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Regression and bandpass filtering in fMRI

June 16, 2020, 8:05 am
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Hi CONN experts,

I normally do a regression in my fMRI data to mitigate the effect of nuisance variables/regressors (e.g. movement, physiological artifacts, white matter, csf, etc.). Sometimes I am also interested to do a band pass filter.
I have read that the correct way to do a "Nuisance regression" with a band pass filter is including the band pass in the regression model. So, all the operations can be done in a single step.
The real problem appears when I try to band pass the data at "0.002 - 0.01" and "0.012 - 0.028".
It seems that band passing at those frequency ranges use at least more than 90% of the degrees of freedom of the data set. Then, if I have more regressors (movement parameters, physiological recordings, etc.) it is not possible or does not make sense to do the regression because the number of regressors exceeds the number of time points.
How could I deal with this problem if I am interested in keeping bandpass in the regression model?
Best regards,
Karel
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First level error - group analysis

June 16, 2020, 10:16 am
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Good morning everyone.
I ran group analysis with three subjects.
After the preprocessing step, I got these warnings in MATLAB Command window.

warning: set-1 data for subject 1 session 1 not found
warning: no valid data for ROI atlas.aITG r (Inferior Temporal Gyrus, anterior division Right) in /Users/fmrineuro/Desktop/prova intrav conn/subject1/rest/s00273285-0008-00001-000034-01.nii (scan # 1/260)
warning: no valid data for ROI networks.Visual.Occipital (0,-93,-4) in /Users/fmrineuro/Desktop/prova intrav conn/subject1/rest/s00273285-0008-00001-000034-01.nii (scan # 1/260)
warning: set-1 data for subject 2 session 1 not found
warning: no valid data for ROI atlas.aITG r (Inferior Temporal Gyrus, anterior division Right) in /Users/fmrineuro/Desktop/prova intrav conn/subject2/REST1/s00299700-0008-00001-000001-01.nii (scan # 1/260)
warning: set-1 data for subject 2 session 2 not found
warning: no valid data for ROI atlas.aITG r (Inferior Temporal Gyrus, anterior division Right) in /Users/fmrineuro/Desktop/prova intrav conn/subject2/REST2/s00299700-0009-00001-000001-01.nii (scan # 1/260)
warning: set-1 data for subject 3 session 1 not found
warning: no valid data for ROI atlas.aITG r (Inferior Temporal Gyrus, anterior division Right) in /Users/fmrineuro/Desktop/prova intrav conn/subject3/rest1/s54654654-0003-00001-000001-01.nii (scan # 1/260)
warning: no valid data for ROI networks.Cerebellar.Anterior (0,-63,-30) in /Users/fmrineuro/Desktop/prova intrav conn/subject3/rest1/s54654654-0003-00001-000001-01.nii (scan # 1/260)
warning: set-1 data for subject 3 session 2 not found
warning: no valid data for ROI atlas.aITG r (Inferior Temporal Gyrus, anterior division Right) in /Users/fmrineuro/Desktop/prova intrav conn/subject3/rest2/s54654654-0004-00001-000001-01.nii (scan # 1/260)
warning: no valid data for ROI networks.Cerebellar.Anterior (0,-63,-30) in /Users/fmrineuro/Desktop/prova intrav conn/subject3/rest2/s54654654-0004-00001-000001-01.nii (scan # 1/260)

When I saw in the first level tab the activation maps, they are not coregistered with the brain, in fact there are activations which are outside the brain. It is curious that, when analyzed singularly few months ago, everything seems to be ok. The version of the software is the same, also the MATLAB version. Could anyone help me?
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How to merge two different analysis

June 16, 2020, 10:16 am
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Hello everyone, 
I have two groups of patient processed with CONN.
I would like to join them in one group to perform the second-level analysis.
The two groups have been acquired using the same MRI protocol, the only difference is that one group has been acquired before the other one.
How can I do it?
Thanks in advance for your help.
Best regards
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RE: FSL preprocessing + conn

June 17, 2020, 3:51 am
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Dear CONN experts,
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA. 
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:  

ERROR DESCRIPTION:

Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end

Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?

Thanks in advance for your precious help,
Giuseppe
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about ROC curve

June 17, 2020, 5:04 am
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sorry but I am new about this analysis. I have dataset for 37 person(17 control 20 patient data). I have analysed them seed to voxel, ROI , ica and dyn ica analysis. i want to test them on ROC curve but didnt know anything much. how can i get data matrix out and take the data to roc analysis of these tests  ???
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Problem creating VDM maps for distortion correction

June 17, 2020, 7:08 am
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Dear all,
When creating VDM maps for distortion correction in my preprocessing, an error occurs in only one patient which is
Error using sqrtm (line 35)
Expected input to be finite (full error message see below).

As a workaround, I added a small constant value of 1/1000 to all 4 files (short and long TE real and imaginary files) as suggested in https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;a6060c5a.1609 and afterwards the preprocessing is working well.
Is this method a reliable way to proceed? Or do I have to consider something else since the values are manipulated now?

Any advice is highly appreciated.
Thank you very much in advance.

Best,
Anna

Error using sqrtm (line 35)
Expected input to be finite.
Error in pm_segment>get_p (line 581)
dst = (cor-ones(size(cor,1),1)*CP.mn(:,i)')/sqrtm(CP.cv(:,:,i));
Error in pm_segment>run_segment (line 364)
[P,ll0] = get_p(cor,msk,s,sums,CP,bf);
Error in pm_segment (line 119)
[CP,BP,SP] = run_segment(CP,BP,SP,VF,sums,x1,x2,x3);
Error in pm_brain_mask (line 48)
VO=pm_segment(P.fname,flags.template,seg_flags);
Error in FieldMap (line 1611)
IP.uflags.bmask = pm_brain_mask(IP.fmagP,IP.mflags);
Error in FieldMap_create (line 146)
IP.fm = FieldMap('CreateFieldMap',IP);
Error in conn_setup_preproc (line 2870)
VDM = FieldMap_create(char(fmap),{filename},pm_def); %[ET1,ET2,0,ERT,-1]
Error in conn (line 1105)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN19.c
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Problem creating Results for Second Level ROI-to-ROI Connectivity

June 17, 2020, 11:14 am
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Hello all,

When attempting to use Results Explorer for any ROI-to-ROI analyses, the following error shows up, and the results are not created as they should be. This error occurs no matter which covariates or seeds I select, and I'm only using one condition.

This is the only major error I've seen that references "angle". Could anybody give me a hand with this? The full error message is below.

ERROR DESCRIPTION:

Error using angle
Too many output arguments.
Error in conn_displayroi (line 2815)
[nill,datarank]=sort(angle(data.xy2(data.displaytheserois,1)+1i*data.xy2(data.displaytheserois,2)));datarank(datarank)=1:numel(datarank);
Error in conn_displayroi (line 438)
conn_displayroi(hfig,[],'displayreduced');
Error in conn (line 9833)
conn_displayroi('init','results_roi',-1); %CONN_x.Results.xX.nsources,-1);
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN19.c
SPM12 + Anatomy DEM FieldMap MEEGtools TOM8 aal cat12 marsbar vbm8 wfupickatlas xjview
Matlab v.2019a
project: CONN19.c<span id="_plain_text_marker"> </span>
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out of storage?

June 18, 2020, 8:44 am
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Hi Alfonso,

I'm having issues with storage—

Without opening a specific project, conn says there is 0% storage. When I open a project, this doesn't change, and I can't run analyses or access completed analyses.

I am running conn locally on my computer and save 2 projects to an external drive that has 2 TB.

Any ideas?

Thanks!
Isabelle
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RE: New Bug/Error with Results since 19c Update

June 18, 2020, 11:39 am
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Hi Alfonso,

Yes this is exactly what I did. I was just unsure if that was the right way to go about creating the design matrix for this scenario. Thank you for your help!

All the best,
Jacinta
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RE: Testing an interaction: split or not & issues with "0" coding

June 18, 2020, 12:59 pm
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[color=#000000]Dear Lucas,[/color]

[color=#000000]You may simply add covariates of no interest to your design (e.g. "males, females, score*males, score*females, age, site1, site2") and enter 0 at the corresponding place in your contrast (e.g. [0 0 -1 1 0 0 0]). If, in addition, you want to also correct for potential covariate-by-group interactions, that is also perfectly fine, and you may do so by entering those interaction terms in the design as additional covariates of no interest (e.g. "males, females, score*males, score*females, age*males, age*females, site1*males, site1*females, site2*males, site2*females" and a contrast [0 0 -1 1 0 0 0 0 0 0]). Of course, you may also do that differentially across covariates (e.g. include the group*age interactions but not the group*site interactions)[/color]

There is no potential confusion regarding continuous vs. categorical covariates here. In both cases you are estimating the expected differential effect in connectivity associated with a unit-increase in scores when everything else (including the covariates) remain constant (i.e. at any arbitrary value of those covariates, whether continuous or categorical), and you are then simply comparing those differential effects between your two groups (males vs. females). 

Hope this helps
Alfonso
[i]Originally posted by Lucas Moro:[/i][quote]Dear Alfonso
Dear Conn-Users

Previous posts suggest the following 2nd level contrast [0 0 1 -1] for testing the gender by score interaction, using "males" , "females", "score_for_males", "score_for_females", respectively. However, how do you test the same interaction, by simultaneously correcting for covariates of no interest, such as age or sites? Doesn't it confuse the Conn with categorical or continuous variables when you put "0" for these e.g. [0 0 0 0 0 1 -1]? I also assume here the scores are coded with either a value or a "0". Does it additionally require spliting each covariate into "age_males", "age_females", "site_1_male", "site_1_female", "site_2_male", "site_2_female"?

I screened the posts for this specific question, but could find no answer and would appreciate any comment. Thank you.

Greetings,
Lucas[/quote]
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Error message in voxel-to-voxel analysis

June 19, 2020, 3:12 am
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Dear all,

I've run a Seed-to-voxel and ROI-to-ROI analyses without problems. Now I'm trying to perform a Voxel-to-voxel analysis using default parameters, but after finishing the analysis, when I press the "Voxel-to-voxel" tap in the 2nd analyses tab, I receive an error message saying: 

"Not ready to display second-level Analyses. Condition (rest ) has not been processed yet. Please re-run previous step (First level analysis)"

Any advice on why this is happening? I can see that a similar problem has been mentioned here: https://www.nitrc.org/forum/forum.php?thread_id=6860&forum_id=1144 and got the advice to try another version of Conn. I tried conn version 18b and 19c, and both versions end up with the same error message.

Best,
Signe
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RE: Bug report: conn_batch

June 19, 2020, 5:20 am
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You're welcome. I'm trying to drive conn_batch() by building the BATCH structure with functions that read parameters from a JSON specification file (which is how I found the bug). This solution would allow users to set up their experiments without knowing coding or entering all data via GUI (which can be error prone). I want to check if there is anything like this already?
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RE: Defining descriptions for L2 covariates (subject effects and groups) - error in docs

June 19, 2020, 5:30 am
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Ok, thank you Alfonso. The solution of running conn_batch() twice is quite suboptimal if the use-case is to drive conn_batch() by building the BATCH structure with functions that read parameters from a JSON specification file - in that case, the function to build BATCH.Setup would have to return the instruction to run conn_batch twice, and somehow handle the update of the Setup struct for each run, to pass the descrip fields as different subfields.

Is there any plan to fix the underlying problem by naming the fields differently?
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Task-residual Functional Connectivity and gPPI

June 19, 2020, 7:35 am
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Dear experts,

I'm trying to use conn for ROI-to-ROI analysis with block-design task. It seems to be two approaches for it.
Approch1: As described in 'Task-residual Functional Connectivity of Language and Attention Networks' and 'A METHOD FOR USING BLOCKED AND EVENT-RELATED FMRI DATA TO STUDY "RESTING STATE" FUNCTIONAL CONNECTIVITY', by denoising the main effect of task, setting a new condition [0, inf] and setting the filter to [0.008,0.09], I can conduct a 'task-residual FC' which emulates resting state fMRI FC.
Approch2: a gPPI analysis as conn manual discribed.

I'm wondering what's the difference between these two approches? Besides, if I conduct a gPPI analysis, what's the difference between ROI-to-ROI and seed-to-voxel analysis? Since the standard PPI tutorial in SPM12 manual seems only support seed-to-voxel analysis.

Thanks!

Best,
Wang
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Reloading a project can't find *dmn.nii file

June 19, 2020, 5:13 pm
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Hi, 

I am trying to reload a previously processed analyses (it was a seed to voxel analysis) as I want to get more information out of the results.  I have tried reloading the .mat file and then showing conn where the structural files are (in the gui).  Conn is now saying that it is missing the *dmn.nii file.  I have no idea what this is, can someone explain?  

Thanks, 

Jennifer
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RE: No Significant Results

June 19, 2020, 5:45 pm
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Dear Laura,

In analysis results window, the threshold you set is for connection level only. In reults explorer, by default, p<0.05 uncorrected for connection level and p<0.05 pFDR corrected for cluster level is applied. You can choose [i]Advanced [/i][i]Family-Wised Error control settings[/i] to find an acceptable threshold for your research. 


Hope this helps!
Wang
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Preprocessing algorithm changes between CONN 17 and 19b?

June 19, 2020, 7:57 pm
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Hi all,
While trying to figure out why I couldn't replicate a coworker's preprocessing output, I tried running identical data and preprocessing setups through CONN 17 and CONN 19b, and found that even with everything appearing identical in terms of input, the two versions of the software gave noticeably different outputs. I used the default preprocessing pipeline without the slice timing correction and smoothing steps (keeping realignment, centering, outlier detection, and structural and functional normalization and segmentation steps). The 'u' outputs were the same, but started to diverge with the 'wu' volumes, and continued to diverge when denoising was run (with CSF, WM, scrubbing, realignment, and effect of rest confounds). I was wondering if there were any preprocessing/denoising algorithm changes between the two versions that could be causing this, and what those changes are?

Also, a secondary question: is there a way to have CONN 19 automatically output the niftiDATA files like CONN 17, rather than converting the DATA .matc files?

Thanks!
Natalie
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RE: FSL preprocessing + conn

June 20, 2020, 11:06 am
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[color=#000000]Dear Alfonso,[/color]
[color=#000000]thank you so much for your feedback.[/color]
[color=#000000]Indeed, while I'm able to open/view that file in mricron or fsleyes, I cannot view it in SPM.[/color]
This is the error I get when trying to display the file in SPM:

Cannot access file "C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii".
Error using spm_slice_vol
Cant map view of file. It may be locked by another program.

[color=#000000]Strangely enough, SPM is perfectly able to open the preprocessd fMRI dataset in the subject's native space ("denoised_func_data_noaggr.nii"), before applying spatial transformations with the following command:  [/color]

applywarp -i denoised_func_data_nonaggr.nii -r standard.nii --premat=example_func2highres.mat -w highres2standard_warp.nii -v -o denoised_func_data_standard.nii

Am I missing something?


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

[color=#000000]That error seems to indicate some general/unspecified problem with the denoised_func_data_standard.nii file. Can you please check whether you are able to open/view that file in SPM or some other software? (e.g. use [/color]

[color=#000000]   spm_check_registration 'C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii'[/color]

Best
[color=#000000]Alfonso[/color]
[i]Originally posted by Giuseppe Pontillo:[/i][quote]Dear CONN experts,
I'm trying to import preprocessed rs-fMRI data into CONN for subsequent analyses.
The data have been preprocessed according to FSL's melodic pipeline (which included motion correction with mcflirt, topup-based EPI distortion correction, high-pass filtering and no slice-timing correction since these are multiband, HCP-style fMRI data) followed by ICA-based denoising using FSL's ICA-AROMA. 
I managed to import MNI-space structural data, as well as segmented tissue maps, motion parameters derived from mcflirt and outliers estimated by fsl_motion_outliers for the subsequent step.
Unfortunately, when trying to import precprocessed fMRI data as the primary functional dataset, I get the following error:  

ERROR DESCRIPTION:

Error using conn_menu>conn_spm_read_vols (line 1091)
Error reading file C:\Users\Giuseppe\Desktop\test\denoised_func_data_standard.nii. File may have been modified or relocated. Please load file again
Error in conn_menu (line 656)
[temp,volhdr]=conn_spm_read_vols(title(n));
Error in conn (line 2049)
conn_menu('updateimage',CONN_h.menus.m_setup_00{5},cfile{3});
Error in conn_filesearchtool (line 222)
if length(h.callback)>1, feval(h.callback{1},h.callback{2:end},names); else, feval(h.callback{1},names); end

Am I missing something?
Once I manage to import the data, my idea is to go through functional smoothing and denoising before statistical analyses, do you suggest any additional step?

Thanks in advance for your precious help,
Giuseppe[/quote][/quote]
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New CONN update and the matrix in the ROI to ROI \How to visualise the matrix with ROI names

June 20, 2020, 2:34 pm
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Hi all

So for the new CONN update in the second level ROI 2 ROI analysis. You can explore the results. When way of showing the result is display the connectivity using a matrix instead of the connected lines.. This is so great in terms of viewing the results.
However I have this problem: I cannot figure out the relation between the regions of the locations and the names of the regions inside the matrix.
CONN does not name the x and y of the matrix and each line by the region name.
So how can I display the region names to be meaningful and make the matrix easy to read?
Thanks

I posted this before but could not find an answer to it.
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reporting a bug in CONN

June 21, 2020, 11:43 am
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Dear Alfonso,
I found a bug in conn. I ran a regression analysis, and "results explorer" window showed a cluster (26,-90,28), the details of this cluster were shown:
size: 160 size p-PWE 0.000263; size p-FDR 0.000231; size p-unc 0.000005; peak p-PWE 0.549599; peak p-unc 0.000004
regions included in this cluster:
138 voxels covering 6% of atlas OP r (Occipital Pole Right),
20 voxels covering 0% of atlas sLOC r (Lateral Occipital Cortex, superior division Right).
2 voxels covering 0% of atlas. not-labeled.

A couple of days later, I want to extract the z values of this cluster, but to my surprise, when I opend, the regions of this cluster became very different (please see attached picture), but other characteristics (i.e., cluster size, coordinate, and p values) of this cluster did not change. I did not change anything in setting. But why regions of this cluster changed (OP r became SCC l)?

Thank you very much in advance!
Best,
Xinyuan
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