Dear Community

I am new to this awesome CONN toolbox, so I have a naive question.
When I load fMRI into ART for motion detection, I am wondering if I should load raw pre-alignment or post-alignment fMRI data before alignment.
Seems like alignment may correct motion among time frames. Please let me know.
Thanks
Li

Dear Sir/Madam,

I am currently using the CONN toolbox (v. 16.b) via MATLAB to perform resting-state analysis. I am at the Setup step right now and have to enter the TR values -- this is where I have a few questions.

Firstly, if my experimental value is 2300ms, should I enter "2.3" or "2,4" or round it up to "2" or "3" to avoid the decimals? Secondly, if I have 40 subjects, should I enter the TR value 40 times and put space between these values or should I enter the TR value only once? Lastly -- in case I can use decimals -- would writing "2" (default TR value) or "3" (most frequent TR value) instead of "2.3" significantly change the results in the end? I looked in the manual, but couldn't find the answers to these questions.

Thanks!

Sincerely,
--
Elmira.

Good afternoon,

I am trying to do a main effects analysis of my patients group, but I have some questions:

1. What does exactly main effects of a group (in my case, patient group) mean in CONN?
2. When I run the analysis and I obtain my results, I have some significant effects. However, when I correct them (p-FDR corrected) they dissipate. Is it necessary to correct them? Which should be the height and cluster thresholds and should both of them be corrected?
3.When I click display values, I obtain a table named REX results. I have different questions about it.
-What does the graphic represent? What do the x and y axis represent? Why the x-axis -which seems to represent volumes/scans- just shows up until 30 volumes/scans (even though I have 100 volumes)? 
-What type of coefficient is beta? What does it represent?

When I compare the patients with all subjects, I obtain the table that I have attached. Why doesn't it compare the groups? As you can see, I obtain results for patients and for all subjects separately.

Thank you so much for your help

Good evening Sir/Madam,

I am currently using CONN toolbox (v. 16.b) via MATLAB to perform resting-state analysis. Once in the Setup, one of the fields required to be filled is the repetition time (TR) -- my experimental value is 2300ms. This is where I have several questions.

First, I was wondering whether I have to simply put "2.3" or whether I have to round it up to "2"/"3" to avoid the decimals? Secondly, in case I should write the decimals, should I use a point or a coma? Third, if I have 100 participants, do I have to put "2.3" hundred times with a space between these values? Lastly, would writing "2" (default value) or "3" (very frequently entered value) instead of "2.3" significantly change the results in the end? I looked in the manual, but couldn't find the answer to my questions.

Thanks!

Sincerely,
--
Elmira.

Good afternoon,

I am trying to add clinical data as a covariate in my analysis. However, I just have data for the patients group but not for the control group. I guess that if I use 0's for the control group (because I have no data), the 0's will be added to the analysis. How can I avoid that?

Thank you for your help

Hello,

I wanted to confirm a task based analysis I ran with the CONN toolbox. With this analysis, I am interested in looking at how the hippocampus is differently connected to other brain regions as a function of three within-subject conditions (A,B,C).

I first ran a seed-to-voxel gPPI analysis using a hippocampal seed established from a conjunction analyses done in SPM between the three conditions.

To see what brain regions were more connected to this seed in condition A in comparison to B and C, i  used the second level contrast 1 -.5 -.5 and then used a threshold of p < 0.005 with cluster threshold FDR corrected to a p < .05 to establish the connectivity pattern. One question I have here is when I export the images so that I can view these patterns, there are three resulting images - is the ROI image the one to use?

I next ran a seed-to-seed analysis to see how different hippocampal regions (subregions of the hippocampus) were connected as function of these three conditions. So here, I chose the ROI-to-ROI tab at the second level (still a gPPI analyses) and manuallly selected only these hippocampal regions to see which connections had a stronger relationship with A as compared to Band C with the same contrasts as noted above. Here, I used a more liberal threshold (p < 0.05) given that I have strong hypotheses about these connections.

I suppose my question is if my analytic approaches with CONN are appropriate?

Best,
Signy

Importing my SPM.mats into CONN toolbox results in me having lots of very specific conditions like:

REDTRIAL_AFTER_ERROR
REDTRIAL_AFTER_CORRECTRESPONSE
REDTRIAL_AFTER_NORESPONSE

How do I define a condition that includes any of those three conditions e.g. REDTRIAL_ALLTYPES?

[color=#000000]Dear Sami,[/color]

[color=#000000]Sorry it was not very clear, yes you may use directly your subject-specific .mgz ROI files (e.g. when entering your ROIs using the GUI simply check the 'subject-specific' checkbox in the [i]Setup.ROIs[/i] tab and then select all subjects, select all your ROI files, and click on 'select' to simultaneously enter all those subject-specific files -one file per subject-). When doing this simply make sure that the 'extract ... from functional dataset #' field for this ROI is set appropriately (e.g. if this ROI is going to be extracting the BOLD signal from dataset-2 just make sure that your dataset-2 in [i]Setup.functional [/i]actually points to the functional data in subject-space; i.e. in the same space as your ROI file for each subject). This procedure works for any arbitrary set of subject-specific ROIs. The linked posts were just referring to an alternative way to enter subject-specific ROIs when those ROIs are derived from freesurfer (the alternative procedures avoid having to resample your ROIs to each subject anatomy, by having CONN explicitly use the freesurfer-generated lh|rh.sphere.reg files to learn the specifics of each subject anatomy)[/color]

[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso [/color]
[i]Originally posted by Sami Abboud:[/i][quote]Dear Alfonso, 

Thank you for the your answer.
If I understood well from reading the two previous posts you mentioned, it seems that I cannot define ROIs from subject-space but only from fsaverage space. Is that so?

What I have as input is a surface overlay file that is created by morphing a specific atlas to each and every single subject (relying on the subject-specific anatomy).
Should I then morph this overlay to fsaverage to be able to using CONN's analysis pipeline?

Cheers,
Sami[/quote]

Dear CONN Experts
We scanned a resting-state fMRI in three subject groups (Control, Patient1, Patient2), 10 subjects for each group.
Each subject has scanned three times, once a year (We use the condition to set this as: Year1, Year2, Year3). After pre- and post-processing, we want to know the following issues.
However, we are not clear how to set the contrast to test several interests.
First, for each group, we want to know how much functional networks (for example, DMN and language network) decrease during the three year period.
Second, we want to find a network which more decreases in the Patient2 group during the three year period compared with the Control.
I appreciate any comments.
Geon-Ho

Dear Alfonso and other conn toolbox experts,

Following the release of V17b I was delighted to see the addition of ALFF added to an already well stoked software package.

However, it is not clear to me from the release notes how you specify the frequency band of interest? Is this done simply by adjusting the frequency band of the bandpass filter?

Many thanks,

John

Dear all,

I'm sorry for disturbing you. Recently we have done a study to investigate the correlation between a cognitive behavior and the connectivity. In CONN, we performed the second-level ROI-to-ROI analysis. The FSL Harvard-Oxford Atlas with maximum likelihood cortical and sub-cortical atlas to divide the whole brain into 106 non-cerebellar anatomical regions of interest (ROI, 91 were cortical and 15 were sub-cortical) was used. We chose FDR corrected IN CONN, and found 5 connectivity being correlated with the cognitive behavior.
Here we have a question: Dose the CONN calculate the correlation between behavior and connectivity using FDR over the entire set of connections (for 106 regions, this would be FDR over a set of 106*105/2 = 5565 p-values)? And of that set of 5565 connections, 5 satisfied FDR-corrected p<0.05?
I'm not sure if my understanding is correct. Would you like to give me some advice. Thank you very much.
Best wishes.
lin

Alfonso,

I actually managed to rectify the issue offline so further troubleshooting will not be needed. Specifically, i re-ran the preprocessing pipeline after manual re-orientation and that seems to have rectified the issue. Thanks so much for your time and consideration nonetheless!

Cheers,
Jeremy

hello,

I am a student new to fMRI analysis. 

I preprocessed my data (functional and structural) using SPM12.

I want to use these already-preprocessed data in CONN for the further seed-voxel correlation analysis.
 
In the manual, it says that I can load it in project-> import and select one SPM.MAT file for each subject, but all the preprocessed data is in .nii format, not .mat format.

Is there any method that I can convert the file format, or am I just in the wrong direction ?

I'd really appreciate it if anyone who can solve this problem answers my question.

Thank you.

Hello CONN experts,

my analysis stops at the last Denoising step 6/6: Updating Analysis variables. I receive an error reading "Run first the Denoising step by pressing "Done" in the Denoising tab", which is of course what I am trying to do, but where the program stops.The matlab command window reads: "Not ready to process step conn_process_9".

Because of previous similar errors, I made sure that all analyses were enabled in the Setup step and the orientations of all functional and structural scans are correct.

Matlab is on my Mac, but the data, CONN and SPM are on an external hard drive. 

I have been stuck here for quite some time now, any help is much appreciated!

Hey all -- 

I created a .csv file that works for importing Setup conditions in the GUI, and I was wondering how I could import this when Batch scripting. If I run "conn_importcondition('file.txt')", the conditions import appropriately. However, I don't think this will work if I try to run it after a "conn_batch(BATCH)" call. Are there any suggestions for imporitng these?

Thanks -
Stephen

Dear CONN developers and users,

I have run CONN for the first time, have performed the preprocessing without troubles, but I am not able to run the analysis after Setup steps. After clicking on Done, I am getting enclosed error message. It seems to me like conn is not able to see the data. But the data are there... :-( 

E.g: CONN_x.Setup.functional{1, 4}{1, 2}{1, 1} = '/md1/NM-RMV/connResults/input_data/swusub_004_rest_sess_02.nii'


From the terminal:

labounek@magellan:~$ ls -l /md1/NM-RMV/connResults/input_data/swusub_004_rest_sess_02.nii
-rw-rw-r-- 1 phlustik mri 346609888 bře 4 00:48 /md1/NM-RMV/connResults/input_data/swusub_004_rest_sess_02.nii
labounek@magellan:~$

User labounek is the member of mri group.

OR

labounek@magellan:~$ fslinfo /md1/NM-RMV/connResults/input_data/swusub_004_rest_sess_01.nii
data_type INT16
dim1 91
dim2 109
dim3 91
dim4 192
datatype 4
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
labounek@magellan:~$

OR

labounek@magellan:~$ ls -l /md1/NM-RMV/connResults/input_data/swusub_002_rest_sess_0*.nii
-rw-rw-r-- 1 phlustik mri 346609888 bře 3 22:40 /md1/NM-RMV/connResults/input_data/swusub_002_rest_sess_01.nii
-rw-rw-r-- 1 phlustik mri 346609888 bře 3 22:53 /md1/NM-RMV/connResults/input_data/swusub_002_rest_sess_02.nii
-rw-rw-r-- 1 phlustik mri 346609888 bře 3 23:08 /md1/NM-RMV/connResults/input_data/swusub_002_rest_sess_03.nii
-rw-rw-r-- 1 phlustik mri 346609888 bře 3 23:22 /md1/NM-RMV/connResults/input_data/swusub_002_rest_sess_04.nii
labounek@magellan:~$

Any idea, why I am getting this error message?

Regards,
Rene

ERROR DESCRIPTION:

ERROR: Subject 2 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 2 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 2 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 3 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 3 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 3 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 3 has no functional data defined for session 2
ERROR: Subject 3 has no functional data defined for session 3
ERROR: Subject 3 has no functional data defined for session 4
ERROR: Subject 3 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 3 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 3 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 4 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 4 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 4 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 4 has no functional data defined for session 2
ERROR: Subject 4 has no functional data defined for session 3
ERROR: Subject 4 has no functional data defined for session 4
ERROR: Subject 4 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 4 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 4 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 5 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 5 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 5 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 5 has no functional data defined for session 2
ERROR: Subject 5 has no functional data defined for session 3
ERROR: Subject 5 has no functional data defined for session 4
ERROR: Subject 5 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 5 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 5 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 6 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 6 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 6 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 6 has no functional data defined for session 2
ERROR: Subject 6 has no functional data defined for session 3
ERROR: Subject 6 has no functional data defined for session 4
ERROR: Subject 6 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 6 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 6 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 7 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 7 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 7 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 7 has no functional data defined for session 2
ERROR: Subject 7 has no functional data defined for session 3
ERROR: Subject 7 has no functional data defined for session 4
ERROR: Subject 7 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 7 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 7 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 8 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 8 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 8 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 8 has no functional data defined for session 2
ERROR: Subject 8 has no functional data defined for session 3
ERROR: Subject 8 has no functional data defined for session 4
ERROR: Subject 8 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 8 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 8 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 9 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 9 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 9 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 9 has no functional data defined for session 2
ERROR: Subject 9 has no functional data defined for session 3
ERROR: Subject 9 has no functional data defined for session 4
ERROR: Subject 9 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 9 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 9 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 10 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 10 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 10 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 10 has no functional data defined for session 2
ERROR: Subject 10 has no functional data defined for session 3
ERROR: Subject 10 has no functional data defined for session 4
ERROR: Subject 10 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 10 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 10 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 11 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 11 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 11 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 11 has no functional data defined for session 2
ERROR: Subject 11 has no functional data defined for session 3
ERROR: Subject 11 has no functional data defined for session 4
ERROR: Subject 11 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 11 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 11 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 12 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 12 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 12 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 12 has no functional data defined for session 2
ERROR: Subject 12 has no functional data defined for session 3
ERROR: Subject 12 has no functional data defined for session 4
ERROR: Subject 12 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 12 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 12 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 13 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 13 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 13 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 13 has no functional data defined for session 2
ERROR: Subject 13 has no functional data defined for session 3
ERROR: Subject 13 has no functional data defined for session 4
ERROR: Subject 13 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 13 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 13 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 14 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 14 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 14 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 14 has no functional data defined for session 2
ERROR: Subject 14 has no functional data defined for session 3
ERROR: Subject 14 has no functional data defined for session 4
ERROR: Subject 14 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 14 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 14 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 15 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 15 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 15 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 15 has no functional data defined for session 2
ERROR: Subject 15 has no functional data defined for session 3
ERROR: Subject 15 has no functional data defined for session 4
ERROR: Subject 15 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 15 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 15 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 16 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 16 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 16 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 16 has no functional data defined for session 2
ERROR: Subject 16 has no functional data defined for session 3
ERROR: Subject 16 has no functional data defined for session 4
ERROR: Subject 16 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 16 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 16 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 17 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 17 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 17 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 17 has no functional data defined for session 2
ERROR: Subject 17 has no functional data defined for session 3
ERROR: Subject 17 has no functional data defined for session 4
ERROR: Subject 17 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 17 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 17 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 18 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 18 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 18 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 18 has no functional data defined for session 2
ERROR: Subject 18 has no functional data defined for session 3
ERROR: Subject 18 has no functional data defined for session 4
ERROR: Subject 18 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 18 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 18 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 19 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 19 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 19 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 19 has no functional data defined for session 2
ERROR: Subject 19 has no functional data defined for session 3
ERROR: Subject 19 has no functional data defined for session 4
ERROR: Subject 19 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 19 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 19 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 20 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 20 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 20 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 20 has no functional data defined for session 2
ERROR: Subject 20 has no functional data defined for session 3
ERROR: Subject 20 has no functional data defined for session 4
ERROR: Subject 20 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 20 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 20 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 21 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 21 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 21 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 21 has no functional data defined for session 2
ERROR: Subject 21 has no functional data defined for session 3
ERROR: Subject 21 has no functional data defined for session 4
ERROR: Subject 21 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 21 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 21 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 22 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 22 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 22 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 22 has no functional data defined for session 2
ERROR: Subject 22 has no functional data defined for session 3
ERROR: Subject 22 has no functional data defined for session 4
ERROR: Subject 22 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 22 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 22 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 23 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 23 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 23 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 23 has no functional data defined for session 2
ERROR: Subject 23 has no functional data defined for session 3
ERROR: Subject 23 has no functional data defined for session 4
ERROR: Subject 23 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 23 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 23 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 24 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 24 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 24 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 24 has no functional data defined for session 2
ERROR: Subject 24 has no functional data defined for session 3
ERROR: Subject 24 has no functional data defined for session 4
ERROR: Subject 24 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 24 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 24 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 25 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 25 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 25 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 25 has no functional data defined for session 2
ERROR: Subject 25 has no functional data defined for session 3
ERROR: Subject 25 has no functional data defined for session 4
ERROR: Subject 25 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 25 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 25 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 26 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 26 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 26 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 26 has no functional data defined for session 2
ERROR: Subject 26 has no functional data defined for session 3
ERROR: Subject 26 has no functional data defined for session 4
ERROR: Subject 26 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 26 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 26 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 27 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 27 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 27 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 27 has no functional data defined for session 2
ERROR: Subject 27 has no functional data defined for session 3
ERROR: Subject 27 has no functional data defined for session 4
ERROR: Subject 27 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 27 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 27 does not have any scan associated with condition post-rest-control-kotnik
ERROR: Subject 28 Session 1 functional data has 0 time-points (scans) defined
ERROR: Subject 28 Session 1 first-level covariate realignment mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 28 Session 1 first-level covariate scrubbing mismatched dimensions (192 rows, while functional data has 0 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 28 has no functional data defined for session 2
ERROR: Subject 28 has no functional data defined for session 3
ERROR: Subject 28 has no functional data defined for session 4
ERROR: Subject 28 does not have any scan associated with condition post-rest-vojta-pata
ERROR: Subject 28 does not have any scan associated with condition pre-rest-control-kotnik
ERROR: Subject 28 does not have any scan associated with condition post-rest-control-kotnik
CONN v.17.a
SPM12 + DEM FieldMap MEEGtools
Matlab v.2016b
storage: 902.4Gb available
Warning: Contents.m overloaded by version in folder /home/labounek/toolbox/matlab/FastICA_25

Hi Alfonso and all

Is it possible to compute and get info about the Eigenvector centrality in conn? If so how please?

Thanks

Aser

Dear all,

I need to include the following two steps in the preprocessing procedure for my data:

-Elimination of odd-even slice intensity differences due to interleaved acquisition
-Frame-censoring with a threshold of 0.5% root-mean-square frame-to-frame intensity change

Does conn support these two preprocessing steps?

Thanks!

Cheers
Sascha

Hi,

I have subjects who underwent resting state fMRI and I am performing a ROI-ROI analysis using conn. I am calculating average intra- and inter-network connectivity values using the individual subject correlation matrices I obtain from the 'resultsROI_subjectx_Condition001.mat' file. However, I wish to calculate average intra and internetwork connectivity after controlling for the effect of Age on the individual correlations between ROI's. Is there a way to obtain an individual subject correlation matrix which contains the correlation values after being adjusted for the effect of Age?
Any direction would be appreciated.

Stefan

Dear Shady,

thank you for you reply. I suppose I was not clear enough in my original post. I was wondering if it is possible to use partial correlation in seed-to-voxel analysis to further investigate the findings obtained in this analysis. In my case that would mean to include the thalamus, which was not present as a seed but was obtained as a result of seed-voxel analysis. The idea was to further investigate, which variance in the data is attributable to the thalamic time course. In brief:

1. Seed-to-voxel analysis using ICA networks as seed
2. Result: Several areas show increased connectivity with this seed, the thalamus is among those regions
3. Use partial correlation to regress out the signal of the thalamus (either the whole thalamus or a cluster)

Does that makes sense? Any help would be highly appreciated