Connectivity Matrix visualization errors

[ds...@bnac.net]

Hi All,

I have been trying to get the visualization of CM in EDTI working, but i am constantly getting errors. I am running the EDTI in Linux. I followed the steps mentioned in the module 14 of EDTI manual to get CM's.

I have performed CM analysis from freesurfer files (trafo.labels.nii and labels_names.txt, both the files i named as mentioned in the module 14 to extract predefined ROI labels from freesurfer data). The real issue is following, i am unable to visualize nodes, with lables in a ring format. Also i always get this MNI space error message.

Also in manual in module 15 it shows randomly how to visualize Nodes in different size by creating a one column random size text file. Can anyone please elaborate on that step?  how can you get this one column size text file?

[stijn m]

Dear ???,

The network you look at is in FreeSurfer (trafo) space and is not the same as MNI. Therefore the coordinates do not match up.

BW.
Stijn

[ds...@bnac.net]

Hi Stijn,

Thank you for your reply. I have the following questions regarding Spaces.

1) How can i find out in which space is my data in?
2) Are Scanner anatomical space, native space, MNI space same or different? If different then can you please explain briefly?
3) Does it mean that if i convert freesurfer converted data in to native(input T1 image) space then it will be in MNI space?
4) Is there an intermediate file (e.g.rawspace.mgz in freesurfer) generated in E_DTI to know the conversion of the space?
5) Can i convert the Explore DTI generated results in to native space(the name here depends on your answer of first question)?

Thank you for your help and time.

Dhaval.

[stijn m]

Dear Dhaval,

1. Check the nifti header and see for the information in there. Or look at the data.
2. Those are different coordinate spaces. Different software means different standard. MNI space is rather common used.
3. If you convert the FS data to native T1, you're in anatomical space. Coregister to an MNI template to get in MNI space.
4. Not that I'am aware of.
5. Yes, the coordinates can be exchanged to different space.

HTH.
BW.
Stijn