1st draft of ROI masks

code/stats2rois

@@ -1,6 +1,7 @@
 #!/usr/bin/python3
 
 import sys
+import os
 from tempfile import mkdtemp
 from os.path import join as _opj
 from os.path import abspath
@@ -8,9 +9,17 @@ from shutil import rmtree
 from configparser import SafeConfigParser
 from subprocess import check_call
 import nibabel as nb
-from scipy.ndimage import label
+from scipy.ndimage import label, center_of_mass, maximum_position
 import numpy as np
 
+
+def ijk2xyz(ijk, aff):
+    tmp = np.ones(4, dtype=ijk.dtype)
+    tmp[:3] = ijk
+    tmp = np.dot(aff, tmp)
+    return tmp[:3]
+
+
 cfg = SafeConfigParser()
 cfg.read(_opj('code', 'stats2rois.cfg'))
 
@@ -22,6 +31,8 @@ if len(sys.argv) > 2:
     mode = 'indi'
     rois = sys.argv[2:]
 
+if not os.path.exists(_opj(subj_code, 'rois')):
+    os.makedirs(_opj(subj_code, 'rois'))
 
 # encode ROI IDs as powers of 2
 roi_ids = {
@@ -77,9 +88,9 @@ for roi in rois:
     # doesn't do casing properly
     roi = roi[:-3] + roi[-3:].upper()
     print(roi)
-    #wdir = mkdtemp(suffix='_stats2roi_%s' % subj_code)
-    wdir = '/tmp/stats2rois'
-    print(wdir)
+    wdir = mkdtemp(suffix='_stats2roi_%s' % subj_code)
+    #wdir = '/tmp/stats2rois'
+    #print(wdir)
     # get particular setting for this ROI
     info = cfg.get(subj_code, roi).split()
     cope = int(info[0])
@@ -97,10 +108,10 @@ for roi in rois:
     # find clusters
     zstat_img = nb.load(zstats_fname)
     clusters, nclusters = label(zstat_img.get_data() > zthresh)
-    print('Cluster sizes:', {i: np.sum(clusters == i) for i in range(1, nclusters + 1)})
+    #print('Cluster sizes:', {i: np.sum(clusters == i) for i in range(1, nclusters + 1)})
 
     # make ROI mask
-    roi_fname = _opj(wdir, '%s.nii.gz' % roi)
+    roi_fname = _opj(subj_code, 'rois', '%s.nii.gz' % roi)
     roi_vol = np.zeros(clusters.shape, dtype=np.bool)
     for cli in cluster_idx:
         roi_vol += clusters == cli
@@ -109,8 +120,47 @@ for roi in rois:
         roisummary_hdr = zstat_img.get_header()
     roisummary_vol += roi_vol.astype(int) * roi_ids[roi]
 
-    nb.save(nb.Nifti1Image(roi_vol.astype('int16'), zstat_img.get_affine()),
-            roi_fname)
+    # save the ROI mask file
+    roi_img = nb.Nifti1Image(roi_vol.astype('int16'), zstat_img.get_affine())
+    nb.save(roi_img, roi_fname)
+    with open(_opj(subj_code, 'rois', '%s_info.txt' % roi), 'w') as infofile:
+        # native space info
+        infofile.write("nvoxels (native): %i\n" % np.sum(roi_vol > 0))
+        infofile.write(
+            "volume (native cm^3): %f\n"
+            % (np.sum(roi_vol > 0) * np.prod(roi_img.get_header().get_zooms()) / 1000.))
+        roi_stats = zstat_img.get_data()[roi_vol > 0]
+        infofile.write(
+            'Z-stats (min, mean, median, max): %.2f, %.2f, %.2f, %.2f\n'
+            % (roi_stats.min(), roi_stats.mean(), np.median(roi_stats), roi_stats.max()))
+        roi_stats = zstat_img.get_data() * (roi_vol > 0)
+        infofile.write("peak Z (native IJK): %i, %i, %i\n" % maximum_position(roi_stats))
+        infofile.write("CoM (native IJK): %i, %i, %i\n" % center_of_mass(roi_stats))
+
+        # MNI space info
+        roi_stats_fname = _opj(wdir, 'roi_stats.nii.gz')
+        nb.save(nb.Nifti1Image(roi_stats, zstat_img.get_affine()), roi_stats_fname)
+        grp_stats_fname = _opj(wdir, 'grp_stats.nii.gz')
+        check_call([
+            'applywarp',
+            '--in=%s' % roi_stats_fname,
+            '--ref=%s' % tmpl_fname,
+            '--warp=%s' % tmplwarp_fname,
+            '--interp=trilinear',
+            '--out=%s' % grp_stats_fname])
+        grp_stats_img = nb.load(grp_stats_fname)
+        infofile.write(
+            "peak Z (MNI mm): %.2f, %.1f, %.1f\n"
+            % tuple(
+                ijk2xyz(
+                    np.array(maximum_position(grp_stats_img.get_data())),
+                    grp_stats_img.get_affine())))
+        infofile.write(
+            "CoM (MNI mm): %.2f, %.1f, %.1f\n"
+            % tuple(
+                ijk2xyz(
+                    np.array(center_of_mass(grp_stats_img.get_data())),
+                    grp_stats_img.get_affine())))
 
     native_clusters_fname = _opj(wdir, 'native_clusters.nii.gz')
     nb.save(zstat_img, _opj(wdir, 'stats.nii.gz'))
@@ -119,8 +169,6 @@ for roi in rois:
     nb.save(nb.Nifti1Image(clusters, zstat_img.get_affine()),
             native_clusters_fname)
 
-
-    print(nclusters)
     #check_call(
     #    ['easythresh', zstats_fname, mask_fname, '%s' % zthresh, '%s' % pthresh,
     #     mask_fname, 'stats2rois'],
@@ -162,28 +210,26 @@ for roi in rois:
             'Greyscale',
         ])
 
-    #rmtree(wdir)
+    rmtree(wdir)
 
 if mode == 'indi':
     sys.exit(0)
 
-roisummary_fname = 'roisummary.nii.gz'
-grp_roisummary_fname = 'grp_roisummary.nii.gz'
+roisummary_fname = _opj(subj_code, 'rois', 'summary.nii.gz')
 nb.save(nb.Nifti1Image(roisummary_vol, roisummary_hdr.get_best_affine()),
         roisummary_fname)
-check_call([
-    'applywarp',
-    '--in=%s' % roisummary_fname,
-    '--ref=%s' % tmpl_fname,
-    '--warp=%s' % tmplwarp_fname,
-    '--interp=nn',
-    '--out=%s' % grp_roisummary_fname])
-check_call([
-    'fslview',
-    '../tnt/templates/grpbold3Tp2/from_mni/MNI152_T1_1mm.nii.gz',
-    grp_roisummary_fname,
-    '-l',
-    'Random-Rainbow',
-])
-
-
+#grp_roisummary_fname = 'grp_roisummary.nii.gz'
+#check_call([
+#    'applywarp',
+#    '--in=%s' % roisummary_fname,
+#    '--ref=%s' % tmpl_fname,
+#    '--warp=%s' % tmplwarp_fname,
+#    '--interp=nn',
+#    '--out=%s' % grp_roisummary_fname])
+#check_call([
+#    'fslview',
+#    '../tnt/templates/grpbold3Tp2/from_mni/MNI152_T1_1mm.nii.gz',
+#    grp_roisummary_fname,
+#    '-l',
+#    'Random-Rainbow',
+#])

code/stats2rois.cfg

@@ -7,15 +7,17 @@ rEBA = 4 3.1 1
 lEBA = 4 3.1 5
 rLOC = 10 2.3 2
 lLOC = 10 2.3 8
+VIS = 6 2.3 1 2
 [sub-02]
 rFFA = 7 3.1 3
-lFFA = 7 3.1 9
+lFFA = 7 3.1 6
 rPPA = 8 2.6 3
 lPPA = 8 2.6 26
 rEBA = 9 3.3 1
 lEBA = 9 2.8 12
 rLOC = 10 2.3 1
 lLOC = 10 2.3 20
+VIS = 6 2.3 5
 [sub-03]
 rFFA = 7 2.0 10 12
 rLOC = 10 2.5 1 3
@@ -29,8 +31,9 @@ lLOC = 10 2.3 7
 rFFA = 7 1.9 14
 rPPA = 8 2.7 5
 rEBA = 9 2.7 2
-lEBA = 9 2.8 11
+lEBA = 9 2.7 11
 rLOC = 10 2.3 3
+VIS = 6 1.7 1
 [sub-06]
 rFFA = 7 2.6 5 6
 lFFA = 7 2.6 9
@@ -48,6 +51,7 @@ rEBA = 9 3.1 2
 lEBA = 9 3.1 13
 rLOC = 10 2.3 4
 lLOC = 10 2.3 14
+VIS = 6 2.3 3
 [sub-10]
 rFFA = 7 2.3 4
 rOFA = 7 2.3 1
@@ -59,6 +63,7 @@ rEBA = 9 2.9 1
 lEBA = 9 2.9 4
 rLOC = 10 2.3 1
 lLOC = 10 2.3 21
+VIS = 6 2.3 2
 [sub-14]
 rFFA = 7 2.3 7
 rOFA = 7 2.3 5
@@ -67,5 +72,61 @@ rPPA = 8 3.3 4
 lPPA = 8 3.3 7
 rEBA = 9 3.1 1
 lEBA = 9 3.1 3
-rLOC = 10 2.4 1
-lLOC = 10 2.4 13
+rLOC = 10 2.5 1
+lLOC = 10 2.5 11
+VIS = 6 2.0 2
+[sub-15]
+rFFA = 7 2.9 5
+lFFA = 7 2.6 38
+rOFA = 7 2.9 1
+lOFA = 7 2.6 36
+rPPA = 8 2.4 1
+lPPA = 8 2.4 10
+rEBA = 9 2.9 3
+lEBA = 9 2.9 13
+rLOC = 10 2.5 3
+lLOC = 10 2.5 14
+VIS = 6 1.7 1 2
+[sub-16]
+rFFA = 7 2.3 21
+rPPA = 8 2.5 2
+lPPA = 8 2.5 14
+rEBA = 9 2.5 1
+lEBA = 9 2.5 29
+rLOC = 10 2.4 7
+lLOC = 10 2.4 73
+VIS = 6 1.8 1
+[sub-17]
+rFFA = 7 2.7 9
+rOFA = 7 2.7 1
+rPPA = 8 2.3 6
+lPPA = 8 2.3 28
+rEBA = 9 2.8 1
+lEBA = 9 2.8 15
+rLOC = 10 2.0 4
+lLOC = 10 2.6 11
+VIS = 6 1.7 1
+[sub-18]
+rEBA = 9 2.4 1
+lEBA = 9 2.4 13
+[sub-19]
+# FFA and OFA in a contiguous blob
+rFFA = 7 2.4 4
+lFFA = 7 2.4 14
+rPPA = 8 2.8 5
+lPPA = 8 2.8 18
+rEBA = 9 2.8 2
+lEBA = 9 2.6 38
+rLOC = 5 2.4 3
+lLOC = 5 2.4 15 17
+VIS = 6 2.3 2
+[sub-20]
+rFFA = 7 2.3 1
+lFFA = 7 2.3 33
+lOFA = 7 2.3 31
+rPPA = 3 2.3 2
+lPPA = 3 2.3 10
+lEBA = 9 2.2 39
+rLOC = 10 2.3 3 7 10 11
+lLOC = 10 2.3 16
+VIS = 6 1.7 1 3

sub-01/rois/VIS.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/XV/Q0/MD5E-s2829--ef821f16b71e2f3ff81dcda5d7b604dd.nii.gz/MD5E-s2829--ef821f16b71e2f3ff81dcda5d7b604dd.nii.gz

sub-01/rois/VIS_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/fq/Zv/MD5E-s235--1120be0e7e2e2d1dff37f6126d3be8ad.txt/MD5E-s235--1120be0e7e2e2d1dff37f6126d3be8ad.txt

sub-01/rois/lEBA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/z4/77/MD5E-s2517--859a9395f9dc408a8c2641c5dc194258.nii.gz/MD5E-s2517--859a9395f9dc408a8c2641c5dc194258.nii.gz

sub-01/rois/lEBA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/3P/4g/MD5E-s241--9cb05bf7e097af2123072d3cb72557fb.txt/MD5E-s241--9cb05bf7e097af2123072d3cb72557fb.txt

sub-01/rois/lLOC.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Pp/2M/MD5E-s2900--aec1471e255113aebaf839a144c3c3ad.nii.gz/MD5E-s2900--aec1471e255113aebaf839a144c3c3ad.nii.gz

sub-01/rois/lLOC_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/9j/Kp/MD5E-s243--776f5ec160d07262dd061b79763fba5a.txt/MD5E-s243--776f5ec160d07262dd061b79763fba5a.txt

sub-01/rois/lPPA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Zf/pm/MD5E-s2425--a05a3738ff4ea8e9ee6457a15b1d4621.nii.gz/MD5E-s2425--a05a3738ff4ea8e9ee6457a15b1d4621.nii.gz

sub-01/rois/lPPA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/2f/WX/MD5E-s239--f36861bbbfcfd81dcd9bd58f62e5ce68.txt/MD5E-s239--f36861bbbfcfd81dcd9bd58f62e5ce68.txt

sub-01/rois/rEBA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/1W/Z8/MD5E-s2544--8d1cd3cc984d8afe2c2a5674fedd5da9.nii.gz/MD5E-s2544--8d1cd3cc984d8afe2c2a5674fedd5da9.nii.gz

sub-01/rois/rEBA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/Jv/P4/MD5E-s240--4ecb11ee113b0c99066eb91643dc929c.txt/MD5E-s240--4ecb11ee113b0c99066eb91643dc929c.txt

sub-01/rois/rFFA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/GQ/J7/MD5E-s2597--66c2ea0b4f3b65c0f33b83f072c24423.nii.gz/MD5E-s2597--66c2ea0b4f3b65c0f33b83f072c24423.nii.gz

sub-01/rois/rFFA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/JF/4M/MD5E-s240--a2a73bbef512cd12a6b64ae78bd87fd5.txt/MD5E-s240--a2a73bbef512cd12a6b64ae78bd87fd5.txt

sub-01/rois/rLOC.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/3q/G9/MD5E-s2661--3a89b1341133a81443df9c3bd42c9073.nii.gz/MD5E-s2661--3a89b1341133a81443df9c3bd42c9073.nii.gz

sub-01/rois/rLOC_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/Ww/7Q/MD5E-s240--c26ab60419ad8ad48d35b57d113d2b25.txt/MD5E-s240--c26ab60419ad8ad48d35b57d113d2b25.txt

sub-01/rois/rPPA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/V6/8z/MD5E-s2580--3896a5b97259734055003810fb861c2f.nii.gz/MD5E-s2580--3896a5b97259734055003810fb861c2f.nii.gz

sub-01/rois/rPPA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/wW/Pz/MD5E-s239--1cedb3a50d855ca70b2fff3a1f4f1111.txt/MD5E-s239--1cedb3a50d855ca70b2fff3a1f4f1111.txt

sub-01/rois/summary.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/PF/6j/MD5E-s4718--95cdceb3221561dd240016dd144ff2af.nii.gz/MD5E-s4718--95cdceb3221561dd240016dd144ff2af.nii.gz

sub-02/rois/VIS.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/12/pj/MD5E-s2937--e5f4c6b48581ea1ef6761cfc36331d98.nii.gz/MD5E-s2937--e5f4c6b48581ea1ef6761cfc36331d98.nii.gz

sub-02/rois/VIS_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/Zp/9P/MD5E-s236--0d38dd16f8e5eaa9e48e4aacfcda1b88.txt/MD5E-s236--0d38dd16f8e5eaa9e48e4aacfcda1b88.txt

sub-02/rois/lEBA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Mq/ZQ/MD5E-s2452--1f90e2d9b8742bfef3fa92f83bc64090.nii.gz/MD5E-s2452--1f90e2d9b8742bfef3fa92f83bc64090.nii.gz

sub-02/rois/lEBA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/6x/3m/MD5E-s237--4014bb31124455676f5dec998fe9c4ce.txt/MD5E-s237--4014bb31124455676f5dec998fe9c4ce.txt

sub-02/rois/lFFA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Kw/63/MD5E-s2370--94f8f483ceb0afd7c517c6c313f1cb9f.nii.gz/MD5E-s2370--94f8f483ceb0afd7c517c6c313f1cb9f.nii.gz

sub-02/rois/lFFA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/kq/V9/MD5E-s241--58425439cbb4ceaae0f0591b0045da80.txt/MD5E-s241--58425439cbb4ceaae0f0591b0045da80.txt

sub-02/rois/lLOC.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/F3/jz/MD5E-s2615--6635bef670321dbf803edf140f75f868.nii.gz/MD5E-s2615--6635bef670321dbf803edf140f75f868.nii.gz

sub-02/rois/lLOC_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/06/FV/MD5E-s239--8300da1299dc976b694e6611ddcbec26.txt/MD5E-s239--8300da1299dc976b694e6611ddcbec26.txt

sub-02/rois/lPPA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/V2/mx/MD5E-s2458--e7b56e3c11663904c69c1e4240c1e62d.nii.gz/MD5E-s2458--e7b56e3c11663904c69c1e4240c1e62d.nii.gz

sub-02/rois/lPPA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/3v/35/MD5E-s242--2c9eadb04f4df56054c6c64463abf23e.txt/MD5E-s242--2c9eadb04f4df56054c6c64463abf23e.txt

sub-02/rois/rEBA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/j5/p1/MD5E-s2554--c19786ff745402617ae2b159f8d3e127.nii.gz/MD5E-s2554--c19786ff745402617ae2b159f8d3e127.nii.gz

sub-02/rois/rEBA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/65/jV/MD5E-s240--b89b67c6e743174bbc7b2474bb462218.txt/MD5E-s240--b89b67c6e743174bbc7b2474bb462218.txt

sub-02/rois/rFFA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/xG/30/MD5E-s2441--4f0625c20dcd67edc50269d54e35230e.nii.gz/MD5E-s2441--4f0625c20dcd67edc50269d54e35230e.nii.gz

sub-02/rois/rFFA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/15/kQ/MD5E-s239--d6446805a430d27a0abab41429bae8ef.txt/MD5E-s239--d6446805a430d27a0abab41429bae8ef.txt

sub-02/rois/rLOC.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/56/XV/MD5E-s2706--ae4879e667fab541fa35cd8043807cec.nii.gz/MD5E-s2706--ae4879e667fab541fa35cd8043807cec.nii.gz

sub-02/rois/rLOC_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/Xg/GG/MD5E-s238--f3e74d10f0b45226fd6dddd99d45812b.txt/MD5E-s238--f3e74d10f0b45226fd6dddd99d45812b.txt

sub-02/rois/rPPA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/6G/mg/MD5E-s2540--f1b46de5dc03f4af6bdd74c59665ffbd.nii.gz/MD5E-s2540--f1b46de5dc03f4af6bdd74c59665ffbd.nii.gz

sub-02/rois/rPPA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/Kx/7p/MD5E-s240--15a00e1fa53441a7ff98cb5bca9eec75.txt/MD5E-s240--15a00e1fa53441a7ff98cb5bca9eec75.txt

sub-02/rois/summary.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/0f/jJ/MD5E-s4439--60c30d3a4a7473dfd1e0d8c7344b7c80.nii.gz/MD5E-s4439--60c30d3a4a7473dfd1e0d8c7344b7c80.nii.gz

sub-03/rois/lLOC.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/38/FK/MD5E-s2568--c701c287e82cc0f9e9c8154f4bb0721f.nii.gz/MD5E-s2568--c701c287e82cc0f9e9c8154f4bb0721f.nii.gz

sub-03/rois/lLOC_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/55/G7/MD5E-s242--f9b68cf38751eb2cc68a073a40b138d5.txt/MD5E-s242--f9b68cf38751eb2cc68a073a40b138d5.txt

sub-03/rois/rFFA.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/2p/zk/MD5E-s2472--46b5a2e1a8425ee31ea9332a9a800d36.nii.gz/MD5E-s2472--46b5a2e1a8425ee31ea9332a9a800d36.nii.gz

sub-03/rois/rFFA_info.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/z5/46/MD5E-s240--be9fe7619494c82e226461f739326039.txt/MD5E-s240--be9fe7619494c82e226461f739326039.txt

sub-03/rois/rLOC.nii.gz

@@ -0,0 +1 @@
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