Dear Alfonso,

First, thank you very much for a wonderful toolbox. I have a couple of questions for you. I have the data 0-2 years old healthy subjects and I want to see the connectivity changing with age. I have done all preprocessing in SPM8. My first question is about normalization. I have used pediatric template ant it is not in MNI space and the rois in conn are MNI space. What should I do for that case? Should I normalize pediatric template to MNI space.

Second, in graph theory analysis I clicked "export data" and I have .dl, .csv, .network, .stats files. I opened .csv file and I have global efficiency, local efficiency... for all subject. First part gives me average values of whole brain right? And then for each rois starting BA1(l).I want to have a trajectory graph to get how global and local efficiency changes with age by choosing all and age subject effects with [0 1] contrast. After that can I use these values to have this trajectory graph in SAS or SPSS. 

Thank you very much again!!
Elveda

Dear Elveda,

Regarding the first question I am not very familiar with this but I believe it would be better to use an age-appropriate atlas for pediatric samples (instead of the default MNI-space parcellation), since the choice of ROI parcels can significantly affect your network measures. 

Regarding the planned analysis steps that sounds perfectly fine. The first part of the .csv file lists the "network-level" measures (properties of the entire network; c.f. properties of each ROI within the network), and in your second-level analyses you can select 'AllSubjects' and 'age' in the subject effects list and enter a contrast [0 1] to look at (linear) age effects for each of the graph measures. Of course you can also take the values in the .csv file (for each subject) and explore these further in other packages for plotting or other more complex analyses.

Hope this helps
Alfonso
Originally posted by Elveda Gozdas:

Dear Alfonso,

Thank you very much for your help!!. I am trying to use age-appropriate atlas. I have created a text file defines the labels, but I got an error:
"Warning: file /Users/elvedagozdas/Desktop/ALL_sleeping/finfant-2yr-aal.txt format not recognized". And I did not get the rois list like I got using /Users/elvedagozdas/Downloads/conn/rois/BA.img. What's wrong with my .txt file? Which format the text file should be?

Thanks,
Elveda

Dear Elveda,

Please attach your atlas *.txt file to better understand what the format problem might be. In general if your atlas myatlas.nii file contains ROI ids/numbers that range, for example, from 1 to 5, and you would like to associated with these numbers the labels "ROI1" to "ROI5", you can define the associated labels file using any of the following methods:

1) create an associated .txt file containing only the associated labels (in order). See for example BA.txt file. E.g.

myatlas.txt
ROI1
ROI2
ROI3
ROI4
ROI5

2) create an associated .txt file containing two tab-separated columns, indicating ROI ids followed by ROI labels (ROIs listed in any order). See for example any freesurfer *LUT.txt file. E.g.

myatlas.txt
3 ROI3
4 ROI4
1 ROI1
2  ROI2
5  ROI5

3) create an associated .csv file containing two comma-separated columns, indicating ROI labels followed by ROI ids (ROIs listed in any order).  E.g.

myatlas.csv
ROI3, 3
ROI4, 4
ROI1, 1
ROI2, 2
ROI5, 5

4) create an associated .xls file containing two columns, indicating ROI ids followed by ROI labels (ROIs listed in any order, columns listed in any order; id's should be numeric, labels should be strings; file may include a first-row header or not). E.g.

myatlas.xls
ROI3 3
ROI4 4
ROI1 1
ROI2 2
ROI5 5

The first format above only works when your atlas file contains sequential numbers from 1 to N, while the last three formats work for any numbering scheme for your ROI atlas file (e.g. non-sequential numbers)

Hope this helps
Alfonso


Originally posted by Elveda Yildirim:

Dear Alfonso,

Thank you so much for a quick reply.  I  have tried again using method 1, but I have the same problem. I attached the *.txt file. Maybe I am missing something. Could you please help me?


Thanks,
Elveda

Dear Alfonso,

Sorry, I forgot to attach.

Thanks,
Elveda

Dear Elveda,

The file looks all right, except perhaps that it uses a somewhat unusual encoding (UTF16-LE), which may be causing problems when read in Matlab, particularly the presence of a byte-order mark at the beginning of the file. Could you please try the attached file instead? (I simply converted your file to ISO-8859-1). If that does not work please send me your .nii file to double-check that it also contains values that are consistent with these labels (integers ranging from 0 to 90). 

Hope this helps
Alfonso

Originally posted by Elveda Yildirim:

Dear Alfonso,

Thank you very much!!. It worked and I have my results now. 

Thanks,
Elveda

Dear Alfonso,

I have 50 subjects and I want to have connectivity changing with age 0-2 years. I am using age-appropriate atlas. When I started the analysis, it takes too much time for the second level analysis. I started to run yesterday, and it is still sunning and it is saying it is going to take 12 ours. Is there anyting  wrong? 

Thank you very much for your help!

Elveda