functional connectivity in individual space

Submitted by Ter Minassian Aram on Fri, 07/31/2009 - 19:48

Hello
First thank you for this toolbox that open new perpectives.
I am trying to perform functional connectivity in non normalized space in patients with glial tumors.
 For this purpose I create a brain mask coregistered with the functional data (same number of slices and voxel size)
However at the last step of computing functional connectivity an exception occured.

Computing functional connectivity with: "C:\Aram\IRM\Brain data base Siemens\chirurgie eveillee\Brossard\resting state raw\rest_detrend_detrend_filtered"
  Read 3D EPI functional images: "C:\Aram\IRM\Brain data base Siemens\chirurgie eveillee\Brossard\resting state raw\rest_detrend_detrend_filtered".........................................

  ROI time course retrieving through "ROI Center(mm)=(-53, -22, 41); Radius=6.00 mm.".
Exception occured. (MATLAB:badsubscript)
 Attempted to access mask(45.9129,18.562,22.2869); index must be a positive integer or logical.
 263#line,  Ball2Mask, in "C:\Program Files\SPM5\spm5\toolbox\REST2007V1.3_090525\REST2007V1.3_090525\rest_SphereROI.m"
 108#line,  rest_SphereROI, in "C:\Program Files\SPM5\spm5\toolbox\REST2007V1.3_090525\REST2007V1.3_090525\rest_SphereROI.m"
 126#line,  fc, in "C:\Program Files\SPM5\spm5\toolbox\REST2007V1.3_090525\REST2007V1.3_090525\fc.m"
 1323#line,  btnComputeFC_Callback, in "C:\Program Files\SPM5\spm5\toolbox\REST2007V1.3_090525\REST2007V1.3_090525\fc_gui.m"
 96#line,  gui_mainfcn, in "C:\Program Files\MATLAB\R2007b\toolbox\matlab\guide\gui_mainfcn.m"
 35#line,  fc_gui, in "C:\Program Files\SPM5\spm5\toolbox\REST2007V1.3_090525\REST2007V1.3_090525\fc_gui.m"
>>

Indeed the seed ROI was centered around -53, -22, -41 using MRIcron : however the coordonates of the native brain mask seemed to be in an other referential and in non integer values.

Is there any solution to perform connectivity in native space?
Thank you for your help
Aram

Submitted by YAN Chao-Gan on Sat, 08/01/2009 - 11:27

Hi!
Is your un-normalized data in NIfTI format?
There is always some orientation matrix (affine matrix) in the un-normalized data.
It's difficult for REST to locate the coordinate if your data with an affine matrix (have non-zero values in the non-diagonal position).
You'd better to re-orient your data (diagonalize the complex affine matrix) before entering the functional connectivity analysis.
Please refer to "Some Useful Programs: http://restfmri.net/forum/node/81" to get the re-orient program.