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BF: mcflirt_2stage couldn't handle missing output dirs

Add all aligned data missing because of this bug
Michael Hanke 8 years ago
parent
a3be1319e6
commit
7d3a693be0
100 changed files with 99 additions and 1 deletions
Split View Show Diff Stats
  1. 1 1
      code/mcflirt_2stage
  2. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-1_bold.nii.gz
  3. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-1_bold_mcparams.txt
  4. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-2_bold.nii.gz
  5. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-2_bold_mcparams.txt
  6. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-3_bold.nii.gz
  7. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-3_bold_mcparams.txt
  8. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-4_bold.nii.gz
  9. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-4_bold_mcparams.txt
  10. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-5_bold.nii.gz
  11. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-5_bold_mcparams.txt
  12. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-6_bold.nii.gz
  13. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-6_bold_mcparams.txt
  14. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-7_bold.nii.gz
  15. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-7_bold_mcparams.txt
  16. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-8_bold.nii.gz
  17. 1 0
      sub-14/in_bold3Tp2/sub-14_task-avmovie_run-8_bold_mcparams.txt
  18. 1 0
      sub-14/in_bold3Tp2/sub-14_task-movielocalizer_run-1_bold.nii.gz
  19. 1 0
      sub-14/in_bold3Tp2/sub-14_task-movielocalizer_run-1_bold_mcparams.txt
  20. 1 0
      sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-1_bold.nii.gz
  21. 1 0
      sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-1_bold_mcparams.txt
  22. 1 0
      sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-2_bold.nii.gz
  23. 1 0
      sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-2_bold_mcparams.txt
  24. 1 0
      sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-3_bold.nii.gz
  25. 1 0
      sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-3_bold_mcparams.txt
  26. 1 0
      sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-4_bold.nii.gz
  27. 1 0
      sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-4_bold_mcparams.txt
  28. 1 0
      sub-14/in_bold3Tp2/sub-14_task-retmap_run-1_bold.nii.gz
  29. 1 0
      sub-14/in_bold3Tp2/sub-14_task-retmap_run-1_bold_mcparams.txt
  30. 1 0
      sub-14/in_bold3Tp2/sub-14_task-retmap_run-2_bold.nii.gz
  31. 1 0
      sub-14/in_bold3Tp2/sub-14_task-retmap_run-2_bold_mcparams.txt
  32. 1 0
      sub-14/in_bold3Tp2/sub-14_task-retmap_run-3_bold.nii.gz
  33. 1 0
      sub-14/in_bold3Tp2/sub-14_task-retmap_run-3_bold_mcparams.txt
  34. 1 0
      sub-14/in_bold3Tp2/sub-14_task-retmap_run-4_bold.nii.gz
  35. 1 0
      sub-14/in_bold3Tp2/sub-14_task-retmap_run-4_bold_mcparams.txt
  36. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-1_bold.nii.gz
  37. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-1_bold_mcparams.txt
  38. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-2_bold.nii.gz
  39. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-2_bold_mcparams.txt
  40. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-3_bold.nii.gz
  41. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-3_bold_mcparams.txt
  42. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-4_bold.nii.gz
  43. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-4_bold_mcparams.txt
  44. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-5_bold.nii.gz
  45. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-5_bold_mcparams.txt
  46. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-6_bold.nii.gz
  47. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-6_bold_mcparams.txt
  48. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-7_bold.nii.gz
  49. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-7_bold_mcparams.txt
  50. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-8_bold.nii.gz
  51. 1 0
      sub-15/in_bold3Tp2/sub-15_task-avmovie_run-8_bold_mcparams.txt
  52. 1 0
      sub-15/in_bold3Tp2/sub-15_task-movielocalizer_run-1_bold.nii.gz
  53. 1 0
      sub-15/in_bold3Tp2/sub-15_task-movielocalizer_run-1_bold_mcparams.txt
  54. 1 0
      sub-15/in_bold3Tp2/sub-15_task-objectcategories_run-1_bold.nii.gz
  55. 1 0
      sub-15/in_bold3Tp2/sub-15_task-objectcategories_run-1_bold_mcparams.txt
  56. 1 0
      sub-15/in_bold3Tp2/sub-15_task-objectcategories_run-2_bold.nii.gz
  57. 1 0
      sub-15/in_bold3Tp2/sub-15_task-objectcategories_run-2_bold_mcparams.txt
  58. 1 0
      sub-15/in_bold3Tp2/sub-15_task-objectcategories_run-3_bold.nii.gz
  59. 1 0
      sub-15/in_bold3Tp2/sub-15_task-objectcategories_run-3_bold_mcparams.txt
  60. 1 0
      sub-15/in_bold3Tp2/sub-15_task-objectcategories_run-4_bold.nii.gz
  61. 1 0
      sub-15/in_bold3Tp2/sub-15_task-objectcategories_run-4_bold_mcparams.txt
  62. 1 0
      sub-15/in_bold3Tp2/sub-15_task-retmap_run-1_bold.nii.gz
  63. 1 0
      sub-15/in_bold3Tp2/sub-15_task-retmap_run-1_bold_mcparams.txt
  64. 1 0
      sub-15/in_bold3Tp2/sub-15_task-retmap_run-2_bold.nii.gz
  65. 1 0
      sub-15/in_bold3Tp2/sub-15_task-retmap_run-2_bold_mcparams.txt
  66. 1 0
      sub-15/in_bold3Tp2/sub-15_task-retmap_run-3_bold.nii.gz
  67. 1 0
      sub-15/in_bold3Tp2/sub-15_task-retmap_run-3_bold_mcparams.txt
  68. 1 0
      sub-15/in_bold3Tp2/sub-15_task-retmap_run-4_bold.nii.gz
  69. 1 0
      sub-15/in_bold3Tp2/sub-15_task-retmap_run-4_bold_mcparams.txt
  70. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-1_bold.nii.gz
  71. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-1_bold_mcparams.txt
  72. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-2_bold.nii.gz
  73. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-2_bold_mcparams.txt
  74. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-3_bold.nii.gz
  75. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-3_bold_mcparams.txt
  76. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-4_bold.nii.gz
  77. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-4_bold_mcparams.txt
  78. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-5_bold.nii.gz
  79. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-5_bold_mcparams.txt
  80. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-6_bold.nii.gz
  81. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-6_bold_mcparams.txt
  82. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-7_bold.nii.gz
  83. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-7_bold_mcparams.txt
  84. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-8_bold.nii.gz
  85. 1 0
      sub-16/in_bold3Tp2/sub-16_task-avmovie_run-8_bold_mcparams.txt
  86. 1 0
      sub-16/in_bold3Tp2/sub-16_task-movielocalizer_run-1_bold.nii.gz
  87. 1 0
      sub-16/in_bold3Tp2/sub-16_task-movielocalizer_run-1_bold_mcparams.txt
  88. 1 0
      sub-16/in_bold3Tp2/sub-16_task-movielocalizer_run-1_bold_tsnr.nii.gz
  89. 1 0
      sub-16/in_bold3Tp2/sub-16_task-objectcategories_run-1_bold.nii.gz
  90. 1 0
      sub-16/in_bold3Tp2/sub-16_task-objectcategories_run-1_bold_mcparams.txt
  91. 1 0
      sub-16/in_bold3Tp2/sub-16_task-objectcategories_run-2_bold.nii.gz
  92. 1 0
      sub-16/in_bold3Tp2/sub-16_task-objectcategories_run-2_bold_mcparams.txt
  93. 1 0
      sub-16/in_bold3Tp2/sub-16_task-objectcategories_run-3_bold.nii.gz
  94. 1 0
      sub-16/in_bold3Tp2/sub-16_task-objectcategories_run-3_bold_mcparams.txt
  95. 1 0
      sub-16/in_bold3Tp2/sub-16_task-objectcategories_run-4_bold.nii.gz
  96. 1 0
      sub-16/in_bold3Tp2/sub-16_task-objectcategories_run-4_bold_mcparams.txt
  97. 1 0
      sub-16/in_bold3Tp2/sub-16_task-retmap_run-1_bold.nii.gz
  98. 1 0
      sub-16/in_bold3Tp2/sub-16_task-retmap_run-1_bold_mcparams.txt
  99. 1 0
      sub-16/in_bold3Tp2/sub-16_task-retmap_run-2_bold.nii.gz
  100. 0 0
      sub-16/in_bold3Tp2/sub-16_task-retmap_run-2_bold_mcparams.txt

+ 1 - 1
code/mcflirt_2stage
View File 

@@ -38,7 +38,7 @@ ignore=$FSLDIR
 
 
 inbold=$(readlink -f $1) || true
 
 ref=$(readlink -f $2) || true
 
-outbold=$(readlink -f $3)
 
+outbold=$(readlink -m $3)
 
 initflirtopts=${4:--dof 6}
 
 
 if [ -z "$inbold" ]; then

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-1_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/9p/W6/MD5E-s92858599--e5de069e9289435f7f89f3e85bda63ee.nii.gz/MD5E-s92858599--e5de069e9289435f7f89f3e85bda63ee.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-1_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/mX/gW/MD5E-s33075--482346fdfeb5b81ae0b57fdad959cefc.txt/MD5E-s33075--482346fdfeb5b81ae0b57fdad959cefc.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-2_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/67/7K/MD5E-s90910628--919aa3869bdb0d6b832969676f33bdd9.nii.gz/MD5E-s90910628--919aa3869bdb0d6b832969676f33bdd9.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-2_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/Vz/W4/MD5E-s32404--8f9b8c77cadfce53bf18a6ab1e02d4e4.txt/MD5E-s32404--8f9b8c77cadfce53bf18a6ab1e02d4e4.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-3_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/pm/xf/MD5E-s90304348--c86c02210615f5213046e7aad010f0de.nii.gz/MD5E-s90304348--c86c02210615f5213046e7aad010f0de.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-3_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/9v/Zf/MD5E-s31470--fac784826b675d5362afb1426ce78afe.txt/MD5E-s31470--fac784826b675d5362afb1426ce78afe.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-4_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/97/pK/MD5E-s101088354--5ff0ddd13b968044a5b6941f73674d27.nii.gz/MD5E-s101088354--5ff0ddd13b968044a5b6941f73674d27.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-4_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/Kk/k4/MD5E-s35068--50d14795f6373959f2ac33556df37e88.txt/MD5E-s35068--50d14795f6373959f2ac33556df37e88.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-5_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/QK/Xv/MD5E-s93018335--9157901aea4ed5d31f61cd1cd6a988cb.nii.gz/MD5E-s93018335--9157901aea4ed5d31f61cd1cd6a988cb.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-5_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/xX/Gg/MD5E-s33651--0ad008b8fdba7c29b10d41b24838f8a3.txt/MD5E-s33651--0ad008b8fdba7c29b10d41b24838f8a3.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-6_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/68/3k/MD5E-s88936881--f8e79fea5a78e37673389a5dcf1deafa.nii.gz/MD5E-s88936881--f8e79fea5a78e37673389a5dcf1deafa.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-6_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/7x/v7/MD5E-s31902--356f2658cd56ca8b9aeb2990a8a776d9.txt/MD5E-s31902--356f2658cd56ca8b9aeb2990a8a776d9.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-7_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/51/fp/MD5E-s109972626--e4c9df70c245da9924595ef51985e71b.nii.gz/MD5E-s109972626--e4c9df70c245da9924595ef51985e71b.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-7_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/jz/8g/MD5E-s39564--c9b92510fd04f8523018d4f566d75156.txt/MD5E-s39564--c9b92510fd04f8523018d4f566d75156.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-8_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/87/zX/MD5E-s68633265--54aa56f9a8cc620924cfe290a27ef23d.nii.gz/MD5E-s68633265--54aa56f9a8cc620924cfe290a27ef23d.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-avmovie_run-8_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/z5/kv/MD5E-s24049--83a4436b5eeb3ca6f06abce017db74a3.txt/MD5E-s24049--83a4436b5eeb3ca6f06abce017db74a3.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-movielocalizer_run-1_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/GQ/f8/MD5E-s9460756--c00c8408d60aeec1f74f22d4650fef61.nii.gz/MD5E-s9460756--c00c8408d60aeec1f74f22d4650fef61.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-movielocalizer_run-1_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/Wq/M6/MD5E-s3596--dac7fed1c14be4beb9c950805d98fe80.txt/MD5E-s3596--dac7fed1c14be4beb9c950805d98fe80.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-1_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/6j/Gj/MD5E-s31413694--83f29e9a612afa97e6bb1ba04a474562.nii.gz/MD5E-s31413694--83f29e9a612afa97e6bb1ba04a474562.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-1_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/Qz/V0/MD5E-s11662--6a0691effa86d54b06512dc660444ae5.txt/MD5E-s11662--6a0691effa86d54b06512dc660444ae5.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-2_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/8m/v1/MD5E-s31287490--ed04185082f51497a8caac9f6c33db34.nii.gz/MD5E-s31287490--ed04185082f51497a8caac9f6c33db34.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-2_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/8j/fM/MD5E-s11306--0b446c2bad714612e69db2067d0804d1.txt/MD5E-s11306--0b446c2bad714612e69db2067d0804d1.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-3_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/Q5/mj/MD5E-s31311882--604eeef6418c4bd87e8f9364a4a445e9.nii.gz/MD5E-s31311882--604eeef6418c4bd87e8f9364a4a445e9.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-3_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/vm/36/MD5E-s11751--66cc3b34178a2c7b674949f1c69e9db1.txt/MD5E-s11751--66cc3b34178a2c7b674949f1c69e9db1.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-4_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/kz/xX/MD5E-s31301957--bc2f7ca51e76ee1ef8f83f8cae844cca.nii.gz/MD5E-s31301957--bc2f7ca51e76ee1ef8f83f8cae844cca.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-objectcategories_run-4_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/4X/XQ/MD5E-s11721--59191679fadd145e3e7a76779b3a7834.txt/MD5E-s11721--59191679fadd145e3e7a76779b3a7834.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-retmap_run-1_bold.nii.gz
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/xP/q8/MD5E-s17797336--95f5bd76baaed2eff6b0675e7aa5fcba.nii.gz/MD5E-s17797336--95f5bd76baaed2eff6b0675e7aa5fcba.nii.gz

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-retmap_run-1_bold_mcparams.txt
View File 

@@ -0,0 +1 @@
 
+../../.git/annex/objects/6m/83/MD5E-s6932--21b5fedb9078d246b5ce767f2af2535d.txt/MD5E-s6932--21b5fedb9078d246b5ce767f2af2535d.txt

+ 1 - 0
sub-14/in_bold3Tp2/sub-14_task-retmap_run-2_bold.nii.gz
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