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Update versaFlow from development repository #3

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merged 59 commits into from
Sep 22, 2023
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7c573d6
Fix apply topup
AlexVCaron Jul 11, 2023
f08b3e6
register epi rev to forward dwi after epi corrections
AlexVCaron Aug 3, 2023
05d9ef0
minor fix
AlexVCaron Aug 3, 2023
79fad2e
minor fix
AlexVCaron Aug 3, 2023
eea06da
Several little fixes
AlexVCaron Aug 2, 2023
2617d87
Update readme
AlexVCaron Aug 15, 2023
9f94e73
Improve registration and segmentation
AlexVCaron Aug 22, 2023
7c662ca
Fix cache invalidation problem on T1 mask
AlexVCaron Aug 24, 2023
f1c8b05
Replace rev image with aligned one when available
AlexVCaron Aug 29, 2023
ff57cf4
Merge branch 'fix/hotfixes' of https://github.com/AlexVCaron/mrHARDIf…
AlexVCaron Aug 29, 2023
6e91121
Fix segmentation (dgm regions m ust be wm for tracking to work),
AlexVCaron Aug 30, 2023
e10e11f
Merge branch 'fix/hotfixes' of https://github.com/AlexVCaron/mrHARDIf…
AlexVCaron Aug 30, 2023
31d0ccf
Create process to generate composite transforms out of ANTs (easier t…
AlexVCaron Sep 1, 2023
90d6328
Minor fixes
AlexVCaron Sep 1, 2023
d4157ac
Stage transforms correctly
AlexVCaron Sep 2, 2023
a49ad0e
minor fixes
AlexVCaron Sep 2, 2023
d79a317
Minor fix
AlexVCaron Sep 2, 2023
9aa0431
add suffix
AlexVCaron Sep 2, 2023
265f523
minor fix
AlexVCaron Sep 2, 2023
bb3e9ed
Fix publish_all
AlexVCaron Sep 7, 2023
0724fec
Overwrite output files on resume
AlexVCaron Sep 7, 2023
a0d5d93
Fix apply topup
AlexVCaron Jul 11, 2023
6994292
register epi rev to forward dwi after epi corrections
AlexVCaron Aug 3, 2023
16cda70
minor fix
AlexVCaron Aug 3, 2023
596957e
minor fix
AlexVCaron Aug 3, 2023
165c2d2
Replace rev image with aligned one when available
AlexVCaron Aug 29, 2023
266c74a
Renaming to versaflow
AlexVCaron Aug 7, 2023
05b16e7
Update readme
AlexVCaron Aug 10, 2023
913500d
register epi rev to forward dwi after epi corrections
AlexVCaron Aug 3, 2023
8156c57
minor fix
AlexVCaron Aug 3, 2023
2bb87f9
minor fix
AlexVCaron Aug 3, 2023
f29735a
Fix ants_ai initialization
AlexVCaron Aug 11, 2023
62577d5
Minor fix for now, will remove later
AlexVCaron Aug 12, 2023
04e8361
Send template to b0 (T1 is registered)
AlexVCaron Aug 13, 2023
9a5a11a
Update registration parameters
AlexVCaron Aug 14, 2023
2c8c5b6
update citation
AlexVCaron Aug 14, 2023
99be78d
Renaming to versaFlow
AlexVCaron Aug 14, 2023
02a2f71
Update image readme
AlexVCaron Aug 14, 2023
507f0a0
Update usage
AlexVCaron Aug 14, 2023
a2f95b3
Minor fix
AlexVCaron Aug 15, 2023
f0baa61
Update readme
AlexVCaron Aug 15, 2023
51ddd51
Improve registration and segmentation
AlexVCaron Aug 22, 2023
9bc92f5
Fix cache invalidation problem on T1 mask
AlexVCaron Aug 24, 2023
c9d0c3d
Fix segmentation (dgm regions m ust be wm for tracking to work),
AlexVCaron Aug 30, 2023
2fb1f2e
Create process to generate composite transforms out of ANTs (easier t…
AlexVCaron Sep 1, 2023
bc84e6d
Minor fixes
AlexVCaron Sep 1, 2023
cbab379
Stage transforms correctly
AlexVCaron Sep 2, 2023
fca8a18
minor fixes
AlexVCaron Sep 2, 2023
c3afdc9
Minor fix
AlexVCaron Sep 2, 2023
81763da
add suffix
AlexVCaron Sep 2, 2023
370f220
minor fix
AlexVCaron Sep 2, 2023
24fa0cb
Fix publish_all
AlexVCaron Sep 7, 2023
92ee506
Overwrite output files on resume
AlexVCaron Sep 7, 2023
32784ea
Reverse order of transforms entering reoder (so its in the right orde…
AlexVCaron Sep 22, 2023
bca16f9
Bad pvf cropping (wm comes after csf in alpha order)
AlexVCaron Sep 22, 2023
9b427db
Merge branch 'fix/hotfixes' of https://github.com/AlexVCaron/mrHARDIf…
AlexVCaron Sep 22, 2023
47bebd3
Reverse transforms inputed to composer
AlexVCaron Sep 22, 2023
e857986
Missing reverse
AlexVCaron Sep 22, 2023
df25263
Apply renaming to versaFlow
AlexVCaron Sep 22, 2023
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minor fix
  • Loading branch information
AlexVCaron committed Sep 2, 2023
commit 265f523bbb474b2204ddd996a6223924d2407087
3 changes: 2 additions & 1 deletion modules/processes/io.nf
Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,8 @@ process rename_sequentially {

input:
tuple val(sid), path(files)
val(suffix), val(start_character)
val(suffix)
val(start_character)
output:
tuple val(sid), path("*_${suffix}*", includeInputs: true)
script:
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