Merge pull request #35 from marcobarilari/main

ENH doc for datalad installation

Author: marcobarilari

.gitignore

@@ -1 +1 @@
-*DS_Store
+*DS_Store

doc/cpp_mriqc.slurm

@@ -17,7 +17,7 @@
 #export OMP_NUM_THREADS=9
 #export MKL_NUM_THREADS=9
 
-## CPP MRIqc script for CECI cluster
+## CPP MRIqc script for CECI cluster v0.2.0
 #
 # writtent by CPP people
 #

doc/install_datalad.md

@@ -45,7 +45,7 @@ cd YOUR-CLONED-REPO
 datalad get .
 ```
 
-it won't probably work since ssh keys to github/gin/etc has to be set up. 
+it won't probably work since ssh keys to github/gin/etc has to be set up.
 
 Set up the einviroment as you did on your personal computer and remebere that if your password is not working is is possible that github/gin/etc are expecting the token code you have to create for each machine.
 

doc/overview.md

@@ -71,9 +71,9 @@ to choose the cluster that best meets your necessities)
 
 ThrFor example two clusters with different characteristics (part of the CECI cluster):
 
-##### Lemaitre3 
+##### Lemaitre3
 
-!!! Warning 
+!!! Warning
 
     SHUTDOWN FORM JULY 1ST 2024 AND REPLACED BY LEMAITRE4 !!!!!
 

doc/run_fmriprep.md

@@ -19,17 +19,17 @@ To contribute see [here](https://cpp-lln-lab.github.io/CPP_HPC/contributing/)
 - install datalad on your user (see [here](https://github.com/cpp-lln-lab/CPP_HPC/install_datalad))
 - get the fmriprep singularity image as follow:
 
-here the example is with `fmriprp version 21.0.1` but check for newer version, list of fmriprep version available [here](https://hub.docker.com/r/nipreps/fmriprep/tags/)
+here the example is with `fmriprp version 24.0.0` but check for newer version, list of fmriprep version available [here](https://hub.docker.com/r/nipreps/fmriprep/tags/)
 
 ```bash
-datalad install https://github.com/ReproNim/containers.git
+datalad install -s https://github.com/ReproNim/containers.git ~/tools/containers
 
-cd containers
+cd tools/containers
 
-datalad get images/bids/bids-fmriprep--21.0.1.sing
+datalad get images/bids/bids-fmriprep--24.0.0.sing
 ```
 
-In case you have installe the repo a while a ago and you want to use a new version of fmriprep., update the `containers` repo via:
+In case you have installed the repo a while a ago and you want to use a new version of fmriprep., update the `containers` repo via:
 
 ```bash
 # go to the repo folder
@@ -41,7 +41,7 @@ datald update --merge
 Depending on the cluster “unlock” is needed or not. No need for `lemaitre3`. !!! TO CHECK ON LEMAITRE4
 
 ```bash
-datalad unlock containers/images/bids/bids-fmriprep--21.0.1.sing
+datalad unlock containers/images/bids/bids-fmriprep--24.0.0.sing
 ```
 
   - get your `freesurfer` license (user specific) for free [here](https://surfer.nmr.mgh.harvard.edu/registration.html) and move it to the cluster
@@ -124,7 +124,7 @@ sbatch --job-name=fmriprep_trial \
     “singularity run --cleanenv \
         -B /scratch/users/m/a/marcobar:/scratch \
         -B ~/sing_temp:/sing_temp \
-        ~/sing_temp/containers/images/bids/bids-fmriprep--21.0.1.sing \
+        ~/sing_temp/containers/images/bids/bids-fmriprep--24.0.0.sing \
         /sing_temp/raw \
         /sing_temp/fmriprep \
         participant \

doc/run_mriqc.md

@@ -24,14 +24,14 @@ To contribute see [here](https://cpp-lln-lab.github.io/CPP_HPC/contributing/)
 - install datalad on your user (see [here](https://github.com/cpp-lln-lab/CPP_HPC/install_datalad))
 - get the fmriprep singularity image as follow:
 
-here the example is with `MRIqc version 23.1.0` but check for newer version, list of fmriprep version available [here](https://hub.docker.com/r/nipreps/fmriprep/tags/)
+here the example is with `MRIqc version 24.0.0` but check for newer version, list of fmriprep version available [here](https://hub.docker.com/r/nipreps/fmriprep/tags/)
 
 ```bash
 datalad install https://github.com/ReproNim/containers.git
 
 cd containers
 
-datalad get images/bids/bids-mriqc--23.1.0.sing
+datalad get images/bids/bids-mriqc--24.0.0.sing
 ```
 
 In case you have installe the repo a while a ago and you want to use a new version of fmriprep., update the `containers` repo via:
@@ -46,7 +46,7 @@ datald update --merge
 Depending on the cluster “unlock” is needed or not. No need for `lemaitre3`. !! TO CHECK ON LEMAITRE4
 
 ```bash
-datalad unlock containers/images/bids/bids-mriqc--23.1.0.sing
+datalad unlock containers/images/bids/bids-mriqc--24.0.0.sing
 ```
 
 ## Submit a MRIqc job via a `slurm` script