Structural connectome for Human Connectome Project (HCP)

Hi all,
I have recently started using the MRtix for structural connectivity of HCP. The toolbox has been installed to Linux Ubuntu by following all the instruction provided in the tutorial section, and it is up to date. The data of HCP based on the tutorial is downloaded and allocate a folder on the desktop for it. When I run the very first line in the HCP tutorial:

5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked

I got the below error.

mehdy@mehdy-OptiPlex-9020:~$ 5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked
5ttgen: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
5ttgen: Generated temporary directory: /tmp/5ttgen-tmp-OTL0V5/
Command: mrconvert /home/mehdy/T1w_acpc_dc_restore_brain.nii.gz /tmp/5ttgen-tmp-OTL0V5/input.mif
5ttgen: [ERROR] Command failed: mrconvert /home/mehdy/T1w_acpc_dc_restore_brain.nii.gz /tmp/5ttgen-tmp-OTL0V5/input.mif
5ttgen: Output of failed command:
mrconvert: [ERROR] cannot access file “/home/mehdy/T1w_acpc_dc_restore_brain.nii.gz”: No such file or directory
mrconvert: [ERROR] error opening image "/home/mehdy/T1w_acpc_dc_restore_brain.nii.gz"
5ttgen: Changing back to original directory (/home/mehdy)
5ttgen: Script failed while executing the command: mrconvert /home/mehdy/T1w_acpc_dc_restore_brain.nii.gz /tmp/5ttgen-tmp-OTL0V5/input.mif
5ttgen: For debugging, inspect contents of temporary directory: /tmp/5ttgen-tmp-OTL0V5/

Any help would be appreciated to solve the issue.

I have added the path of the fsl but now a new error is getting appeared which is Atlases required for FSL’s FIRST program not installed;
Please install fsl-first-data using your relevant package manager
I am using ubuntu 16.04

Hi Mehdy,

You have to install fsl-complete from the neurodebian repository.


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