September 28, 2016 at 10:11 pm #363wwu94Participant
I am using BrainSuite command line version under ssh server Linux environment:
I encountered the following problem when I try to perform Cerebrum labeling using the default atlas: brainsuite.icbm452.lpi.v08a.img and brainsuite.icbm452.v15a.label.img:
Initializing brain volume
Performing linear alignment of atlas brain to subject brain
Performing warp alignment (order=5) of atlas brain to subject brain
Problem with file ./brainLETN3m/scale.init
The specified file does not exist. (AIR_NO_FILE_READ_ERROR)
warp process failed.
error during warping
unable to finish making label output.
I am not sure where the problem is, but the process was working fine in the GUI version on my own computer.
Thanks for helping!
September 28, 2016 at 10:18 pm #364David ShattuckKeymaster
Can you provide the specific command line call that you are making, including all arguments?
If that stage works in the GUI, the best thing to do is to use the cortical_extraction.cmd script. It is configured to have settings that match those in the GUI, and will produce identical results.
September 28, 2016 at 10:29 pm #365wwu94Participant
Thanks for replying!
Here is the code I used:
## DIR is where I put all the skull-stripped volume (output from skull-stripping function).
## of and of2 are just formatted output file names.
for f in “$DIR”/*_mri.nii.gz
/home/share/BrainSuite16a/bin/cerebro -i “$f” –atlas “/home/share/BrainSuite16a/atlas/brainsuite.icbm452.lpi.v08a.img” –atlaslabels “/home/share/BrainSuite16a/atlas/brainsuite.icbm452.v15a.label.img” -l “$DIR/$of” -o “$DIR/$of2”
For cortical_extraction.cmd: can that be executed in Linux environment? I thought it’s for windows platform. If it can, can you be a little more specific on that?
Thanks a lot for helping!
October 28, 2016 at 9:00 pm #549David ShattuckKeymaster
There is also cortical_extraction.sh, which can be run from bash on Mac or Linux. It sets all of the parameters to be the same as the GUI. If necessary, you can copy it and edit it if you need to make any changes. If you do edit it, then you will want to make sure that BrainSuiteDir is set to the installation path. If it is not set, then the script will try to find the files based on location of the script.
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