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Antonio Ulloa
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Added several visualization scripts
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‎analysis/avg_FC_TVB_ROIs_across_subjects.py‎

Lines changed: 382 additions & 126 deletions
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‎analysis/compute_BOLD_balloon_66_regions.py‎

Lines changed: 49 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -38,7 +38,7 @@
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#
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# Author: Antonio Ulloa
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#
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# Last updated by Antonio Ulloa on November 20 2016
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# Last updated by Antonio Ulloa on January 3 2017
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#
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# **************************************************************************/
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@@ -929,12 +929,17 @@ def balloon_function(y, t, syn):
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# round of mr time for display purposes
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mr_time = np.round(mr_time, decimals=0)
931931

932-
# create a numpy array of timeseries, using only the 33 ROIs in the right hemisphere
932+
# create a numpy array of timeseries, using the 66 ROIs
933933
lsnm_BOLD = np.array([BOLD_0, BOLD_1, BOLD_2, BOLD_3, BOLD_4, BOLD_5, BOLD_6, BOLD_7,
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BOLD_8, BOLD_9, BOLD_10, BOLD_11, BOLD_12, BOLD_13, BOLD_14, BOLD_15,
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BOLD_16, BOLD_17, BOLD_18, BOLD_19, BOLD_20, BOLD_21, BOLD_22, BOLD_23,
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BOLD_24, BOLD_25, BOLD_26, BOLD_27, BOLD_28, BOLD_29, BOLD_30, BOLD_31,
937-
BOLD_32])
937+
BOLD_32,
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BOLD_33, BOLD_34, BOLD_35, BOLD_36, BOLD_37, BOLD_38, BOLD_39, BOLD_40,
939+
BOLD_41, BOLD_42, BOLD_43, BOLD_44, BOLD_45, BOLD_46, BOLD_47, BOLD_48,
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BOLD_49, BOLD_50, BOLD_51, BOLD_52, BOLD_53, BOLD_54, BOLD_55, BOLD_56,
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BOLD_57, BOLD_58, BOLD_59, BOLD_60, BOLD_61, BOLD_62, BOLD_63, BOLD_64,
942+
BOLD_65 ])
938943

939944
print 'Size of BOLD time-series after removing scans: ', BOLD_0.size
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@@ -1001,7 +1006,41 @@ def balloon_function(y, t, syn):
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'rMT' ,
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'rBSTS',
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'rST' ,
1004-
'rTT']
1009+
'rTT' ,
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'lLOF' ,
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'lPORB',
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'lFP' ,
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'lMOF' ,
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'lPTRI',
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'lPOPE',
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'LRMF' ,
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'lSF' ,
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'lCMF' ,
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'lPREC',
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'lPARC',
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'lRAC' ,
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'lCAC' ,
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'lPC' ,
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'lISTC',
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'lPSTC',
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'lSMAR',
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'lSP' ,
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'lIP' ,
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'lPCUN',
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'lCUN' ,
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'lPCAL',
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'lLOC' ,
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'lLING',
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'lFUS' ,
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'lPARH',
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'lENT' ,
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'lTP' ,
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'lIT' ,
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'lMT' ,
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'lBSTS',
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'lST' ,
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'lTT'
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]
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10061045
#initialize new figure for correlations
10071046
fig = plt.figure()
@@ -1011,12 +1050,12 @@ def balloon_function(y, t, syn):
10111050
#plt.rcParams.update({'font.size': 15})
10121051

10131052
# plot correlation matrix as a heatmap
1014-
mask = np.tri(corr_mat.shape[0], k=-1)
1015-
mask = np.transpose(mask)
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corr_mat = np.ma.array(corr_mat, mask=mask) # mask out the upper triangle
1053+
#mask = np.tri(corr_mat.shape[0], k=0)
1054+
#mask = np.transpose(mask)
1055+
#corr_mat = np.ma.array(corr_mat, mask=mask) # mask out the upper triangle
10171056
cmap = CM.get_cmap('jet', 10)
1018-
cmap.set_bad('w')
1019-
cax = ax.imshow(corr_mat, vmin=-0.6, vmax=1.0, interpolation='nearest', cmap=cmap)
1057+
#cmap.set_bad('w')
1058+
cax = ax.imshow(corr_mat, vmin=-1, vmax=1.0, interpolation='nearest', cmap=cmap)
10201059
ax.grid(False)
10211060
plt.colorbar(cax)
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@@ -1056,7 +1095,7 @@ def balloon_function(y, t, syn):
10561095

10571096
plt.xlabel('Correlation Coefficient')
10581097
plt.ylabel('Number of occurrences')
1059-
plt.axis([-0.6, 0.6, 0, 100])
1098+
plt.axis([-1, 1, 0, 100])
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10611100
# calculate and print kurtosis
10621101
print 'Fishers kurtosis: ', kurtosis(corr_mat, fisher=True)

‎visual_model/circle_tvb_lsnm_dms_fc.png‎

94.1 KB

‎visual_model/circle_tvb_lsnm_pv_fc.png‎

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‎visual_model/circle_tvb_lsnm_rs_fc.png‎

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‎visual_model/circle_tvb_rs_fc.png‎

95.5 KB

‎visual_model/subject_12/output.RestingState/log.txt‎

Lines changed: 5 additions & 5 deletions
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* Simulation Start Time: Fri Oct 14 14:40:19 2016
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* Simulation End Time: Sat Oct 15 02:57:40 2016
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* Simulation Start Time: Fri Dec 9 11:26:40 2016
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* Simulation End Time: Fri Dec 9 18:26:13 2016
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* Simulation duration (timesteps): 39600
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* Model description used: /Users/Antonio/Documents/NEURALBYTES/NIHPROJECT2/lsnm_in_python/visual_model/model.txt
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* Weights list used: /Users/Antonio/Documents/NEURALBYTES/NIHPROJECT2/lsnm_in_python/visual_model/subject_12/weightslist.txt
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* Model description used: /home/ulloa/SIMULATIONS.120916/lsnm_in_python/visual_model/model.txt
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* Weights list used: /home/ulloa/SIMULATIONS.120916/lsnm_in_python/visual_model/subject_12/weightslist.txt
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* Neural net used:
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* Simulation script used: /Users/Antonio/Documents/NEURALBYTES/NIHPROJECT2/lsnm_in_python/visual_model/script_resting_state_198_seconds.py
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* Simulation script used: /home/ulloa/SIMULATIONS.120916/lsnm_in_python/visual_model/script_resting_state_198_seconds.py
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* Were weights changed to generate a new subject? NO
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* Was TVB Connectome used in the simulation? YES

‎visual_model/subject_12/output.RestingStateOLD/log.txt‎

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* Simulation Start Time: Fri Oct 14 14:40:19 2016
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* Simulation End Time: Sat Oct 15 02:57:40 2016
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* Simulation duration (timesteps): 39600
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* Model description used: /Users/Antonio/Documents/NEURALBYTES/NIHPROJECT2/lsnm_in_python/visual_model/model.txt
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* Weights list used: /Users/Antonio/Documents/NEURALBYTES/NIHPROJECT2/lsnm_in_python/visual_model/subject_12/weightslist.txt
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* Neural net used:
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* Simulation script used: /Users/Antonio/Documents/NEURALBYTES/NIHPROJECT2/lsnm_in_python/visual_model/script_resting_state_198_seconds.py
8+
* Were weights changed to generate a new subject? NO
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* Was TVB Connectome used in the simulation? YES

‎visual_model/subject_12/output.RestingStateOLD/neuralnet.json‎

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‎visual_model/subject_13/output.PassiveViewing/log.txt‎

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* Simulation Start Time: Fri Dec 9 13:24:18 2016
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* Simulation End Time: Fri Dec 9 20:53:14 2016
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* Simulation duration (timesteps): 39600
4+
* Model description used: /home/ulloa/SIMULATIONS.120916/lsnm_in_python/visual_model/model.txt
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* Weights list used: /home/ulloa/SIMULATIONS.120916/lsnm_in_python/visual_model/subject_13/weightslist.txt
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* Neural net used:
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* Simulation script used: /home/ulloa/SIMULATIONS.120916/lsnm_in_python/visual_model/script_passive_viewing_198_seconds.py
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* Were weights changed to generate a new subject? NO
9+
* Was TVB Connectome used in the simulation? YES

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