Hi,

I was trying to make a mask for large blood vessles from Angio dataset and found this was discussed in "Analysis and use of FMRI response delays" by Saad, Z.S., et al., Human Brain Mapping, 2001. 13(2): p. 74-93)

The paper talked about the separation of voxels into vascular and parenchymal pools: "In the first method, we imaged blood vessels directly using 2D-TOF sequence capable of resolving blood vessels greater then 2 mm in diameter. To isolate blood vessels from other tissue, we applied an image intensity threshold (It) followed by a 3D-cluster volume threshold of 10 ml, the equivalent of 8 contiguous voxels. 2D-TOF voxels that exceeded It and formed clusters larger than 10 ml were categorized as blood vessels..."

I think this method can be implemented using 3dmerge with option "-1noneg -dxyz=1 -1clust 1.01 8", but can't figure out how the intensity threshold(0.2, 0.4 and 0.8 in the paper) was applied on Angio dataset. Could you give me some hint?

I tried to use an arbitary intensity clip value with "-1clip XX". Then any advice on how to decide this intensity value for different subjects?

Also, the mask will be used on the functional dataset, but the Angio dataset is in different resolution with functional dataset, should I use the 3dresample and 3dvolreg before making the mask or after?

Thanks for your advice.