[Camino-users] generate atlas_mask problem

[Philip A Cook]

Hi,

1.

It looks like you're trying to binarize a mask. There's a bunch of tools to do this, since you are using FSL you might try fslmaths. I recommend avoiding Analyze, stick with NIfTI.


2. 

Camino can perform various types of tractography, please see the documentation and the tutorials at

http://cmic.cs.ucl.ac.uk/camino



On May 24, 2013, at 9:44 AM, lujiao luo wrote:

> Hello experts,
> 
> I was trying to do connectivity-based segmentation using camino, but I couldn't obtain the atlas_mask.nii.gz properly. When I tried to view the image in mricron, it said the atlas_mask.img file was smaller than described in header. This is what I have done:
> 1. My atlas which contain label information was obtained by using wfu_pickatlas TD_label.nii. The file was registered to nodif_brain.nii.gz by using fsl flirt. Then I used code below to obtain an atlas_mask.nii.gz file.
> 
> >> fid = fopen('/scans/atlas_subject.img', 'r');
> >> atlas = fread(fid, 'int');
> >> fclose(fid);
> >> mask = atlas ./ atlas;
> >> fid = fopen('/scans/atlas_mask.img', 'w', 'b');
> >> fwrite(fid, mask, 'int16');
> >> fclose(fid);
> 
> Then  run command (I used the voxeldims and datadims of our data)
> analyzeheader -voxeldims 1.7 1.7 2.3 -datadims 128 128 60 -datatype short > scans/atlas_mask.hdr 
> 
> 
> But I was confused that what's the atlas_subject.img since the tutorial mentioned both of them.
> 
> 2. When doing fiber tracking, if camino was using a probabilistic algorithm just like fsl, or using a multifiber tracking algorithm?
> 
> 
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