already processed steps". Can I somehow change the parameters alone based on the already preprocessed data (e.g. to run this step and smooth)? By the way, is there any golden standard for ART parameters? The quality of my data is good, however using 3SD and 1mm instead of previous liberal 9SD and 2mm made my results weaker, particularly influenced dramatically the MVPA (the only other difference was having effects of conditions on the confound list), what makes me a bit confused. The question is of course, whether the lower threshold reduced the artifacts or functionally meaningful effects.

[b]3. MVPA[/b]: Should I limit the dimensionality (default is 64) or put "inf" there? Should I keep the centrality on? I don't exactly understand which consequences it has. Moreover, I try to understand what is, so to speak obligatory and what optional, because this choice impacts the results: for creating seeds for post hoc seed-to-voxel analysis, do I need to load all the components at the same time (e.g. eye(8)) or am I allowed to look at each component separately? Are both parametric and non-parametric stats accepted and which height and cluster thresholds should be used there? In my data, the non-parametric stats result much more conservative.

[b]4. ICA: CONN and GIFT[/b]: next to the variety of resting state analysis performed in CONN, I want to run ICA using GIFT, because it still offers a few additional options for visualization and statistical sorting of components. I preprocessed and denoised data with CONN. As I understand, the swau files are the ones to use as input for GIFT, however, how can I consider all the fine denoising steps, CompCor, ART, etc.? Or maybe there is an elegant way to switch between CONN and GIFT allowing for the maximal use of GIFT features, such as MDL criteria, ICASSO and statistical sorting of components and making statistics in CONN (or something like this)?

[b]5. Matlab warning:[/b] Should I bother with the following Matlab warning (appearing after the first-level step)?
Warning: Returning NaN for out of range arguments
> In spm_Fcdf (line 108)
In conn_glm (line 152)
In conn_process (line 4151)
In conn_process (line 46)
In conn (line 5396)
In conn_contrasthelp>conn_contrasthelpcallback (line 86)
In conn_contrasthelp>@(varargin)conn_contrasthelpcallback(handle,contrasts,get
(gcbo,'value')-1) (line 64

Again, I apologize for the long list. I would be highly grateful for your advice.

Best, Lucas
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Naming convention preprocessing COND

April 29, 2016, 1:32 pm
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Hi Alfonso,

Could you help me out by explaining the naming convention used by CONN to store results for different conditions?

I had previously processed my data with a single condition, this provided me with a DATA_SubjectXXX_Condition001.mat file that had a 'softlink' variable pointing to the DATA_SubjectXX_Condition000.matc file containing the actual data.

I added a second condition to process the data with a different bandpass filter, and now I see several more files appearing that don't make much sense to me.

There are the two DATA_SubjectXXX_Condition001.mat and DATA_SubjectXX_Condition000.matc files as described above. Then there is a DATA_SubjectXXX_Condition002.mat but the 'softlink' variable is empty (i.e. '[]'), and there is [i]no[/i] DATA_SubjectXXX_Condition001.matc file. Next, there is a DATA_SubjectXXX_Condition003.mat file, but the 'softlink' variable point to the DATA_SubjectXX_Condition000.matc file (same file as used by DATA_SubjectXXX_Condition001.mat). And finally, there is a DATA_SubjectXXX_Condition002.matc file with actual data, but it is not referred to by any of the other mat files.

CONN does generate a niftiDATA_SubjectXXX_Condition000.nii and niftiDATA_SubjectXXX_Condition002.nii files, and the contents of these files are distinct by MD% hash, so I assume the data for the two conditions are there. Which files belong to which condition?

Kind regards,
Jalmar
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RE: 2x2 ANOVA setup

May 2, 2016, 5:25 am
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Dear Alfredo,

after reading several posts I'm still a bit puzzled how to report the results of a mixed-design ANOVA.

I set up a 2x2x2 model (group, condition, roi). The 3-way interaction gives me a T-value instead of F-values which would be expected for a rmANOVA for example.

group: <span style="white-space: pre;"> </span>[1 -1]
condition: <span style="white-space: pre;"> </span>[1 -1]
roi: <span style="white-space: pre;"> </span>[1 -1]

If I understand correctly this is founded in the way results are calculated (t-tests for within-subject-effects on 1st-level, subsequent results in t-tests on 2nd level (between-subjects-effects))
If I want to report F-values is it the correct way to calculate the F=t^2 as indicated in that post (https://www.nitrc.org/forum/message.php?msg_id=13780)? 

I hope the specifications are sufficient.

Thanks in advance and best wishes,
Bruno
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7 T MRI masked ICA

May 2, 2016, 8:13 pm
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Dear Alfonso,

Before starting to process my 7T MRI data, I have several question that I am hoping you can help me out with.
We have about 40 datasets of whole brain 7T MRI resting-state data (1.25 mm isotropic).
I now would like to run an ICA within a specific region (masked ICA) and then take the output for a seed-to-voxel analyses.

But several issues come to my mind:
1. Should I do something special as this was scanned with multiband imaging?
2. I also have a short sequence where the phase-encoding direction was reversed (in FSL I would run topup). How should I deal with that in Conn?
3. To run the masked ICA, should I add the mask to the ROIs in the setup page? How to proceed then?

Many thanks!
Heidi
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RE: 1 -1 comparison between sessions

May 3, 2016, 11:00 am
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[color=#000000]Dear Christopher,[/color]

[color=#000000]For this design you would typically create two conditions in the [i]Setup.Conditions [/i]tab (e.g. 'control' and 'experimental') and assign the stimulation blocks onsets/durations during the first-run only to the 'control' condition (e.g. select all subjects in the 'subjects' list and 'control' in the conditions list, then select 'session1' in the sessions list and enter there the corresponding onsets/durations; last select 'session2' in the sessions list and leave empty -or enter empty brackets [ ]- in the onset/duration fields) , and the stimulation blocks onsets/durations during the second-run only to the 'experimental' condition (e.g. same as above but now select session1 and leave empty the onset/durations and then select session2 and enter the appropriate onset/duration values there). [/color]

[color=#000000]Then when you get to the [i]second-level results[/i] tab you will have the 'control' and 'experimental' conditions listed there in the 'conditions' list, and you can specify any desired within- and between-subject contrasts there (e.g. select both conditions and a [-1 1] contrast to evaluate the difference in connectivity between the two conditions; doing this while selecting 'AllSubjects' in the subject-effects list performs a paired t-test between your two conditions; doing the same while selecting 'Group1' and 'Group2' in the subject-effects list and entering there also a [-1 1] contrast will look at the 2x2 ANOVA interaction between groups -a between-subjects factor- and conditions -a within-subjects factor-). [/color]

note: I am assuming that the VAS-rating blocks are to be treated as nuisance effects so you could simply include those as an additional first-level covariates, if you prefer to look at the connectivity values within those blocks as well you could instead simply define two additional conditions (e.g. 'control_VAS' and 'experimental_VAS' with the corresponding onset/duration values for the first and second sessions, respectively)

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Christopher Milde:[/i][quote]Dear CONN experts,

I started using CONN to perform task-related fc analysis with a blocked-design. I can perform nice between group comparisons. However I get stucked when trying to formulate a between session comparison within subjects.
At which stage an how can I contrast both sessions (run 1 versus run 2 corresponding to experimental versus control condition within subject)?

I have the following design: 2 groups (patients, yoked controls) x 2 conditions (2 runs: first experimental condition, second control condition) both runs have a regressor of interest (stimulation) and an additional nuisance regressor (blocks were VAS-ratings were performed). 
I used two session per subject were I upload the run with the experimental run (session 1) and the control run (session 2). For both runs per subject I formulated a stimulation and rating regressor as condition names


Many thanks for your support,

Chris[/quote]
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RE: reporting 3-way interaction

May 3, 2016, 11:31 am
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[color=#000000]Dear Bruno[/color]

[color=#000000]If you want to use F-stats (and that is typically the best choice for this sort of interaction analyses, unless you have an a priori hypothesis about the directionality of the expected interaction effect) simply switch the option in the [i]results explorer [/i]window that reads 'one-sided (positive)' to 'two-sided', and that will be exactly equivalent to the standard F-test (which is blind to the directionality of the interaction effect) for this same interaction analysis. [/color]

If in doubt, or if you prefer to have F-stat values directly, you could also simply enter in the 'between-subjects contrast' field [1 -1; 1 -1] (instead of just [1 -1]), and that will give you exactly the same results as the analysis above, but now all statistics will be reported using F-stats instead of T-stats. Another alternative would be, in the original analysis [i]results explorer [/i]window, click on the 'display SPM' button and define there a new F-contrast with the [-1 1] values. Again, all of these options will produce exactly the same second-level results as your original analyses (using the 'two-sided' option), you will see exactly the same significant clusters, the same cluster-level statistics, etc. (they will only vary in the choice of voxel-level statistics being reported -either T(dof) or F(1,dof) stats-) 

Hope this helps
Alfonso

[i]Originally posted by Bruno Baumann:[/i][quote]Dear Alfredo,

after reading several posts I'm still a bit puzzled how to report the results of a mixed-design ANOVA.
I set up a 2x2x2 model (group, condition, roi). The 3-way interaction gives me a T-value instead of F-values which would be expected for a rmANOVA for example.
group: [1 -1]
condition: [1 -1]
roi: [1 -1]
If I understand correctly this is founded in the way results are calculated (t-tests for within-subject-effects on 1st-level, subsequent results in t-tests on 2nd level (between-subjects-effects))
If I want to report F-values is it the correct way to calculate the F=t^2 as indicated in that post (https://www.nitrc.org/forum/message.php?...)?
I hope the specifications are sufficient.
Thanks in advance and best wishes,
Bruno[/quote]
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spm.ps file

May 3, 2016, 2:58 pm
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Hi Alfonso,

Hope you're well, and thank you, as always, for your excellent support. 

I don't know if this is more of a question for the spm listserv, but when using the latest version of Conn it seems that a spm.ps file isn't generated. This appears during the realignment stage for each subject:

"Figure not found; nothing has been printed",

and I can't locate one in the subject (or other) directories.

We've always gotten a post script file before with version 14, so thought I'd ask. (We use them for judging whether there is too much motion, but can also refer to the realignment params text file.

Thanks and all best,
Mary
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RE: scrubbing in setup but not denoising

May 3, 2016, 6:30 pm
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[color=#000000]Hi Federico,[/color]

[color=#000000]Just to give me some additional information about your project, could you please do the following:[/color]

[color=#000000]a) in the Denoising tab, select one subject/session that "should" have outliers (but does not show them)[/color]
[color=#000000]b) in Matlab command window type:[/color]

[color=#000000]  global CONN_h;[/color]
[color=#000000]  save infofile.mat CONN_h;[/color]

[color=#000000]and c) send me the newly generated infofile.mat file as well as your original conn_*.mat project file.[/color]

[color=#000000]Thanks[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Federico Nemmi:[/i][quote]Hi Alfonso,
thank for your quick reply.
I followed your advice, but the scrubbing continue to be present only in the setup step and not in the denoising.
I am also having another strange behavior, but I opened a different thread for that. I start doubting about how I implemented the whole pipeline.[/quote]
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RE: Average within / between network connectivity

May 3, 2016, 6:40 pm
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[color=#000000]Hi Ruth,[/color]

[color=#000000]Currently there is a separate script (part of the CONN package but not yet integrated into CONN's gui) that would allow you to perform these sort of within- and between- network analyses. To use it you should:[/color]

[color=#000000]1) in CONN's gui [i]second-level results [/i]tab, define there the specific model that you would like to test (i.e. select the subject-effects and associated between-subjects contrast, and the desired conditions and associated between-conditions contrast)[/color]

[color=#000000]2) then in Matlab command line type[/color]
[color=#000000]  conn_withinbetweenROItest;[/color]

That will prompt you to select two networks (e.g. select the 5 ROIs that belong to each of your first two networks) and then it will output a file containing the within- and between- network connectivities (averaged across all the ROIs within each network) for each subject, as well as the statistics associated with your selected second-level model again for the within- and between- network connectivity values. 

Let me know if this is what you had in mind.

Best
Alfonso

[i]Originally posted by Ruth Shaffer:[/i][quote]Hello,

I am looking into second level ROI-to-ROI analyses and am hoping to calculate average within- and between- network correlations for each of the networks of ROIs in two separate RSFC runs.  

For example, if I had 3 networks, each with 5 ROIs, I would be trying to do two things:

1)  to obtain an average within-network correlation during run1 and during run2 for each of the three networks (specifically I am looking for a single average correlation among the 5 ROIs in network 1 at run1 and then their average correlation at run 3--and then I would do the same calculation for the other two networks separately).  

2)  to obtain between network average correlations for each network (specifically I am looking for a single average correlation for 5 ROIs in network 1 with the 10 ROIs comprising networks 2 and 3, calculating this at run1 and then again at run 3--and tthen I would do the same calculation for the other two networks separately).

Is this possible to do in CONN, and, if so, how might I go about obtaining these measures?

Thank you so much for such a great program and for any help on this question you can give me!

Best,

Ruth[/quote]
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RE: Surface Based Analysis - Setup Error (??)

May 3, 2016, 6:45 pm
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[color=#000000]Hi Shady,[/color]

[color=#000000]Yes, I think so. This error message means that the white matter mask for that subject was empty, again indicating (assuming that the gray/white/csf masks had been imported from the freesurfer folders for your subjects) that freesurfer might have run through some issues with the registration and/or segmentation of this subject data, so I would probably suggest to re-run recon-all and visually inspect the results to make sure that everything looks fine. [/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[i]Originally posted by Shady El Damaty:[/i][quote]Thanks Alfonso,

I will try rerunning this subject again with recon-all.  After excluding this subject, I noticed the following error when processing my ROIs:

ERROR DESCRIPTION:[quote]
Error using conn_process (line 597)
No suprathreshold voxels in ROI file /Volumes/Archive/Research/ADS/data/ads.subjects/402568-w1/mri/c2brainmask.nii (this typically indicates a problem during normalization/segmentation for this subject; please try re-running normalization/segmentation step after manually re-aligning the structural volumes to better match the default template orientation)
Error in conn_process (line 14)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
Error in conn (line 2977)
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.15.h
SPM12 + DEM FieldMap MEEGtools
Matlab v.2015b
storage: 2968.7Gb available
[/quote]Is this a related problem, probably due to copying files?  I can probably just rerun recon-all and it should be fine?[/quote]
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RE: Surface display questions

May 3, 2016, 7:21 pm
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[color=#000000]Hi Sami,[/color]

[color=#000000]To generate the 'surface display' view from the mask just generated you may use:[/color]

[color=#000000]conn_mesh_display('masfilenamePos.nii','');[/color]

[color=#000000]Programmatically printing without any gui interaction is a little bit more involved but it can be done using something like (for example, to print a 4-view mosaic):[/color]

conn_print('print01.jpg',...
                '-nogui',...
                '-mosaic',...
                   get(findobj(gcf,'label','Left view'),'callback'),...
                   get(findobj(gcf,'label','Left medial view'),'callback'),...
                   get(findobj(gcf,'label','Right view'),'callback'),...
                   get(findobj(gcf,'label','Right medial view'),'callback'));

Let me know if you would like me to clarify the associate commands for other actions available in the surface-display GUI.

Hope this helps
Alfonso


[i]Originally posted by Sami Abboud:[/i][quote]Hello Alfonso,

This works now, thank you. I get the exported .nii file with the results.

Back to my initial question then: Could I open the surface view and execute a Print -> Current view from the command line?
In other words, is there an easy way to call conn_mesh_display() on the exported image above that would lead to a saved .tiff file from a certain view point?

Thanks again for your help and for saving me hours of looking into the code.

Cheers,
Sami[/quote]
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