Michiel Cottaar (bec77a9f) at 27 Mar 16:21
build based on 0abc71ab
Michiel Cottaar (0abc71ab) at 27 Mar 16:14
Call LinearPart for any number
Support the following features:
Given a file-tree
sub-{subject}
T1w.nii.gz
T1w_bet.nii.gz
I want the following to work:
for FT_subject in A B ; do
bet $(. file-tree get T1w) $(. file-tree get T1w_bet)
done
This should in effect call:
bet ./sub-A/T1w.nii.gz ./sub-A/T1w_bet.nii.gz
bet ./sub-B/T1w.nii.gz ./sub-B/T1w_bet.nii.gz
We should also support iteration.
call_bet() {
bet $(. file-tree get T1w) $(. file-tree get T1w_bet)
}
. file-tree iter T1w call_bet --glob
This will call bet
for any sub-*/T1w.nii.gz
file.
This will require file-tree
to be a shell script, which is sourced from the pipeline script. It will internally call a python script called file-tree-helper
, which will actually read and interpret the file-tree.
ENVSTRING=$(file-tree-helper ENVSTRING)
echo $(eval $ENVSTRING file-tree-helper get $@)
file-tree-helper ENVSTRING
will return a string like: "FT_subject=$FT_subject FT_session=$FT_session
" for a file-tree containing 2 placeholders (subject
and session
).file-tree-helper get
will return the full filename using the environmental variables $FT_subject
and $FT_session
.Implementation for iter:
for SETENV in $(file-tree-helper SETENV $1); do
eval $SETENV $2
done
file-tree-helper SETENV <template>
will return a string like: "FT_subject=A FT_session=01
" presuming that the <template>
depends on subject and session.
I think there should be a new top-level topic called "Pipeline tools", which will contain 4 sections:
fsl_sub
fslpy
file-tree
fsl-pipe
The first is currently a section in "Other tools", while the others are in "Other tools > FSL Python libraries". This would make these tools much easier to find.
Michiel Cottaar (21e633fd) at 25 Mar 17:20
build based on 955ccb5f
Michiel Cottaar (955ccb5f) at 25 Mar 17:14
Convert InstantGradient1D to InstantGradient3D
... and 2 more commits
Michiel Cottaar (b6c27dc5) at 25 Mar 17:02
build based on bc49bcb5
Michiel Cottaar (709d73a7) at 25 Mar 15:30
build based on e4f501dd
Michiel Cottaar (e4f501dd) at 25 Mar 15:24
Allow scanner to be unset
Michiel Cottaar (8347a725) at 25 Mar 15:05
build based on 8a9bd7ff
Michiel Cottaar (8a9bd7ff) at 25 Mar 14:58
Fix start time effect on block duration for gradients
... and 6 more commits
Michiel Cottaar (d23d975b) at 21 Mar 16:51
build based on 0bfa5869
Michiel Cottaar (0bfa5869) at 21 Mar 16:45
Store instants in dense vector form
... and 5 more commits
Michiel Cottaar (349c62d0) at 21 Mar 12:13
build based on 8642eb54
Michiel Cottaar (0e3db36c) at 08 Mar 13:44
Michiel Cottaar (0e3db36c) at 08 Mar 10:25