Browse Source

T1w, grpbold3Tp2 templates

plus associated transformations from and to these images spaces
Michael Hanke 8 years ago
parent
commit
fac413eaa8
100 changed files with 333 additions and 3 deletions
  1. 3 0
      .gitmodules
  2. 54 0
      code/mk_subjtmpl_t1w
  3. 54 0
      code/mk_subjtmpl_t1w.submit
  4. 76 0
      code/mk_xfm_bold3Tp2_vs_t1w
  5. 42 0
      code/mk_xfm_bold3Tp2_vs_t1w.submit
  6. 1 1
      code/ofhelpers
  7. 11 2
      code/proc.cfg
  8. 1 0
      raw/structural
  9. 1 0
      sub-01/bold3Tp2/dil_occ_mask.nii.gz
  10. 1 0
      sub-01/bold3Tp2/in_grpbold3Tp2/brain_mask.nii.gz
  11. 1 0
      sub-01/bold3Tp2/in_grpbold3Tp2/head.nii.gz
  12. 1 0
      sub-01/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz
  13. 1 0
      sub-01/bold3Tp2/in_grpbold3Tp2/tmpl2subj_warp.nii.gz
  14. 1 0
      sub-01/bold3Tp2/in_t1w/brain.nii.gz
  15. 1 0
      sub-01/bold3Tp2/in_t1w/brain_occ.nii.gz
  16. 1 0
      sub-01/bold3Tp2/in_t1w/xfm_6dof.mat
  17. 1 0
      sub-01/bold3Tp2/in_t1w/xfm_6dof_occ.mat
  18. 1 0
      sub-01/t1w/brain.nii.gz
  19. 1 0
      sub-01/t1w/brain_csf_stdspace.nii.gz
  20. 1 0
      sub-01/t1w/brain_gray_stdspace.nii.gz
  21. 1 0
      sub-01/t1w/brain_mask.nii.gz
  22. 1 0
      sub-01/t1w/brain_mixeltype.nii.gz
  23. 1 0
      sub-01/t1w/brain_nobias.nii.gz
  24. 1 0
      sub-01/t1w/brain_prob_csf.nii.gz
  25. 1 0
      sub-01/t1w/brain_prob_gray.nii.gz
  26. 1 0
      sub-01/t1w/brain_prob_white.nii.gz
  27. 1 0
      sub-01/t1w/brain_pve_csf.nii.gz
  28. 1 0
      sub-01/t1w/brain_pve_gray.nii.gz
  29. 1 0
      sub-01/t1w/brain_pve_white.nii.gz
  30. 1 0
      sub-01/t1w/brain_pveseg.nii.gz
  31. 1 0
      sub-01/t1w/brain_seg.nii.gz
  32. 1 0
      sub-01/t1w/brain_seg_csf.nii.gz
  33. 1 0
      sub-01/t1w/brain_seg_gray.nii.gz
  34. 1 0
      sub-01/t1w/brain_seg_white.nii.gz
  35. 1 0
      sub-01/t1w/brain_white_stdspace.nii.gz
  36. 1 0
      sub-01/t1w/dil_occ_mask.nii.gz
  37. 1 0
      sub-01/t1w/head.nii.gz
  38. 1 0
      sub-01/t1w/in_bold3Tp2/brain.nii.gz
  39. 1 0
      sub-01/t1w/in_bold3Tp2/brain_occ.nii.gz
  40. 1 0
      sub-01/t1w/in_bold3Tp2/xfm_6dof.mat
  41. 1 0
      sub-01/t1w/in_bold3Tp2/xfm_6dof_occ.mat
  42. 1 0
      sub-01/t1w/in_mni152/afnitest.nii.gz
  43. 1 0
      sub-01/t1w/in_mni152/afnitest_WARP.nii.gz
  44. 1 0
      sub-01/t1w/in_mni152/brain.nii.gz
  45. 1 0
      sub-01/t1w/in_mni152/dil_occ_mask.nii.gz
  46. 1 0
      sub-01/t1w/in_mni152/subj2tmpl.mat
  47. 1 0
      sub-01/t1w/in_mni152/tmpl2subj.mat
  48. 1 0
      sub-02/bold3Tp2/dil_occ_mask.nii.gz
  49. 1 0
      sub-02/bold3Tp2/in_grpbold3Tp2/brain_mask.nii.gz
  50. 1 0
      sub-02/bold3Tp2/in_grpbold3Tp2/head.nii.gz
  51. 1 0
      sub-02/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz
  52. 1 0
      sub-02/bold3Tp2/in_grpbold3Tp2/tmpl2subj_warp.nii.gz
  53. 1 0
      sub-02/bold3Tp2/in_t1w/brain.nii.gz
  54. 1 0
      sub-02/bold3Tp2/in_t1w/brain_occ.nii.gz
  55. 1 0
      sub-02/bold3Tp2/in_t1w/xfm_6dof.mat
  56. 1 0
      sub-02/bold3Tp2/in_t1w/xfm_6dof_occ.mat
  57. 1 0
      sub-02/t1w/brain.nii.gz
  58. 1 0
      sub-02/t1w/brain_csf_stdspace.nii.gz
  59. 1 0
      sub-02/t1w/brain_gray_stdspace.nii.gz
  60. 1 0
      sub-02/t1w/brain_mask.nii.gz
  61. 1 0
      sub-02/t1w/brain_mixeltype.nii.gz
  62. 1 0
      sub-02/t1w/brain_nobias.nii.gz
  63. 1 0
      sub-02/t1w/brain_prob_csf.nii.gz
  64. 1 0
      sub-02/t1w/brain_prob_gray.nii.gz
  65. 1 0
      sub-02/t1w/brain_prob_white.nii.gz
  66. 1 0
      sub-02/t1w/brain_pve_csf.nii.gz
  67. 1 0
      sub-02/t1w/brain_pve_gray.nii.gz
  68. 1 0
      sub-02/t1w/brain_pve_white.nii.gz
  69. 1 0
      sub-02/t1w/brain_pveseg.nii.gz
  70. 1 0
      sub-02/t1w/brain_seg.nii.gz
  71. 1 0
      sub-02/t1w/brain_seg_csf.nii.gz
  72. 1 0
      sub-02/t1w/brain_seg_gray.nii.gz
  73. 1 0
      sub-02/t1w/brain_seg_white.nii.gz
  74. 1 0
      sub-02/t1w/brain_white_stdspace.nii.gz
  75. 1 0
      sub-02/t1w/dil_occ_mask.nii.gz
  76. 1 0
      sub-02/t1w/head.nii.gz
  77. 1 0
      sub-02/t1w/in_bold3Tp2/brain.nii.gz
  78. 1 0
      sub-02/t1w/in_bold3Tp2/brain_occ.nii.gz
  79. 1 0
      sub-02/t1w/in_bold3Tp2/xfm_6dof.mat
  80. 1 0
      sub-02/t1w/in_bold3Tp2/xfm_6dof_occ.mat
  81. 1 0
      sub-02/t1w/in_mni152/brain.nii.gz
  82. 1 0
      sub-02/t1w/in_mni152/dil_occ_mask.nii.gz
  83. 1 0
      sub-02/t1w/in_mni152/subj2tmpl.mat
  84. 1 0
      sub-02/t1w/in_mni152/tmpl2subj.mat
  85. 1 0
      sub-03/bold3Tp2/dil_occ_mask.nii.gz
  86. 1 0
      sub-03/bold3Tp2/in_grpbold3Tp2/brain_mask.nii.gz
  87. 1 0
      sub-03/bold3Tp2/in_grpbold3Tp2/head.nii.gz
  88. 1 0
      sub-03/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz
  89. 1 0
      sub-03/bold3Tp2/in_grpbold3Tp2/tmpl2subj_warp.nii.gz
  90. 1 0
      sub-03/bold3Tp2/in_t1w/brain.nii.gz
  91. 1 0
      sub-03/bold3Tp2/in_t1w/brain_occ.nii.gz
  92. 1 0
      sub-03/bold3Tp2/in_t1w/xfm_6dof.mat
  93. 1 0
      sub-03/bold3Tp2/in_t1w/xfm_6dof_occ.mat
  94. 1 0
      sub-03/t1w/brain.nii.gz
  95. 1 0
      sub-03/t1w/brain_csf_stdspace.nii.gz
  96. 1 0
      sub-03/t1w/brain_gray_stdspace.nii.gz
  97. 1 0
      sub-03/t1w/brain_mask.nii.gz
  98. 1 0
      sub-03/t1w/brain_mixeltype.nii.gz
  99. 1 0
      sub-03/t1w/brain_nobias.nii.gz
  100. 0 0
      sub-03/t1w/brain_prob_csf.nii.gz

+ 3 - 0
.gitmodules

@@ -4,3 +4,6 @@
 [submodule "code/ofhelpers"]
 	path = code/ofhelpers
 	url = /home/data/exppsy/forrest_gump/git/openfmri_code
+[submodule "raw/structural"]
+	path = raw/structural
+	url = ../structural

+ 54 - 0
code/mk_subjtmpl_t1w

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+set -e
+set -u
+
+subj=$1
+betopts="${2:--R -f 0.1 -g 0.0}"
+
+subjdir="${subj}/t1w"
+mkdir -p "${subjdir}"
+# this will produce the input to the freesurfer recon-all pipeline
+$FSLDIR/bin/fslreorient2std \
+	raw/structural/$subj/anat/${subj}_T1w \
+	${subjdir}/head
+
+$FSLDIR/bin/bet \
+	${subjdir}/head \
+	${subjdir}/brain \
+	-m ${betopts}
+
+mkdir -p "${subjdir}/in_mni152"
+$FSLDIR/bin/flirt -dof 12 \
+	-in ${subjdir}/brain \
+	-ref /usr/share/data/fsl-mni152-templates/MNI152_T1_1mm_brain.nii.gz \
+	-omat "${subjdir}/in_mni152/subj2tmpl.mat" \
+	-out "${subjdir}/in_mni152/brain"
+
+$FSLDIR/bin/convert_xfm \
+	-omat "${subjdir}/in_mni152/tmpl2subj.mat" \
+	-inverse "${subjdir}/in_mni152/subj2tmpl.mat"
+
+## make the brain image's sform transform to MNI space
+#PYTHONPATH=code/ofhelpers python -c \
+#	"import os; os.chdir(\"${subjdir}\"); from openfmri.nipype_helpers import update_sform2mni; update_sform2mni(\"brain.nii.gz\", \"in_mni152/subj2tmpl.mat\", \"/usr/share/data/fsl-mni152-templates/MNI152_T1_1mm_brain.nii.gz\")"
+#mv "${subjdir}/updated_sform.nii.gz" "${subjdir}/brain.nii.gz"
+
+$FSLDIR/bin/fast -n 3 -t 1 -g -B -p \
+	-a "${subjdir}/in_mni152/tmpl2subj.mat" \
+	-o "${subjdir}/brain" \
+	"${subjdir}/brain"
+
+# rename FAST output
+mv "${subjdir}/brain_seg_0.nii.gz" "${subjdir}/brain_seg_csf.nii.gz"
+mv "${subjdir}/brain_seg_1.nii.gz" "${subjdir}/brain_seg_gray.nii.gz"
+mv "${subjdir}/brain_seg_2.nii.gz" "${subjdir}/brain_seg_white.nii.gz"
+mv "${subjdir}/brain_pve_0.nii.gz" "${subjdir}/brain_pve_csf.nii.gz"
+mv "${subjdir}/brain_pve_1.nii.gz" "${subjdir}/brain_pve_gray.nii.gz"
+mv "${subjdir}/brain_pve_2.nii.gz" "${subjdir}/brain_pve_white.nii.gz"
+mv "${subjdir}/brain_prob_0.nii.gz" "${subjdir}/brain_prob_csf.nii.gz"
+mv "${subjdir}/brain_prob_1.nii.gz" "${subjdir}/brain_prob_gray.nii.gz"
+mv "${subjdir}/brain_prob_2.nii.gz" "${subjdir}/brain_prob_white.nii.gz"
+mv "${subjdir}/brain_restore.nii.gz" "${subjdir}/brain_nobias.nii.gz"
+mv "${subjdir}/brain_gm_stdspace.nii.gz" "${subjdir}/brain_gray_stdspace.nii.gz"
+mv "${subjdir}/brain_wm_stdspace.nii.gz" "${subjdir}/brain_white_stdspace.nii.gz"

+ 54 - 0
code/mk_subjtmpl_t1w.submit

@@ -0,0 +1,54 @@
+universe = vanilla
+output = condor_logs/$(CLUSTER).$(PROCESS).out
+error = condor_logs/$(CLUSTER).$(PROCESS).err
+log = condor_logs/$(CLUSTER).$(PROCESS).log
+initialdir = /home/data/psyinf/forrest_gump/collection/tnt
+getenv = True
+request_cpus = 1
+request_memory = 8000
+should_transfer_files = NO
+transfer_executable = False
+executable = /home/data/psyinf/forrest_gump/collection/tnt/code/mk_subjtmpl_t1w
+
+arguments = sub-01
+queue
+arguments = sub-02
+queue
+arguments = sub-03
+queue
+arguments = sub-04
+queue
+arguments = sub-05
+queue
+arguments = sub-06
+queue
+arguments = sub-07
+queue
+arguments = sub-08
+queue
+arguments = sub-09
+queue
+arguments = sub-10
+queue
+arguments = sub-11
+queue
+arguments = sub-12
+queue
+arguments = sub-13
+queue
+arguments = sub-14
+queue
+arguments = sub-15
+queue
+arguments = sub-16
+queue
+arguments = sub-17
+queue
+arguments = sub-18
+queue
+arguments = sub-19
+queue
+arguments = sub-20
+queue
+arguments = sub-21
+queue

+ 76 - 0
code/mk_xfm_bold3Tp2_vs_t1w

@@ -0,0 +1,76 @@
+#!/bin/bash
+
+set -e
+set -u
+
+subj=$1
+
+t1dir="${subj}/t1w"
+bolddir="${subj}/bold3Tp2"
+
+mkdir -p "${bolddir}/in_t1w"
+mkdir -p "${t1dir}/in_bold3Tp2"
+
+
+#$FSLDIR/bin/flirt -dof 6 \
+#	-in ${bolddir}/brain \
+#	-ref ${t1dir}/brain_nobias \
+#	-omat "${bolddir}/in_t1w/xfm_6dof.mat" \
+#	-out "${bolddir}/in_t1w/brain"
+#
+#$FSLDIR/bin/convert_xfm \
+#	-omat "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
+#	-inverse "${bolddir}/in_t1w/xfm_6dof.mat"
+#
+#$FSLDIR/bin/flirt \
+#	-in "${t1dir}/brain_nobias" \
+#	-ref "${bolddir}/brain" \
+#	-applyxfm \
+#	-init "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
+#	-out "${t1dir}/in_bold3Tp2/brain"
+
+#
+# occiptal focus
+#
+
+$FSLDIR/bin/fslmaths \
+	/usr/share/data/mni-structural-atlas/MNI/MNI-maxprob-thr0-2mm.nii.gz \
+	-thr 5 -uthr 5 -bin -dilF -dilF \
+	${t1dir}/in_mni152/dil_occ_mask.nii.gz
+
+$FSLDIR/bin/flirt \
+	-in ${t1dir}/in_mni152/dil_occ_mask.nii.gz \
+	-ref "${t1dir}/brain" \
+	-applyxfm \
+	-init "${t1dir}/in_mni152/tmpl2subj.mat" \
+	-out "${t1dir}/dil_occ_mask"
+
+$FSLDIR/bin/flirt \
+	-in "${t1dir}/dil_occ_mask" \
+	-ref "${bolddir}/brain" \
+	-applyxfm \
+	-init "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
+	-out "${bolddir}/dil_occ_mask"
+
+$FSLDIR/bin/flirt -dof 6 \
+	-in ${bolddir}/brain \
+	-ref ${t1dir}/brain_nobias \
+	-refweight ${t1dir}/dil_occ_mask \
+	-inweight ${bolddir}/dil_occ_mask \
+	-init "${bolddir}/in_t1w/xfm_6dof.mat" \
+	-searchrx -20 20 \
+	-searchry -20 20 \
+	-searchrz -20 20 \
+	-omat "${bolddir}/in_t1w/xfm_6dof_occ.mat" \
+	-out "${bolddir}/in_t1w/brain_occ"
+
+$FSLDIR/bin/convert_xfm \
+	-omat "${t1dir}/in_bold3Tp2/xfm_6dof_occ.mat" \
+	-inverse "${bolddir}/in_t1w/xfm_6dof_occ.mat"
+
+$FSLDIR/bin/flirt \
+	-in "${t1dir}/brain_nobias" \
+	-ref "${bolddir}/brain" \
+	-applyxfm \
+	-init "${t1dir}/in_bold3Tp2/xfm_6dof_occ.mat" \
+	-out "${t1dir}/in_bold3Tp2/brain_occ"

+ 42 - 0
code/mk_xfm_bold3Tp2_vs_t1w.submit

@@ -0,0 +1,42 @@
+universe = vanilla
+output = condor_logs/$(CLUSTER).$(PROCESS).out
+error = condor_logs/$(CLUSTER).$(PROCESS).err
+log = condor_logs/$(CLUSTER).$(PROCESS).log
+initialdir = /home/data/psyinf/forrest_gump/collection/tnt
+getenv = True
+request_cpus = 1
+request_memory = 1000
+should_transfer_files = NO
+transfer_executable = False
+executable = /home/data/psyinf/forrest_gump/collection/tnt/code/mk_xfm_bold3Tp2_vs_t1w
+
+arguments = sub-01
+queue
+arguments = sub-02
+queue
+arguments = sub-03
+queue
+arguments = sub-04
+queue
+arguments = sub-05
+queue
+arguments = sub-06
+queue
+arguments = sub-09
+queue
+arguments = sub-10
+queue
+arguments = sub-14
+queue
+arguments = sub-15
+queue
+arguments = sub-16
+queue
+arguments = sub-17
+queue
+arguments = sub-18
+queue
+arguments = sub-19
+queue
+arguments = sub-20
+queue

+ 1 - 1
code/ofhelpers

@@ -1 +1 @@
-Subproject commit 83f529f08efb3caeceab1e89b1cc2de20bb27fa2
+Subproject commit bb29cf28a5e25b9e97a0bb0a97a2eddef46d8a7f

+ 11 - 2
code/proc.cfg

@@ -22,7 +22,6 @@ output base directory = %%(subj)s
 [group template grpbold3Tp2]
 # whitespace-separated list of floats
 resolution = 2.5 2.5 2.5
-exclude subjects = 7 8 11 12 13
 linear iterations = 2
 non-linear iterations = 2
 # whitespace-separated list of integers
@@ -33,4 +32,14 @@ subject bet frac = 0.1
 template bet frac = 0.3
 apply mni sform = yes
 initial reference brain = /usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz
-input expression = raw/phase2/%%(subj)s/templates/bold3Tp2/head.nii.gz
+input expression = %%(subj)s/bold3Tp2/head.nii.gz
+
+[align2tmpl subjbold3Tp2_to_grpbold3Tp2]
+template = grpbold3Tp2
+input expression = %%(subj)s/bold3Tp2/head\.nii.*
+search radius = 15
+non-linear = yes
+use qform = yes
+warp resolution = 10
+motion correction = False
+input is subject template = yes

+ 1 - 0
raw/structural

@@ -0,0 +1 @@
+Subproject commit 54e555acea857acdb2a8b713cc4c7c7b09607b3d

+ 1 - 0
sub-01/bold3Tp2/dil_occ_mask.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/V8/jv/MD5E-s61396--83d0a3818c83cd318b1825c74159a486.nii.gz/MD5E-s61396--83d0a3818c83cd318b1825c74159a486.nii.gz

+ 1 - 0
sub-01/bold3Tp2/in_grpbold3Tp2/brain_mask.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/WV/9j/MD5E-s11755--999270e32c1107692ff412b72ae7387b.nii.gz/MD5E-s11755--999270e32c1107692ff412b72ae7387b.nii.gz

+ 1 - 0
sub-01/bold3Tp2/in_grpbold3Tp2/head.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/37/8W/MD5E-s739342--9786906d20f30c4bb053d3453d81e871.nii.gz/MD5E-s739342--9786906d20f30c4bb053d3453d81e871.nii.gz

+ 1 - 0
sub-01/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/47/7F/MD5E-s3556165--227fde355895be0c2bf26949116d5ffe.nii.gz/MD5E-s3556165--227fde355895be0c2bf26949116d5ffe.nii.gz

+ 1 - 0
sub-01/bold3Tp2/in_grpbold3Tp2/tmpl2subj_warp.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/84/4z/MD5E-s2487687--52d4472b516f86b135ae72259a93c974.nii.gz/MD5E-s2487687--52d4472b516f86b135ae72259a93c974.nii.gz

+ 1 - 0
sub-01/bold3Tp2/in_t1w/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/FM/5w/MD5E-s17828551--9e5a010e940e48118ea0d8acd691341a.nii.gz/MD5E-s17828551--9e5a010e940e48118ea0d8acd691341a.nii.gz

+ 1 - 0
sub-01/bold3Tp2/in_t1w/brain_occ.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/1J/VX/MD5E-s17833346--3eee2b35ad722790b1eef229c6768a28.nii.gz/MD5E-s17833346--3eee2b35ad722790b1eef229c6768a28.nii.gz

+ 1 - 0
sub-01/bold3Tp2/in_t1w/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/FZ/7F/MD5E-s191--b14c19ecd551b60d6714ee4650b11bf3.mat/MD5E-s191--b14c19ecd551b60d6714ee4650b11bf3.mat

+ 1 - 0
sub-01/bold3Tp2/in_t1w/xfm_6dof_occ.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/F6/6j/MD5E-s186--22759cf2fb0caa6606037d185fd9929b.mat/MD5E-s186--22759cf2fb0caa6606037d185fd9929b.mat

+ 1 - 0
sub-01/t1w/brain.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/f8/pv/MD5E-s6119787--a7826fb6084596f46e7c5e4b8e8fd7da.nii.gz/MD5E-s6119787--a7826fb6084596f46e7c5e4b8e8fd7da.nii.gz

+ 1 - 0
sub-01/t1w/brain_csf_stdspace.nii.gz

@@ -0,0 +1 @@
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