Hi

I found an option called INTRINSC CONNECTIVITY on the fmri Menu. I am trying to do functinal connectivity to identify brain areas interconnected. Hoerver, I am not sure that Intrinsic connecty is functional connecting. generally and roi is defined and the application will identify areas that follow activation in other brain regions. I could not find further explanation on how to use this option of Biomage. I would appreciate if you can refer me to that documentation.

best Regards

Magno R. Guillen, PhD
FIU

Dear Magno,

Thanks. We are working on an updated manual for the fMRI tool to describe the functional connectivity tools, hopefully this will be out in the next week or so and will describe things in more detail. Intrinsic Connectivity effectively computes the correlation (there are some abstracts from our group describing this and is similar to a recent paper by Buckner et al) from each voxel to each other and then for each voxel counts how many voxels had correlation above a certain threshold (typically 0.25) to compute a degree measure which is then normalized.

Xenios

Thank you
I am looking forward to read the new manual.
 
Best regards

HI Again.
 
i am trying to generate a series of slices automatically using the movie tools, which support scripting. Are you planing to include the movie tool in the new manual? Do you have any reference or example script to learn how to use it.
Thanks

Please clarify. What do you mean by slices? The movie tool really only supports parameters to do with the camera position and orientation not the contents of the scene.

There is a description of the movie tools here

http://www.bioimagesuite.org/doc/node8.h...

XP

Hi

I am sorry I could not explain myselft clearly. I am using the animation tool  (Display-AnimationTool) in a manual way. Setting the view to axial and the delay time to 500 ms, then I startr the frame grabber and I scroll the axial slices and I get a stack of axial images. Since the animation tool works automatically with scripts, my question was regarding to how to generate a scriot that does that, capture the axial slice (or cor or sag) and then moves to next slices and records it.

I hope this clarify my question.

Best Regards

magno

Thanks. The script tool only allows the automatic manipulation of the camera position for 3D scenes -- unfortunately the axial, sag, coronal sliders are not scriptable right now.

Xenios

Thanks for the explanation. I will continue doing the manual operation to capture the slices.

As for the 3D manipulation of images (automatic rotation), do you have a sample script to understand its usage. Is it going to be available in the new release of the manual?

Thanks

Hello!

I would also like to know something about using BioImageSuit for intrinsic connectivity analysis. Can you share it with me? Thanks a million.

Best Wishes!

Hi Zhou,

Once your data is preprocessed and you have transformations mapping your data to the reference space, you can use legacy BIS to estimate connectivity. The legacy manual will get you much of the way there—see "Chapter 13: The Single Subject fMRI Tool":
https://medicine.yale.edu/bioimaging/sui... Please note that this will require legacy BIS—it is not yet possible to estimate matrices or GLM-based activation in BISWeb.

Essentially this will guide you in the process of creating a "setupfile" to estimate parameters for a GLM, but you can instead change some parameters in this file to estimate functional connectivity*. You can then run the setupfile to estimate FC like this:
bis_fmrisetup.tcl my_setupfile.xmlg matrix

Feel free to reach out if you encounter any issues going through these steps.

Best,
Stephanie

* Functional connectivity-specific parameters in the setupfile + example arguments:
#-----------------------------------------------------
#Resting State Connectivity Extra Inputs
#-----------------------------------------------------
#VOI Definition
/my_dir/shen_1mm_368_parcellation.nii.gz
#VOI Definition Space (Reference,Anatomical,Conventional,Functional)
Reference
#Inverse Reference Transformation
/my_dir/i.matr
#-----------------------------------------------------
#Connectivity Parameters
#-----------------------------------------------------
#Mask Level (% of max intensity)
masklevel : 0.05
#Polynomial Drift
driftpol : 3
# Slice Mean Removal
slicemeanremoval : 0
# Volume Mean Removal
volumemeanremoval : 1
#Raw Correlation
rawcorrelation : 0
#Z Transform
ztransform : 0
#Process Runs Individually
individualruns : 0
#Temporal Smoothing Sigma (Frames)
temporalsigma : 1
#Intrinsic Connectivity Threshold
threshold : 0.25
#Intrinsic Connectivity Range
range : Positive
#Intrinsic Connectivity Mode
mode : Sqr
#Use VOI Image as mask For Intrinsic Connectivity
usermask : 1
#Preprocess (Eliminate Motion Parameters)
usemotionparams : 1
#Preprocess (Eliminate CSF/White Matter Mean)
usecsfmean : 1