Daer all,
I was able to install Hammer and run the sample datasets without any problems. Thank you for a good job!
Allow me a few newbie questions to help me analyze my own data.

1) Intensity values of tissue classes
I segment my data using FAST which outputs values 1 for CSF, 2 for GM and 3 for WM. I was not able to find any way to change the values to comply with the Hammer standard - could you suggest any solution?

2) Models supplied
Is there any descriptions of the models? All the "VN" models comes without headers and I am not able to use them. Do the "VN" models mean Ventricles and are they used for the segmentation and labeling of ventricles? Could you sent me any hints how to do that?

3) Image dimensions
Is it necessary to resample the data to be of the same dimension as the model used? Is it what you mean that it is necessary to have in-plane resolution 256x256?

Thank you for your comments,

Tomas Kasparek
Dep. of Psychiatry, Masaryk University
Brno, the Czech Republic

Hello Tomas,

For 1) you can use the program: changelinevalueinimg included with
HAMMER, although it is only available for the CLI (Command Line
Interface).

You can run 3 commands such as:

changelinevalueinimg mysegmentedimage.img mysegmentedimage.img -o 15 -c
10
changelinevalueinimg mysegmentedimage.img mysegmentedimage.img -o 155 -c
150
changelinevalueinimg mysegmentedimage.img mysegmentedimage.img -o 253 -c
250

where 15,155,253 are the values of your current segmented images.

For 2) Yes, indeed VN stands for ventricles. I will post the headers
soon, also we have a beta version of the HAMMER CLI coming soon that
does take the ventricle masks into account. Depending on your time frame
you may want to try this. I must note that this functionality requires
FSL.

Finally for 3) Yes you need to have the same XY dimensions.

Cheers

Andres

Hi,

The model headers for VN images have been included, you can obtain the
updated archive at:

https://www.rad.upenn.edu/sbia/software-...
s.zip=20

Cheers,

Andres

Hi Anders,
thank you for the updated models and your answers.
The problem is I cannot find changelinevalueinimg executable in my hammer instalation (1_0 version downloaded last week).

As for the new beta version of CLI Hammer, I would appreciate a lot if I can try it.

Best,

Tomas