[Camino-users] generate atlas_mask problem

[lujiao luo]

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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