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Use of CONN through remote server

July 26, 2017, 2:13 pm
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Hello,
I am analyzing rsfMRI data and generally I use CONN locally (with Matlab and CONN of my computer). Because I have a lot of data to analyse, I would like to use CONN (with the GUI) of a remote server (killdevil) which have matlab with CONN. I copied my data on the remote server and I connected to it. I was able to open matlab and CONN (with GUI). I prepared my setup and launched the preprocessing pipeline. But it stopped and it put a message of error:
ERROR DESCRIPTION:

Error using subsasgn_check (line 49)
Input file lists to cfg_getfile('filter',...) must be a column cellstr.
Error in subsasgn (line 80)
Error in initialise (line 48)
Error in initialise>initialise_job (line 54)
Error in initialise (line 27)
Error in initialise>initialise_job (line 81)
Error in initialise (line 34)
Error in initialise>initialise_job (line 81)
Error in initialise (line 34)
Error in initialise>initialise_job (line 116)
Error in initialise (line 31)
Error in cfg_util>local_initjob/@(ucjob)initialise(cjd,ucjob,false)
Error in cfg_util>local_initjob (line 1534)
Error in cfg_util (line 802)
Error in spm_jobman (line 246)
Error in conn_setup_preproc (line 793)
Error in conn (line 504)
Error in conn_menumanager (line 102)
CONN v.14.n
SPM12 + DEM FieldMap MEEGtools
Matlab v.2013a

Somebody have an idea of what happen?
Maybe it is problem of path...

Thanks
Celia
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HELP! Covariate problems that invert results

July 27, 2017, 6:44 am
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Hey All great scientists and minds alike

I have a few questions regarding using "age" and other co variates on a second level analysis
as the age difference between the groups I am studying are significantly different...
 
1) when using age as a covariate why does the results differ so much when using A) 1 -1 0 vs B) 1 -1 0 0 in CONN?
...for A) the 0 involves the whole list of ages whereas B) the ages are seperated according to their groups 
for example I tried both inputs and the functional connectivity results were inverted and totally different? What is happening here?
(please see attached)
 
2) Also what would happen if you use 0 0 1 -1 for example where by the ages are allocated as 1s and the groups I wish to look at are 0s... e.g. 0 0 = group A and B. 1 = Group A Ages. -1 = Group B ages.  What would CONN explore and compute in this setting?
 
3) Also is it possible and does it make sense to regress more than one covariate that are independent of each other in CONN? for example subject age and subjects time since injury like this: 1 -1 0 0 (with 0s being age and time since injury respectively)
 
4) How would you control complicated scores such as motor or sensory scores when we only have values for one group (patients). Would you then have to either present a maximal score for healthy (e.g. 100) or would you put NaN for healthys instead? (although these scores are not missing, we would like to present the healthys as having a maximum score since they are healthy)
 
 
thanks so much for your time and attention, I know that this is a lot but I think it will help us all also!
 
Best wishes
Vincent
 
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RE: CONN preprocessing :normalization error

July 27, 2017, 7:52 am
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Thank you very much it is worked very well ....
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Subject-specific implicit masks

July 27, 2017, 11:36 am
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Greetings CONN experts,

I have changed the masking variable in my spm_defauts.m file to disable voxel signal-dependent thresholding (defaults.mask.thresh = -Inf), but alas there are still "holes" in my preprocessed "niftiDATA_Subject..." files.

I would like to use subject-specific implicit masks, or alternatively turn off all masking, because parts of the brain are being masked out of some of my subjects. I know that I could get around this by using an explicit mask, but that's not an option for this subject-space analysis.

Any help would be greatly appreciated!

Jennifer
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RE: "NORMS_" output files from denoising

July 28, 2017, 6:17 am
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Hello all,

I'm also curious about these NORMS files and would love to know what they are for.

Thanks!

Jennifer
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RE: error importing ROI data

July 28, 2017, 7:59 am
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Hi Young,
 I am having a similar issue  - did you have any luck with this?

 Thank you

 Kayla
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preprocessing data in SPM for rsFC and tbFC

July 29, 2017, 6:50 am
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Hello,

We use a standardized pipeline in spm that uses a combination of ART and ArtRepair to address subject motion and noise.  We detect outlier volumes in ART using a 1mm threshold for rsFC data, and 4mm for task data, and then use ArtRepair to interpolate the motion outlier volumes.  For task data, we also use art_despike to despike the data at 4% of the global mean. Our task data is either long block (eg 40 sec) or fast event-related. We leave the rsFC data alone and use despiking in conn.  Then, we load the art_regression_outliers_and_movement.mat file into conn as a 1st level confound.  

Do you see any issue with this approach in terms of denoising?

Many thanks in advance,
Patrick
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Inconsistencies between CONN NBS and NBS tool

July 31, 2017, 2:21 am
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Dear Alfonso and other CONN users,

I have been comparing NBS results obtained using CONN and those obtained using the NBS toolbox (https://www.nitrc.org/projects/nbs/), and find the results with the two methods are somewhat different. I am using the same connectivity matrices and design matrices in both.

It seems that using the same initial threshold in both leads to a larger maximum network size in CONN (e.g. using p<0.05 one sided in CONN, and t<1.72 in NBS gives networks of 190 and 95 connections respectively). Also regardless of the edge level threshold, when calculating the p value for the network CONN seems to be less stringent than NBS (e.g. the 190 edge network has a p value of 0.0037 in CONN, while the 95 edge NBS one has a P value of 0.06. If one reduces the edge threshold to get a 190 edge network in NBS its p value is 0.09).

I was wondering does CONN use exactly the same methods as NBS, or is there a difference that explains this discrepancy?

Many thanks

Rob
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Effect size

July 31, 2017, 11:05 am
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Hi,

I would like to better understand what the effect size is and how it is interpreted for a comparison of ROI-to-ROI connectivity between 2 sessions in within-subject design?


Thank you,

Florence
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how to combine two or more projects in conn

August 1, 2017, 12:30 am
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Hi Alfonso

I am using Conn in my project where I am operating functional MRI of controls and patients.

I have made two different projects for controls and patients to pre-process them individually, in Conn. Now I want to combine them together and analyse them.
Please help me how I can combine them and operate combinedly. 

Thanks in advance

Regards
Shivali
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First-level ICC output

August 1, 2017, 1:49 pm
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Hi all, 

I am currently running a voxel-to-voxel ICC analysis across two different drug conditions. I want to see whether there is a correlation between ICC and symptom scales given to the participants in the regions which were found to be different across drug conditions. First of all, what is the statistical output for the first-level analysis with ICC? Is this just an average r-value or r-squared across all other voxels? 

And second, is there a way that I can access a matrix of this first-level statistic across all participants from the voxel-to-voxel results? Or could I do a seed-to-voxel analysis using the voxels pulled out by ICC to get this information and somehow calculate the averaged global connectivity from that?

Thanks in advance for your help! 

Best, 
Leah
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CONN: second level one group different ROI

August 2, 2017, 3:01 am
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Hi
we have one group and different ROIs , we would like to check the connectivity different by using different ROIs, we used (1 1) and (1 -1) in the Between-sources contrast  field ,  and not show any different in the results .
So, we would like to compare different ROIs and their connecting  to AAL regions ?!
 
 
Regards
 
Njoud
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Details for ROIs available in "networks.nii"

August 7, 2017, 1:41 am
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Dear Alfonso,

Would you please provide further details regarding the ROIs part of the file networks.nii available in the CONN package? The only piece of information I seem to be able to find in the networks.info file is that these ROIs have been derived from the HCP dataset with N=497. It would be great, for instance, if you could talk a bit about the parameters that went into the ICA, and perhaps more importantly, the preprocessing steps that were involved. I imagine it would be very helpful for the users to know these details, particularly if they want to publish their results using these default ROIs.  

I am posting this question because, although there have been multiple posts (e.g., http://www.nitrc.org/forum/forum.php?offset=125&max_rows=25&style=nested&forum_id=1144) related to this issue, it does not seem that it has been clarified yet. 

Thank you very much in advance,
Yuta
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Sliding Window Dynamic RSFC

August 7, 2017, 1:36 pm
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Hello conn experts,

I had some questions about sliding window resting state connectivity analyses.

First, a basic question, when I enter in the onsets, does conn typically start at 0 or at 1. So for a resting scan, if I wanted to start a sliding window right at the beginning, would it be 0 or 1? So say I would like to have 36-second long sliding windows, sliding the onset of each window by 18 s. I could set my onsets as 0, 18, 36, and so on in the onsets box.

Second, after I have generated the sliding window Fischer's Z-maps, I have generated a script that will provide me with the standard deviation over all of the sliding windows. Can I feed in the SD maps into conn and run the second level analyses on these maps?

Thanks!!!

Emily
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NBS: number of permutations?

August 7, 2017, 5:36 pm
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Dear CONN experts

I have 14 ROIs (connectivity matrix: 14x14 ROIs) and I would like to examine 2 group differences using network based statistics, by clicking "Enable permutation tests". Is there any option of specifying the number of permutations? If not, how many permutation tests are performed by default?

Thank you
Kwanghyuk
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I'm unable to correctly use dcm2nii code

August 9, 2017, 5:45 pm
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Hello. I'm having difficulty on the seemingly simple task of converting dcm files to nii files.
I'm using Bash on Ubuntu on Windows.
My Windows version is Windows 10 Pro.

From ~/c9image/NDARAF706DLN/s796950,
I have i796951.MRDC.1 ~ i796951.MRDC.166 files
I want to convert these dcm? image into nii format so that I can start image processing.
However, the command doesn't work the same way as my intuition.
When I entered the following command, it didn't work. (nothing happened)
Even though the instructions appear when using dcm2nii command,
I don't clearly understand as I was unable to find concrete examples of the usage.
 
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN$ dcm2nii -v s796950
Chris Rorden's dcm2nii :: 4AUGUST2014 (Debian) 64bit BSD License
reading preferences file /home/eternal/.dcm2nii/dcm2nii.ini
[b]0 /usr/bin/dcm2nii ERROR: unable to find[/b]
Either drag and drop or specify command line options:
  dcm2nii
OPTIONS:
-4 Create 4D volumes, else DTI/fMRI saved as many 3D volumes: Y,N = Y
-a Anonymize [remove identifying information]: Y,N = Y
-b load settings from specified inifile, e.g. '-b C:\set\t1.ini'
-c Collapse input folders: Y,N = Y
-d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = Y
-e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = Y
-f Source filename [e.g. filename.par -> filename.nii]: Y,N = N
-g gzip output, filename.nii.gz [ignored if '-n n']: Y,N = Y
-i ID  in filename [filename.dcm -> johndoe.nii]: Y,N = N
-m manually prompt user to specify output format [NIfTI input only]: Y,N = Y
-n output .nii file [if no, create .hdr/.img pair]: Y,N = Y
-o Output Directory, e.g. 'C:\TEMP' (if unspecified, source directory is used)
-p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y
-r Reorient image to nearest orthogonal: Y,N
-s SPM2/Analyze not SPM5/NIfTI [ignored if '-n y']: Y,N = N
-t Text report (patient and scan details): Y,N = N
-v Convert every image in the directory: Y,N = Y
-x Reorient and crop 3D NIfTI images: Y,N = N
  You can also set defaults by editing /home/eternal/.dcm2nii/dcm2nii.ini
EXAMPLE: dcm2nii -a y /Users/Joe/Documents/dcm/IM_0116
 
When I enter the code below, I get the same error as above.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN$ dcm2nii -4 s796950 
<span>I would appreciate it if someone knows the correct way of using the dcm2nii code to convert dcm files to nii format. </span>
<span>I've heard that there are also dcm2niigui and also the matlab versions<span id="_plain_text_marker"> </span></span>
<span><span>I can't seem to use dcm2niigui since I'm using Linux command line.</span></span>
<span><span>I would appreciate it if someone knows how to use dcm2niigui on Bash on Ubuntu on Linux.</span></span>
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Combining and comparing 2nd level analysis

August 10, 2017, 4:11 am
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I have done 2nd level analysis for a single subject over several sessions (entered in CONN as subjects) and each session having multiple fMRI runs (entered in CONN as sessions). Since I used the SPM.mat for importing data I preserved this structure.

This has been done for both experimental and control subjects.
Now I wish to:
(i) Compare changes in connectivity over time for each subject or group.
(ii) Combine the connectivity network/data for all subjects in the experimental/control group
(iii) Find the differences between groups for the combined connectivity.
Further is there a tool which can take the 2nd level results and perform statistical analyses on them.
Thanks, SS.
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intrepretation of [1 -1] contrast

August 10, 2017, 4:35 pm
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Hi,

I have an experiment with four conditions A, B, C and D and would like to check if seed-voxel connectivity is greater for condition A than condition B. I selected bivariate correlations at first level and at second level set Results.AllSubjects=1 and Results.between_conditions.contrast=[1 -1]. Is this correct? In the secondlevel folder I have corr_*.img files with the Fisher-transformed correlations. But how should I interpret these values? If the contrast was just [1], it would be the correlation coefficient between seed and voxel xyz for condition A, right? But what do the coefficients mean for the contrast [1 -1]?
Best regards,
Michael
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RE: PCA decomposition of behavioural scores

August 11, 2017, 6:08 am
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Hi Alfonso, 

I am sorry to keep bothering you about this, but I am having a lot of trouble finding the answer to my question elsewhere. I am completely done the analysis and just need to know what my component represents. Is it an amalgamation of scores from the original scale or does it represent something that I can identify from the original scale? (i.e., a specific score?) 

If there is any way you can let me know how to go about finding this information or point me to a resource I would really appreciate it. 

Thank you as always, 

Jenna
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Sessions with different durations

August 11, 2017, 11:11 am
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Dear all,

I want to compare functional connectivity between sessions with different durations. In my current data set, the number of data-points varies not only between sessions but also between subjects. I would prefer to use all data rather than reducing it to the minimum number of available data-points and would be glad to know what do you think about it. Instead of disregarding data-points that exceeds the minimum, is there any other way to control for potential differences due to different standard errors between the sessions and subjects?

Thank you in advance,

Ella
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