soyfrien

$ sudo fmriprep-docker -i poldracklab/fmriprep:latest -u 12218:12218 -w /louis/temp-151rc1 /louis/raw_bids /louis/derivatives-151rc1 participant --fs-license-file=/usr/local/freesurfer/license.txt --ignore slicetiming --output-spaces MNI152NLin2009cAsym:res-2 T1w fsaverage5 --participant-label 12345
[sudo] password for louis: 
RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.09.7 -u 12218:12218 -v /usr/local/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /louis/raw_bids:/data:ro -v /louis/derivatives-151rc1:/out -v /louis/temp-151rc1:/scratch poldracklab/fmriprep:latest /data /out participant --ignore slicetiming --output-spaces MNI152NLin2009cAsym:res-2 T1w fsaverage5 --participant-label 12345 -w /scratch
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
	1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

	Please visit https://neurostars.org/search?q

soyfrien

$ sudo fmriprep-docker -i poldracklab/fmriprep:1.5.0 -u 12218:12218 -w /louis/temp-run2 /louis/raw_bids /louis/derivatives-run2 participant --fs-license-file=/usr/local/freesurfer/license.txt --ignore slicetiming --output-spaces MNI152NLin2009cAsym:res-2 T1w fsaverage5 --participant-label 12345
RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.09.7 -u 12218:12218 -v /usr/local/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /louis/raw_bids:/data:ro -v /louis/derivatives-run2:/out -v /louis/temp-run2:/scratch poldracklab/fmriprep:1.5.0 /data /out participant --ignore slicetiming --output-spaces MNI152NLin2009cAsym:res-2 T1w fsaverage5 --participant-label 12345 -w /scratch
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
  1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

  Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing co

soyfrien

$ sudo fmriprep-docker -i poldracklab/fmriprep:1.5.0 -u 12218:12218 -w /louis/temp /louis/raw_bids /louis/derivatives2 participant --fs-license-file=/usr/local/freesurfer/license.txt --ignore slicetiming --output-spaces MNI152NLin2009cAsym:res-2 T1w fsaverage5 --participant-label 12345
RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.09.7 -u 12218:12218 -v /usr/local/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /louis/raw_bids:/data:ro -v /louis/derivatives2:/out -v /louis/temp:/scratch poldracklab/fmriprep:1.5.0 /data /out participant --ignore slicetiming --output-spaces MNI152NLin2009cAsym:res-2 T1w fsaverage5 --participant-label 12345 -w /scratch
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
	1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

	Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about th

soyfrien

Homebrew and Symlink Issues

If you see this:

Error: An unexpected error occurred during the `brew link` step
The formula built, but is not symlinked into /usr/local
Permission denied @ dir_s_mkdir - /usr/local/Frameworks
Error: Permission denied @ dir_s_mkdir - /usr/local/Frameworks

soyfrien

#FREESURFER SETUP
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
#END FREESURFER SETUP

soyfrien

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/opt/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/opt/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/opt/anaconda3/bin:$PATH"

soyfrien

When seeing these types of messages, it may be helpful to remove the failed service using zmprov. See below.

  ----- The following addresses had permanent fatal errors -----
<email address>
    (reason: 554 5.7.1 Service unavailable; Client host [IP] blocked using dnsbl.njabl.org)

   ----- Transcript of session follows -----
... while talking to MAIL.SERVER.HOSTNAME:
>>> DATA
<<< 554 5.7.1 Service unavailable; Client host [IP] blocked using dnsbl.njabl.org

soyfrien

#!/bin/bash
ls -la $1 | awk '{print $1, $3, $4,  $9}'

soyfrien

# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
	. ~/.bashrc
fi

# User specific environment and startup programs
PATH=$PATH:$HOME/.local/bin:$HOME/bin
export PATH

soyfrien

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=