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--- calcoloscientifico:userguide:fsl [28/01/2026 15:14] – fabio.spataro
+++ calcoloscientifico:userguide:fsl [28/01/2026 16:14] (versione attuale) – fabio.spataro
@@ Linea 3: / Linea 3: @@
 [[https://fsl.fmrib.ox.ac.uk/fsl|FSL]]
-FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces).
+FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. Most of the tools can be run both from the command line and as GUIs (''point-and-click'' graphical user interfaces).
 === Job FSL 6.0.7.19 (single node, multitasks) for CPU ===
@@ Linea 42: / Linea 42: @@
 === Interactive FSL 6.0.7.19 session ===
+To run an interactive work session, you need to connect to the ''[[gui|gui.hpc.unipr.it]]'' server via RDP (Remote Desktop Protocol), change your keyboard layout (if necessary), open a terminal window. The following commands must be run in the terminal window.
+To work in ''Group'' mode, run the newgrp command.
+Example:
+<code>
+[foo@ui03 ~]$ groups
+Person G_BAR
+[foo@ui03 ~]$ newgrp G_BAR
+</code>
+In case you want to work in the ''$GROUP'' directory:
+<code>
+(G_BAR)[foo@ui03 ~]$ echo $GROUP
+/hpc/group/G_BAR
+(G_BAR)[foo@ui03 ~]$ cd $GROUP
+(G_BAR)[foo@ui03 G_BAR]$ ...
+</code>
+In case you want to work in the ''$ARCHIVE'' directory:
+<code>
+(G_BAR)[foo@ui03 ~]$ echo $ARCHIVE
+/hpc/archive/G_BAR
+(G_BAR)[foo@ui03 ~]$ cd $ARCHIVE
+(G_BAR)[foo@ui03 G_BAR]$ ...
+</code>
 == Interactive FSL 6.0.7.19 session (single node, multitasks) for CPU ==
@@ Linea 62: / Linea 90: @@
     bash
 </code>
+Once you have access to the compute node, run these commands:
+<code>
+module load apptainer fsl
+fsl.sh
+fsleyes
+</code>
+Example:
+<code>
+[foo@wn82 ~]$ module load apptainer fsl
+[foo@wn82 ~]$ fsl.sh
+(fsl-6.0.7.19.sif)[foo@wn82 ~]$ fsleyes
+</code>
+To close your work session, run the ''exit'' command twice. The first command exits the ''[[calcoloscientifico:userguide:apptainer|Apptainer]]'' container, while the second exits the remote node.
 == Interactive FSL 6.0.7.19 session (single node, multitasks) for GPU ==
-Command to run ''fsl'' on 1 node of the ''gpu'' partition using 4 cores, at most 16 GB of memory and 1 ''NVIDIA P100 GPU'':
+Command to run ''fsl'' on 1 node of the ''gpu'' partition using 4 cores, at most 16 GB of memory and 1 ''NVIDIA P100'' GPU:
 <code>
@@ Linea 82: / Linea 128: @@
     bash
 </code>
+Once you have access to the compute node, run these commands:
+<code>
+module load apptainer fsl
+fsl.sh
+fsleyes
+</code>
+Example:
+<code>
+[foo@wn41 ~]$ module load apptainer fsl
+[foo@wn41 ~]$ fsl.sh
+(fsl-6.0.7.19.sif)[foo@wn41 ~]$ fsleyes
+</code>
+To close your work session, run the ''exit'' command twice. The first command exits the ''[[calcoloscientifico:userguide:apptainer|Apptainer]]'' container, while the second exits the remote node.