Hi, I wonder if you can help me figure out a problem I'm having.

A couple of seconds after starting the analysis I get the following error:

sh-4.1$ ./run_hallucination_v13b.sh T1template.nii,T2template.nii T1toconvert.nii regression 5E4 100 0.01 3x3x3 24 0 yes 550 1500 out.nii ~/MCR/bin/glnxa64/v81
...
...

Index exceeds matrix dimensions.

Error in Crop3D (line 89)
Error in image_hallucination_v13b (line 310)
Error in run_hallucination_v13b (line 191)
MATLAB:badsubscript

Thanks for any help you can provide

Josh

The new release (2015 January 7th) should resolve this issue.

This is the procedure I've used. I've two images from the same subject with different modalities (0001.nii and 0001AREG.nii) which have been rigidly registered to each other. The skull is still present so I found peak intensity. However, I just read the other post and realize that there are not restricted to the WM, so these peak values are probably wrong. When I run the scripts here is the output:

[jaa@mb]$ ./run_hallucination_v13b.sh 0001.nii,0001AREG.nii toconvert.nii regression 5E4 150 0.01 3x3x3 12 100 yes 2126 855 converted.nii ~/MCR/bin/glnxa64/v81
Setting up environment variables
MCR ROOT is /home/local/AD3/jaa/MCR/bin/glnxa64/v81
Atlas volume: 0001.nii,0001AREG.nii
Subject volume: toconvert.nii
./run_hallucination_v13b 0001.nii,0001AREG.nii toconvert.nii regression 5E4 150 0.01 3x3x3 12 100 yes 2126 855 converted.nii
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
This is a parallelized code. Make sure you use all the processors.
Do not run more than one subject simultaneously if you are using all the processors.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Setting Params
Atlas volumes = 0001.nii,0001AREG.nii.
2 atlas inputs detected.
1 subject inputs detected.
Using regression.
Using lambda = 0.010.
Using 3 x 3 x 3 sized patches.
Using 50000 atlas patches.
Using 150 nearest neighbors.
Atlas slice range =[100, 115].
Subject and atlas images contain skull. WM peaks must be provided.
Atlas WM peaks are: 2126.00
Subject WM peaks are: 855.00
Using 12 cpu.
Output will be written in
converted.nii
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
------------------------WARNING WARNING--------------------
If any of your subject or atlas volume contains a Brainweb phantom
check the WM peak calculated inside the code (will be displayed next).
Most likely it would be wrong. So use the options param.subjectwmpeak
or param.atlaswmpeak to feed the WM peak info.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
----------------------------------------------------------------
Using 12 parallel processes.
WM peaks are mentioned. No default normalization applied.
Working on atlas: 0001.nii
Atlas : 256 x 256 x 208 volume
Working on atlas: 0001AREG.nii
Atlas : 256 x 256 x 208 volume
Scaling by 2126.000..Some extra outlier removal..
For atlas with skull, outliers are bounded for robustness.
Index exceeds matrix dimensions.

Error in Crop3D (line 89)
Error in image_hallucination_v13b (line 310)
Error in run_hallucination_v13b (line 191)
MATLAB:badsubscript


--
Because the error occurs in Crop3D (which I presumed removed background voxels) I didn't suspect an issue with peak WM parameters...However, the executables are binary so I have no idea yet until I try later today.

Thanks for your time,

Most Sincerely,
Joshua

Thanks!

Can you please post the full output?

Note that this issue that is frustrating me doesn't go away if I change the starting slice position in the command.