HPC check

Login

ssh netid@login.storrs.hpc.uconn.edu

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Copy a file

On your computer

touch testcopy

scp testcopy netid@login.storrs.hpc.uconn.edu:/home/NETID

or

scp testcopy netid@login.storrs.hpc.uconn.edu:~

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Editing at the Terminal

ssh netid@login.storrs.hpc.uconn.edu
nano testcopy

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Dataset

• Gorgolewski et al (2013)
• Test-retest dataset of various functional localizers
• Stored in /scratch/psyc5171/dataset1
• New BIDS level: session
  • sub-01/ses-test
• Already in BIDS form
• Metadata is at the study level
• Your output and related files will go in /scratch/psyc5171/NETID

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Goal

• Today: run a single subject afni_proc on the cluster
• Next week: run the entire dataset

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Steps

• Fork and clone hw7
• Figure out slice timing (non-multiband)
• Create event timing files
• Write afni_proc.py command
• Copy to cluster
• As a job:
  • Run afni_proc.py
  • Generate proc script
  • Run proc script

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Slice timing

• Look at dataset1/task-fingerfootlips_bold.json
• How are the slices being acquired?

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Slice timing

• Slice times start at 0 and increase
• If we checked, the first slice would be inferior (=ascending)
• But not monotonically (=interleaved)
• Slice code is alt+z
• No timing file needed: use -tpattern alt+z

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Events

• Block design motor localizer (fingerfootlips)
• 15 second blocks
• Timing for all subjects/sessions in dataset1/task-fingerfootlips_events.tsv
• Create a timing file (think back to HW1 or last class)
• Which convolution function should be used with 3dDeconvolve?

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'BLOCK(15)'

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Creating a timing file

• This can be done with a shell command similarly to HW1
• Use awk 'BEGIN { ORS=" " }; {print $1}' as part of the command

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Creating a timing file

• Let's modify log2times.py from the last class

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Contrasts

• finger-foot
• finger-lips
• foot-lips

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Modify ap.sh

• afni_proc.py generates processing scripts
• The afni_proc.py command is generated by uber_subject.py
• Edit ap.sh to work with the current data
• Paths for input data should start with /scratch/psyc5171/dataset1

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Edit the sbatch script

• Customize sbatch_ap.sh and sbatch_proc.sh
• Push your hw7 repository
• Login to HPC
• cd /scratch/psyc5171/NETID
• Clone your hw7 repository on the cluster

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Submit your job

To generate afni_proc.py script

sbatch sbatch_ap.sh

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Submit your job

To run the proc script:

sbatch sbatch_proc.sh

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