Note
Click here to download the full example code
Callosal bundles using AFQ API#
An example using the AFQ API to find callosal bundles using the templates from: http://hdl.handle.net/1773/34926
import os.path as op
import plotly
from AFQ.api.group import GroupAFQ
import AFQ.api.bundle_dict as abd
from AFQ.definitions.image import RoiImage
import AFQ.data.fetch as afd
Get some example data#
Retrieves Stanford HARDI dataset.
afd.organize_stanford_data(clear_previous_afq=True)
Set tractography parameters (optional)#
We make this tracking_params which we will pass to the GroupAFQ object which specifies that we want 100,000 seeds randomly distributed in the ROIs of every bundle.
We only do this to make this example faster and consume less space.
tracking_params = dict(seed_mask=RoiImage(),
n_seeds=10000,
random_seeds=True,
rng_seed=42)
Set segmentation parameters (optional)#
We make this segmentation_params which we will pass to the GroupAFQ object which specifies that we want to clip the extracted tract profiles to only be between the two ROIs.
We do this because tract profiles become less reliable as the bundles approach the gray matter-white matter boundary. On some of the non-callosal bundles, ROIs are not in a good position to clip edges. In these cases, one can remove the first and last nodes in a tract profile.
segmentation_params = {"clip_edges": True}
Initialize a GroupAFQ object:#
We specify bundle_info as the callosal bundles only (abd.CALLOSUM_BUNDLES). If we want to segment both the callosum and the other bundles, we would pass abd.CALLOSUM_BUNDLES + abd.BUNDLES instead. This would tell the GroupAFQ object to use bundles from both the standard and callosal templates.
myafq = GroupAFQ(
bids_path=op.join(afd.afq_home, 'stanford_hardi'),
preproc_pipeline='vistasoft',
bundle_info=abd.CALLOSUM_BUNDLES,
tracking_params=tracking_params,
segmentation_params=segmentation_params,
viz_backend_spec='plotly_no_gif')
# Calling export all produces all of the outputs of processing, including
# tractography, scalar maps, tract profiles and visualizations:
myafq.export_all()
Out:
0%| | 0/145758.0 [00:00<?, ?it/s]
0%| | 67/145758.0 [00:00<03:37, 669.74it/s]
0%| | 208/145758.0 [00:00<02:11, 1103.53it/s]
0%| | 466/145758.0 [00:00<01:21, 1774.31it/s]
1%| | 762/145758.0 [00:00<01:04, 2241.57it/s]
1%| | 1076/145758.0 [00:00<00:56, 2562.61it/s]
1%| | 1373/145758.0 [00:00<00:53, 2700.64it/s]
1%|1 | 1678/145758.0 [00:00<00:51, 2811.92it/s]
1%|1 | 1997/145758.0 [00:00<00:49, 2930.49it/s]
2%|1 | 2296/145758.0 [00:00<00:48, 2946.93it/s]
2%|1 | 2611/145758.0 [00:01<00:47, 3009.35it/s]
2%|2 | 2935/145758.0 [00:01<00:46, 3077.33it/s]
2%|2 | 3255/145758.0 [00:01<00:45, 3111.71it/s]
2%|2 | 3567/145758.0 [00:01<00:46, 3091.08it/s]
3%|2 | 3885/145758.0 [00:01<00:45, 3115.78it/s]
3%|2 | 4210/145758.0 [00:01<00:44, 3154.57it/s]
3%|3 | 4526/145758.0 [00:01<00:44, 3145.83it/s]
3%|3 | 4843/145758.0 [00:01<00:44, 3151.42it/s]
4%|3 | 5178/145758.0 [00:01<00:43, 3209.30it/s]
4%|3 | 5510/145758.0 [00:01<00:43, 3239.98it/s]
4%|4 | 5835/145758.0 [00:02<00:43, 3241.33it/s]
4%|4 | 6160/145758.0 [00:02<00:43, 3226.34it/s]
4%|4 | 6496/145758.0 [00:02<00:42, 3264.25it/s]
5%|4 | 6832/145758.0 [00:02<00:42, 3290.37it/s]
5%|4 | 7181/145758.0 [00:02<00:41, 3348.80it/s]
5%|5 | 7517/145758.0 [00:02<00:41, 3351.66it/s]
5%|5 | 7853/145758.0 [00:02<00:41, 3290.47it/s]
6%|5 | 8199/145758.0 [00:02<00:41, 3338.27it/s]
6%|5 | 8543/145758.0 [00:02<00:40, 3368.12it/s]
6%|6 | 8899/145758.0 [00:02<00:39, 3423.55it/s]
6%|6 | 9242/145758.0 [00:03<00:39, 3423.76it/s]
7%|6 | 9585/145758.0 [00:03<00:40, 3371.04it/s]
7%|6 | 9928/145758.0 [00:03<00:40, 3388.11it/s]
7%|7 | 10283/145758.0 [00:03<00:39, 3432.70it/s]
7%|7 | 10643/145758.0 [00:03<00:38, 3481.09it/s]
8%|7 | 11005/145758.0 [00:03<00:38, 3521.93it/s]
8%|7 | 11358/145758.0 [00:03<00:38, 3498.34it/s]
8%|8 | 11708/145758.0 [00:03<00:39, 3427.58it/s]
8%|8 | 12065/145758.0 [00:03<00:38, 3467.95it/s]
9%|8 | 12431/145758.0 [00:03<00:37, 3523.80it/s]
9%|8 | 12802/145758.0 [00:04<00:37, 3575.13it/s]
9%|9 | 13163/145758.0 [00:04<00:36, 3584.62it/s]
9%|9 | 13522/145758.0 [00:04<00:37, 3561.86it/s]
10%|9 | 13879/145758.0 [00:04<00:37, 3500.85it/s]
10%|9 | 14239/145758.0 [00:04<00:37, 3527.77it/s]
10%|# | 14599/145758.0 [00:04<00:36, 3548.77it/s]
10%|# | 14970/145758.0 [00:04<00:36, 3594.83it/s]
11%|# | 15339/145758.0 [00:04<00:36, 3619.88it/s]
11%|# | 15702/145758.0 [00:04<00:36, 3583.82it/s]
11%|#1 | 16061/145758.0 [00:04<00:36, 3530.37it/s]
11%|#1 | 16420/145758.0 [00:05<00:36, 3544.47it/s]
12%|#1 | 16801/145758.0 [00:05<00:35, 3621.93it/s]
12%|#1 | 17169/145758.0 [00:05<00:35, 3637.69it/s]
12%|#2 | 17537/145758.0 [00:05<00:35, 3649.32it/s]
12%|#2 | 17903/145758.0 [00:05<00:35, 3598.48it/s]
13%|#2 | 18264/145758.0 [00:05<00:35, 3579.75it/s]
13%|#2 | 18629/145758.0 [00:05<00:35, 3599.28it/s]
13%|#3 | 19011/145758.0 [00:05<00:34, 3662.85it/s]
13%|#3 | 19387/145758.0 [00:05<00:34, 3687.09it/s]
14%|#3 | 19759/145758.0 [00:05<00:34, 3695.97it/s]
14%|#3 | 20129/145758.0 [00:06<00:34, 3689.12it/s]
14%|#4 | 20498/145758.0 [00:06<00:33, 3685.58it/s]
14%|#4 | 20867/145758.0 [00:06<00:34, 3598.96it/s]
15%|#4 | 21261/145758.0 [00:06<00:33, 3698.02it/s]
15%|#4 | 21640/145758.0 [00:06<00:33, 3722.68it/s]
15%|#5 | 22020/145758.0 [00:06<00:33, 3745.25it/s]
15%|#5 | 22397/145758.0 [00:06<00:32, 3750.92it/s]
16%|#5 | 22774/145758.0 [00:06<00:32, 3755.24it/s]
16%|#5 | 23150/145758.0 [00:06<00:33, 3702.80it/s]
16%|#6 | 23521/145758.0 [00:06<00:33, 3628.08it/s]
16%|#6 | 23891/145758.0 [00:07<00:33, 3648.85it/s]
17%|#6 | 24271/145758.0 [00:07<00:32, 3691.91it/s]
17%|#6 | 24657/145758.0 [00:07<00:32, 3738.47it/s]
17%|#7 | 25032/145758.0 [00:07<00:32, 3741.47it/s]
17%|#7 | 25411/145758.0 [00:07<00:32, 3755.43it/s]
18%|#7 | 25787/145758.0 [00:07<00:32, 3702.11it/s]
18%|#7 | 26158/145758.0 [00:07<00:32, 3657.70it/s]
18%|#8 | 26525/145758.0 [00:07<00:33, 3608.59it/s]
18%|#8 | 26892/145758.0 [00:07<00:32, 3626.37it/s]
19%|#8 | 27272/145758.0 [00:07<00:32, 3676.32it/s]
19%|#8 | 27649/145758.0 [00:08<00:31, 3701.99it/s]
19%|#9 | 28035/145758.0 [00:08<00:31, 3748.33it/s]
19%|#9 | 28411/145758.0 [00:08<00:31, 3740.52it/s]
20%|#9 | 28786/145758.0 [00:08<00:31, 3717.12it/s]
20%|## | 29158/145758.0 [00:08<00:31, 3651.69it/s]
20%|## | 29524/145758.0 [00:08<00:31, 3634.87it/s]
21%|## | 29913/145758.0 [00:08<00:31, 3708.27it/s]
21%|## | 30298/145758.0 [00:08<00:30, 3747.86it/s]
21%|##1 | 30688/145758.0 [00:08<00:30, 3791.83it/s]
21%|##1 | 31068/145758.0 [00:09<00:30, 3787.75it/s]
22%|##1 | 31447/145758.0 [00:09<00:30, 3776.59it/s]
22%|##1 | 31825/145758.0 [00:09<00:30, 3693.88it/s]
22%|##2 | 32195/145758.0 [00:09<00:30, 3669.23it/s]
22%|##2 | 32563/145758.0 [00:09<00:30, 3670.04it/s]
23%|##2 | 32954/145758.0 [00:09<00:30, 3739.97it/s]
23%|##2 | 33352/145758.0 [00:09<00:29, 3809.52it/s]
23%|##3 | 33744/145758.0 [00:09<00:29, 3840.09it/s]
23%|##3 | 34129/145758.0 [00:09<00:29, 3830.47it/s]
24%|##3 | 34513/145758.0 [00:09<00:29, 3788.12it/s]
24%|##3 | 34892/145758.0 [00:10<00:29, 3727.67it/s]
24%|##4 | 35266/145758.0 [00:10<00:29, 3708.04it/s]
24%|##4 | 35648/145758.0 [00:10<00:29, 3739.82it/s]
25%|##4 | 36048/145758.0 [00:10<00:28, 3815.75it/s]
25%|##5 | 36452/145758.0 [00:10<00:28, 3880.31it/s]
25%|##5 | 36841/145758.0 [00:10<00:28, 3833.99it/s]
26%|##5 | 37225/145758.0 [00:10<00:28, 3834.94it/s]
26%|##5 | 37609/145758.0 [00:10<00:29, 3725.55it/s]
26%|##6 | 37986/145758.0 [00:10<00:28, 3738.37it/s]
26%|##6 | 38377/145758.0 [00:10<00:28, 3788.76it/s]
27%|##6 | 38782/145758.0 [00:11<00:27, 3865.92it/s]
27%|##6 | 39197/145758.0 [00:11<00:26, 3948.33it/s]
27%|##7 | 39593/145758.0 [00:11<00:27, 3895.06it/s]
27%|##7 | 39983/145758.0 [00:11<00:27, 3842.66it/s]
28%|##7 | 40368/145758.0 [00:11<00:27, 3826.36it/s]
28%|##7 | 40751/145758.0 [00:11<00:27, 3761.85it/s]
28%|##8 | 41128/145758.0 [00:11<00:28, 3727.60it/s]
28%|##8 | 41532/145758.0 [00:11<00:27, 3817.83it/s]
29%|##8 | 41930/145758.0 [00:11<00:26, 3864.08it/s]
29%|##9 | 42321/145758.0 [00:11<00:26, 3876.88it/s]
29%|##9 | 42709/145758.0 [00:12<00:26, 3845.37it/s]
30%|##9 | 43094/145758.0 [00:12<00:26, 3832.14it/s]
30%|##9 | 43478/145758.0 [00:12<00:27, 3763.89it/s]
30%|### | 43855/145758.0 [00:12<00:27, 3720.62it/s]
30%|### | 44228/145758.0 [00:12<00:27, 3687.71it/s]
31%|### | 44626/145758.0 [00:12<00:26, 3773.35it/s]
31%|### | 45021/145758.0 [00:12<00:26, 3825.32it/s]
31%|###1 | 45411/145758.0 [00:12<00:26, 3845.72it/s]
31%|###1 | 45799/145758.0 [00:12<00:25, 3854.86it/s]
32%|###1 | 46185/145758.0 [00:12<00:25, 3836.43it/s]
32%|###1 | 46569/145758.0 [00:13<00:26, 3774.32it/s]
32%|###2 | 46947/145758.0 [00:13<00:26, 3708.73it/s]
32%|###2 | 47326/145758.0 [00:13<00:26, 3731.95it/s]
33%|###2 | 47738/145758.0 [00:13<00:25, 3844.93it/s]
33%|###3 | 48136/145758.0 [00:13<00:25, 3882.47it/s]
33%|###3 | 48547/145758.0 [00:13<00:24, 3949.80it/s]
34%|###3 | 48946/145758.0 [00:13<00:24, 3959.71it/s]
34%|###3 | 49343/145758.0 [00:13<00:24, 3950.44it/s]
34%|###4 | 49739/145758.0 [00:13<00:25, 3827.89it/s]
34%|###4 | 50123/145758.0 [00:14<00:25, 3776.28it/s]
35%|###4 | 50502/145758.0 [00:14<00:25, 3762.87it/s]
35%|###4 | 50905/145758.0 [00:14<00:24, 3840.02it/s]
35%|###5 | 51322/145758.0 [00:14<00:23, 3935.82it/s]
35%|###5 | 51717/145758.0 [00:14<00:23, 3936.36it/s]
36%|###5 | 52111/145758.0 [00:14<00:23, 3919.50it/s]
36%|###6 | 52504/145758.0 [00:14<00:24, 3879.72it/s]
36%|###6 | 52893/145758.0 [00:14<00:24, 3753.53it/s]
37%|###6 | 53274/145758.0 [00:14<00:24, 3766.42it/s]
37%|###6 | 53677/145758.0 [00:14<00:23, 3842.06it/s]
37%|###7 | 54075/145758.0 [00:15<00:23, 3881.43it/s]
37%|###7 | 54483/145758.0 [00:15<00:23, 3938.63it/s]
38%|###7 | 54890/145758.0 [00:15<00:22, 3974.84it/s]
38%|###7 | 55288/145758.0 [00:15<00:23, 3922.55it/s]
38%|###8 | 55681/145758.0 [00:15<00:23, 3806.06it/s]
38%|###8 | 56063/145758.0 [00:15<00:23, 3743.65it/s]
39%|###8 | 56449/145758.0 [00:15<00:23, 3776.61it/s]
39%|###8 | 56841/145758.0 [00:15<00:23, 3817.38it/s]
39%|###9 | 57228/145758.0 [00:15<00:23, 3830.78it/s]
40%|###9 | 57635/145758.0 [00:15<00:22, 3900.71it/s]
40%|###9 | 58030/145758.0 [00:16<00:22, 3914.44it/s]
40%|#### | 58422/145758.0 [00:16<00:23, 3790.81it/s]
40%|#### | 58803/145758.0 [00:16<00:23, 3759.95it/s]
41%|#### | 59180/145758.0 [00:16<00:23, 3755.41it/s]
41%|#### | 59581/145758.0 [00:16<00:22, 3828.61it/s]
41%|####1 | 59965/145758.0 [00:16<00:22, 3830.76it/s]
41%|####1 | 60349/145758.0 [00:16<00:22, 3802.52it/s]
42%|####1 | 60730/145758.0 [00:16<00:34, 2499.20it/s]
42%|####1 | 61091/145758.0 [00:17<00:30, 2740.64it/s]
42%|####2 | 61437/145758.0 [00:17<00:28, 2910.83it/s]
42%|####2 | 61799/145758.0 [00:17<00:27, 3088.16it/s]
43%|####2 | 62173/145758.0 [00:17<00:25, 3259.84it/s]
43%|####2 | 62555/145758.0 [00:17<00:24, 3413.45it/s]
43%|####3 | 62945/145758.0 [00:17<00:23, 3550.11it/s]
43%|####3 | 63327/145758.0 [00:17<00:22, 3623.90it/s]
44%|####3 | 63700/145758.0 [00:17<00:22, 3635.42it/s]
44%|####3 | 64071/145758.0 [00:17<00:23, 3538.09it/s]
44%|####4 | 64431/145758.0 [00:17<00:23, 3513.78it/s]
44%|####4 | 64799/145758.0 [00:18<00:22, 3559.89it/s]
45%|####4 | 65188/145758.0 [00:18<00:22, 3654.98it/s]
45%|####4 | 65556/145758.0 [00:18<00:21, 3661.60it/s]
45%|####5 | 65926/145758.0 [00:18<00:21, 3672.73it/s]
45%|####5 | 66295/145758.0 [00:18<00:21, 3652.42it/s]
46%|####5 | 66662/145758.0 [00:18<00:21, 3599.60it/s]
46%|####5 | 67023/145758.0 [00:18<00:22, 3535.93it/s]
46%|####6 | 67378/145758.0 [00:18<00:22, 3497.76it/s]
46%|####6 | 67743/145758.0 [00:18<00:22, 3541.43it/s]
47%|####6 | 68117/145758.0 [00:18<00:21, 3596.68it/s]
47%|####6 | 68485/145758.0 [00:19<00:21, 3620.44it/s]
47%|####7 | 68848/145758.0 [00:19<00:21, 3611.56it/s]
47%|####7 | 69210/145758.0 [00:19<00:21, 3522.77it/s]
48%|####7 | 69577/145758.0 [00:19<00:21, 3564.19it/s]
48%|####7 | 69934/145758.0 [00:19<00:21, 3553.61it/s]
48%|####8 | 70302/145758.0 [00:19<00:21, 3589.76it/s]
48%|####8 | 70669/145758.0 [00:19<00:20, 3612.40it/s]
49%|####8 | 71043/145758.0 [00:19<00:20, 3646.10it/s]
49%|####8 | 71408/145758.0 [00:19<00:20, 3635.71it/s]
49%|####9 | 71772/145758.0 [00:20<00:20, 3591.57it/s]
49%|####9 | 72132/145758.0 [00:20<00:21, 3492.67it/s]
50%|####9 | 72482/145758.0 [00:20<00:21, 3460.20it/s]
50%|####9 | 72834/145758.0 [00:20<00:20, 3474.50it/s]
50%|##### | 73202/145758.0 [00:20<00:20, 3534.34it/s]
50%|##### | 73589/145758.0 [00:20<00:19, 3633.17it/s]
51%|##### | 73982/145758.0 [00:20<00:19, 3718.93it/s]
51%|#####1 | 74370/145758.0 [00:20<00:18, 3766.46it/s]
51%|#####1 | 74747/145758.0 [00:20<00:19, 3633.14it/s]
52%|#####1 | 75112/145758.0 [00:20<00:19, 3591.10it/s]
52%|#####1 | 75472/145758.0 [00:21<00:19, 3518.64it/s]
52%|#####2 | 75825/145758.0 [00:21<00:19, 3518.66it/s]
52%|#####2 | 76205/145758.0 [00:21<00:19, 3599.63it/s]
53%|#####2 | 76587/145758.0 [00:21<00:18, 3663.78it/s]
53%|#####2 | 76963/145758.0 [00:21<00:18, 3689.07it/s]
53%|#####3 | 77338/145758.0 [00:21<00:18, 3707.07it/s]
53%|#####3 | 77709/145758.0 [00:21<00:18, 3652.60it/s]
54%|#####3 | 78075/145758.0 [00:21<00:18, 3598.34it/s]
54%|#####3 | 78436/145758.0 [00:21<00:18, 3562.79it/s]
54%|#####4 | 78801/145758.0 [00:21<00:18, 3586.46it/s]
54%|#####4 | 79177/145758.0 [00:22<00:18, 3636.01it/s]
55%|#####4 | 79545/145758.0 [00:22<00:18, 3648.82it/s]
55%|#####4 | 79911/145758.0 [00:22<00:18, 3614.73it/s]
55%|#####5 | 80273/145758.0 [00:22<00:18, 3544.14it/s]
55%|#####5 | 80628/145758.0 [00:22<00:18, 3490.76it/s]
56%|#####5 | 80978/145758.0 [00:22<00:18, 3475.02it/s]
56%|#####5 | 81326/145758.0 [00:22<00:18, 3475.34it/s]
56%|#####6 | 81701/145758.0 [00:22<00:18, 3555.42it/s]
56%|#####6 | 82084/145758.0 [00:22<00:17, 3634.80it/s]
57%|#####6 | 82455/145758.0 [00:22<00:17, 3656.27it/s]
57%|#####6 | 82829/145758.0 [00:23<00:17, 3680.50it/s]
57%|#####7 | 83198/145758.0 [00:23<00:17, 3576.75it/s]
57%|#####7 | 83557/145758.0 [00:23<00:17, 3575.55it/s]
58%|#####7 | 83917/145758.0 [00:23<00:17, 3582.23it/s]
58%|#####7 | 84284/145758.0 [00:23<00:17, 3606.88it/s]
58%|#####8 | 84671/145758.0 [00:23<00:16, 3684.06it/s]
58%|#####8 | 85053/145758.0 [00:23<00:16, 3721.73it/s]
59%|#####8 | 85437/145758.0 [00:23<00:16, 3755.03it/s]
59%|#####8 | 85814/145758.0 [00:23<00:15, 3756.19it/s]
59%|#####9 | 86190/145758.0 [00:24<00:16, 3635.34it/s]
59%|#####9 | 86556/145758.0 [00:24<00:16, 3640.54it/s]
60%|#####9 | 86922/145758.0 [00:24<00:16, 3642.66it/s]
60%|#####9 | 87313/145758.0 [00:24<00:15, 3720.34it/s]
60%|###### | 87704/145758.0 [00:24<00:15, 3775.94it/s]
60%|###### | 88087/145758.0 [00:24<00:15, 3788.80it/s]
61%|###### | 88467/145758.0 [00:24<00:15, 3780.93it/s]
61%|###### | 88849/145758.0 [00:24<00:15, 3790.90it/s]
61%|######1 | 89229/145758.0 [00:24<00:15, 3727.97it/s]
61%|######1 | 89603/145758.0 [00:24<00:15, 3727.55it/s]
62%|######1 | 89986/145758.0 [00:25<00:14, 3754.76it/s]
62%|######2 | 90386/145758.0 [00:25<00:14, 3826.86it/s]
62%|######2 | 90782/145758.0 [00:25<00:14, 3865.35it/s]
63%|######2 | 91176/145758.0 [00:25<00:14, 3885.70it/s]
63%|######2 | 91577/145758.0 [00:25<00:13, 3921.74it/s]
63%|######3 | 91970/145758.0 [00:25<00:13, 3863.01it/s]
63%|######3 | 92357/145758.0 [00:25<00:14, 3798.49it/s]
64%|######3 | 92738/145758.0 [00:25<00:13, 3790.33it/s]
64%|######3 | 93134/145758.0 [00:25<00:13, 3839.39it/s]
64%|######4 | 93531/145758.0 [00:25<00:13, 3875.89it/s]
64%|######4 | 93940/145758.0 [00:26<00:13, 3939.11it/s]
65%|######4 | 94335/145758.0 [00:26<00:13, 3908.21it/s]
65%|######4 | 94733/145758.0 [00:26<00:12, 3925.49it/s]
65%|######5 | 95126/145758.0 [00:26<00:13, 3844.43it/s]
66%|######5 | 95511/145758.0 [00:26<00:13, 3816.72it/s]
66%|######5 | 95916/145758.0 [00:26<00:12, 3884.07it/s]
66%|######6 | 96316/145758.0 [00:26<00:12, 3916.74it/s]
66%|######6 | 96712/145758.0 [00:26<00:12, 3928.22it/s]
67%|######6 | 97106/145758.0 [00:26<00:12, 3918.75it/s]
67%|######6 | 97524/145758.0 [00:26<00:12, 3994.21it/s]
67%|######7 | 97924/145758.0 [00:27<00:12, 3935.00it/s]
67%|######7 | 98318/145758.0 [00:27<00:12, 3904.23it/s]
68%|######7 | 98713/145758.0 [00:27<00:12, 3915.89it/s]
68%|######8 | 99127/145758.0 [00:27<00:11, 3980.76it/s]
68%|######8 | 99528/145758.0 [00:27<00:11, 3988.89it/s]
69%|######8 | 99928/145758.0 [00:27<00:11, 3981.26it/s]
69%|######8 | 100334/145758.0 [00:27<00:11, 4003.70it/s]
69%|######9 | 100735/145758.0 [00:27<00:11, 3966.70it/s]
69%|######9 | 101132/145758.0 [00:27<00:11, 3897.33it/s]
70%|######9 | 101523/145758.0 [00:27<00:11, 3874.08it/s]
70%|######9 | 101933/145758.0 [00:28<00:11, 3938.20it/s]
70%|####### | 102337/145758.0 [00:28<00:10, 3966.07it/s]
70%|####### | 102734/145758.0 [00:28<00:10, 3954.07it/s]
71%|####### | 103130/145758.0 [00:28<00:10, 3944.51it/s]
71%|#######1 | 103525/145758.0 [00:28<00:10, 3933.70it/s]
71%|#######1 | 103919/145758.0 [00:28<00:10, 3831.39it/s]
72%|#######1 | 104303/145758.0 [00:28<00:10, 3833.74it/s]
72%|#######1 | 104700/145758.0 [00:28<00:10, 3872.04it/s]
72%|#######2 | 105102/145758.0 [00:28<00:10, 3915.32it/s]
72%|#######2 | 105496/145758.0 [00:28<00:10, 3919.23it/s]
73%|#######2 | 105889/145758.0 [00:29<00:10, 3895.05it/s]
73%|#######2 | 106279/145758.0 [00:29<00:10, 3883.38it/s]
73%|#######3 | 106668/145758.0 [00:29<00:10, 3841.05it/s]
73%|#######3 | 107053/145758.0 [00:29<00:10, 3797.96it/s]
74%|#######3 | 107442/145758.0 [00:29<00:10, 3822.04it/s]
74%|#######3 | 107836/145758.0 [00:29<00:09, 3855.35it/s]
74%|#######4 | 108241/145758.0 [00:29<00:09, 3912.34it/s]
75%|#######4 | 108633/145758.0 [00:29<00:09, 3904.64it/s]
75%|#######4 | 109024/145758.0 [00:29<00:09, 3859.19it/s]
75%|#######5 | 109411/145758.0 [00:29<00:09, 3839.95it/s]
75%|#######5 | 109796/145758.0 [00:30<00:09, 3701.68it/s]
76%|#######5 | 110168/145758.0 [00:30<00:09, 3697.94it/s]
76%|#######5 | 110545/145758.0 [00:30<00:09, 3717.43it/s]
76%|#######6 | 110931/145758.0 [00:30<00:09, 3755.00it/s]
76%|#######6 | 111314/145758.0 [00:30<00:09, 3776.21it/s]
77%|#######6 | 111692/145758.0 [00:30<00:09, 3775.65it/s]
77%|#######6 | 112084/145758.0 [00:30<00:08, 3815.05it/s]
77%|#######7 | 112466/145758.0 [00:30<00:08, 3744.05it/s]
77%|#######7 | 112841/145758.0 [00:30<00:09, 3654.97it/s]
78%|#######7 | 113217/145758.0 [00:31<00:08, 3684.12it/s]
78%|#######7 | 113609/145758.0 [00:31<00:08, 3752.31it/s]
78%|#######8 | 114004/145758.0 [00:31<00:08, 3807.38it/s]
78%|#######8 | 114386/145758.0 [00:31<00:08, 3796.28it/s]
79%|#######8 | 114766/145758.0 [00:31<00:08, 3796.57it/s]
79%|#######8 | 115146/145758.0 [00:31<00:08, 3731.19it/s]
79%|#######9 | 115520/145758.0 [00:31<00:08, 3589.03it/s]
80%|#######9 | 115881/145758.0 [00:31<00:08, 3581.60it/s]
80%|#######9 | 116269/145758.0 [00:31<00:08, 3667.60it/s]
80%|######## | 116662/145758.0 [00:31<00:07, 3743.76it/s]
80%|######## | 117050/145758.0 [00:32<00:07, 3783.83it/s]
81%|######## | 117434/145758.0 [00:32<00:07, 3799.80it/s]
81%|######## | 117815/145758.0 [00:32<00:07, 3775.47it/s]
81%|########1 | 118193/145758.0 [00:32<00:07, 3648.31it/s]
81%|########1 | 118570/145758.0 [00:32<00:07, 3682.76it/s]
82%|########1 | 118951/145758.0 [00:32<00:07, 3719.96it/s]
82%|########1 | 119339/145758.0 [00:32<00:07, 3766.31it/s]
82%|########2 | 119738/145758.0 [00:32<00:06, 3831.84it/s]
82%|########2 | 120128/145758.0 [00:32<00:06, 3850.07it/s]
83%|########2 | 120514/145758.0 [00:32<00:06, 3811.50it/s]
83%|########2 | 120896/145758.0 [00:33<00:06, 3750.22it/s]
83%|########3 | 121296/145758.0 [00:33<00:06, 3822.29it/s]
83%|########3 | 121685/145758.0 [00:33<00:06, 3836.57it/s]
84%|########3 | 122071/145758.0 [00:33<00:06, 3843.28it/s]
84%|########4 | 122477/145758.0 [00:33<00:05, 3907.29it/s]
84%|########4 | 122868/145758.0 [00:33<00:05, 3834.65it/s]
85%|########4 | 123252/145758.0 [00:33<00:05, 3757.84it/s]
85%|########4 | 123629/145758.0 [00:33<00:06, 3672.03it/s]
85%|########5 | 124019/145758.0 [00:33<00:05, 3737.29it/s]
85%|########5 | 124401/145758.0 [00:33<00:05, 3760.47it/s]
86%|########5 | 124790/145758.0 [00:34<00:05, 3798.24it/s]
86%|########5 | 125175/145758.0 [00:34<00:05, 3813.09it/s]
86%|########6 | 125557/145758.0 [00:34<00:05, 3760.10it/s]
86%|########6 | 125934/145758.0 [00:34<00:05, 3681.82it/s]
87%|########6 | 126312/145758.0 [00:34<00:05, 3708.77it/s]
87%|########6 | 126684/145758.0 [00:34<00:05, 3700.09it/s]
87%|########7 | 127062/145758.0 [00:34<00:05, 3722.16it/s]
87%|########7 | 127440/145758.0 [00:34<00:04, 3738.33it/s]
88%|########7 | 127815/145758.0 [00:34<00:04, 3695.27it/s]
88%|########7 | 128185/145758.0 [00:35<00:04, 3653.92it/s]
88%|########8 | 128551/145758.0 [00:35<00:04, 3595.82it/s]
88%|########8 | 128920/145758.0 [00:35<00:04, 3622.93it/s]
89%|########8 | 129299/145758.0 [00:35<00:04, 3670.33it/s]
89%|########8 | 129672/145758.0 [00:35<00:04, 3687.37it/s]
89%|########9 | 130041/145758.0 [00:35<00:04, 3669.68it/s]
89%|########9 | 130411/145758.0 [00:35<00:04, 3678.63it/s]
90%|########9 | 130779/145758.0 [00:35<00:04, 3579.98it/s]
90%|########9 | 131138/145758.0 [00:35<00:04, 3578.06it/s]
90%|######### | 131523/145758.0 [00:35<00:03, 3656.15it/s]
91%|######### | 131914/145758.0 [00:36<00:03, 3728.07it/s]
91%|######### | 132288/145758.0 [00:36<00:03, 3703.91it/s]
91%|#########1| 132659/145758.0 [00:36<00:03, 3665.53it/s]
91%|#########1| 133026/145758.0 [00:36<00:03, 3536.67it/s]
92%|#########1| 133383/145758.0 [00:36<00:03, 3545.87it/s]
92%|#########1| 133760/145758.0 [00:36<00:03, 3610.78it/s]
92%|#########2| 134134/145758.0 [00:36<00:03, 3647.54it/s]
92%|#########2| 134500/145758.0 [00:36<00:03, 3621.76it/s]
93%|#########2| 134863/145758.0 [00:36<00:03, 3530.92it/s]
93%|#########2| 135217/145758.0 [00:36<00:02, 3514.60it/s]
93%|#########3| 135572/145758.0 [00:37<00:02, 3524.64it/s]
93%|#########3| 135945/145758.0 [00:37<00:02, 3584.96it/s]
94%|#########3| 136309/145758.0 [00:37<00:02, 3599.23it/s]
94%|#########3| 136670/145758.0 [00:37<00:02, 3564.83it/s]
94%|#########4| 137027/145758.0 [00:37<00:02, 3524.00it/s]
94%|#########4| 137385/145758.0 [00:37<00:02, 3540.20it/s]
95%|#########4| 137747/145758.0 [00:37<00:02, 3561.27it/s]
95%|#########4| 138108/145758.0 [00:37<00:02, 3574.33it/s]
95%|#########4| 138466/145758.0 [00:37<00:02, 3531.70it/s]
95%|#########5| 138820/145758.0 [00:37<00:01, 3517.54it/s]
95%|#########5| 139188/145758.0 [00:38<00:01, 3562.73it/s]
96%|#########5| 139558/145758.0 [00:38<00:01, 3601.96it/s]
96%|#########5| 139919/145758.0 [00:38<00:01, 3563.80it/s]
96%|#########6| 140276/145758.0 [00:38<00:01, 3491.29it/s]
96%|#########6| 140628/145758.0 [00:38<00:01, 3499.31it/s]
97%|#########6| 140979/145758.0 [00:38<00:02, 2269.89it/s]
97%|#########6| 141328/145758.0 [00:38<00:01, 2530.34it/s]
97%|#########7| 141662/145758.0 [00:38<00:01, 2718.92it/s]
97%|#########7| 142006/145758.0 [00:39<00:01, 2899.20it/s]
98%|#########7| 142357/145758.0 [00:39<00:01, 3058.75it/s]
98%|#########7| 142693/145758.0 [00:39<00:00, 3139.35it/s]
98%|#########8| 143030/145758.0 [00:39<00:00, 3203.78it/s]
98%|#########8| 143386/145758.0 [00:39<00:00, 3304.55it/s]
99%|#########8| 143726/145758.0 [00:39<00:00, 3309.42it/s]
99%|#########8| 144066/145758.0 [00:39<00:00, 3334.19it/s]
99%|#########9| 144410/145758.0 [00:39<00:00, 3363.49it/s]
99%|#########9| 144750/145758.0 [00:39<00:00, 3341.45it/s]
100%|#########9| 145087/145758.0 [00:39<00:00, 3348.67it/s]
100%|#########9| 145424/145758.0 [00:40<00:00, 3314.33it/s]
100%|#########9| 145757/145758.0 [00:40<00:00, 3281.20it/s]
100%|##########| 145758/145758.0 [00:40<00:00, 3624.68it/s]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
0%| | 0/8114 [00:00<?, ?it/s]
0%| | 4/8114 [00:02<1:22:02, 1.65it/s]
3%|2 | 204/8114 [00:02<01:10, 112.41it/s]
13%|#2 | 1036/8114 [00:02<00:09, 710.05it/s]
25%|##5 | 2060/8114 [00:02<00:03, 1588.68it/s]
51%|##### | 4108/8114 [00:02<00:01, 3458.90it/s]
76%|#######5 | 6156/8114 [00:03<00:00, 5536.97it/s]
100%|##########| 8114/8114 [00:03<00:00, 2647.30it/s]
0%| | 0/8114 [00:00<?, ?it/s]
25%|##5 | 2040/8114 [00:00<00:00, 15157.40it/s]
50%|##### | 4088/8114 [00:00<00:00, 16513.43it/s]
100%|##########| 8114/8114 [00:00<00:00, 25168.45it/s]
0%| | 0/8114 [00:00<?, ?it/s]
3%|3 | 252/8114 [00:00<00:03, 2481.09it/s]
19%|#8 | 1532/8114 [00:00<00:00, 8489.73it/s]
38%|###7 | 3068/8114 [00:00<00:00, 10586.84it/s]
51%|##### | 4110/8114 [00:00<00:00, 9874.04it/s]
76%|#######5 | 6140/8114 [00:00<00:00, 12869.92it/s]
100%|##########| 8114/8114 [00:00<00:00, 14674.91it/s]
0%| | 0/8114 [00:00<?, ?it/s]
25%|##5 | 2040/8114 [00:00<00:00, 15569.03it/s]
50%|##### | 4088/8114 [00:00<00:00, 14878.29it/s]
100%|##########| 8114/8114 [00:00<00:00, 22761.80it/s]
0%| | 0/8114 [00:00<?, ?it/s]
5%|4 | 380/8114 [00:00<00:02, 3623.98it/s]
25%|##5 | 2044/8114 [00:00<00:00, 8647.40it/s]
50%|##### | 4092/8114 [00:00<00:00, 10068.92it/s]
100%|##########| 8114/8114 [00:00<00:00, 15156.28it/s]
0%| | 0/8114 [00:00<?, ?it/s]
2%|2 | 184/8114 [00:00<00:04, 1761.80it/s]
13%|#2 | 1016/8114 [00:00<00:01, 4372.54it/s]
25%|##5 | 2040/8114 [00:00<00:01, 5024.64it/s]
38%|###7 | 3064/8114 [00:00<00:00, 6281.71it/s]
50%|##### | 4088/8114 [00:00<00:00, 5527.67it/s]
63%|######3 | 5112/8114 [00:00<00:00, 5208.38it/s]
76%|#######5 | 6136/8114 [00:01<00:00, 4837.83it/s]
88%|########8 | 7160/8114 [00:01<00:00, 4200.16it/s]
100%|##########| 8114/8114 [00:01<00:00, 5278.60it/s]
0%| | 0/8114 [00:00<?, ?it/s]
3%|3 | 252/8114 [00:00<00:03, 2415.90it/s]
25%|##5 | 2044/8114 [00:00<00:00, 9521.16it/s]
50%|##### | 4092/8114 [00:00<00:00, 11930.67it/s]
100%|##########| 8114/8114 [00:00<00:00, 16950.13it/s]
0%| | 0/8114 [00:00<?, ?it/s]
3%|3 | 252/8114 [00:00<00:03, 2491.18it/s]
25%|##5 | 2044/8114 [00:00<00:00, 9599.60it/s]
50%|##### | 4092/8114 [00:00<00:00, 10612.02it/s]
100%|##########| 8114/8114 [00:00<00:00, 15812.83it/s]
0%| | 0/8 [00:00<?, ?it/s]
12%|#2 | 1/8 [00:00<00:01, 6.35it/s]
25%|##5 | 2/8 [00:00<00:00, 6.63it/s]
38%|###7 | 3/8 [00:00<00:01, 4.18it/s]
50%|##### | 4/8 [00:00<00:00, 4.90it/s]
62%|######2 | 5/8 [00:00<00:00, 5.57it/s]
75%|#######5 | 6/8 [00:01<00:00, 6.01it/s]
88%|########7 | 7/8 [00:01<00:00, 6.25it/s]
100%|##########| 8/8 [00:01<00:00, 6.57it/s]
100%|##########| 8/8 [00:01<00:00, 5.89it/s]
0%| | 0/8 [00:00<?, ?it/s]
12%|#2 | 1/8 [00:00<00:01, 6.52it/s]
25%|##5 | 2/8 [00:00<00:00, 6.97it/s]
38%|###7 | 3/8 [00:00<00:00, 6.90it/s]
50%|##### | 4/8 [00:00<00:00, 6.86it/s]
62%|######2 | 5/8 [00:00<00:00, 6.83it/s]
75%|#######5 | 6/8 [00:00<00:00, 6.83it/s]
88%|########7 | 7/8 [00:01<00:00, 6.84it/s]
100%|##########| 8/8 [00:01<00:00, 7.00it/s]
100%|##########| 8/8 [00:01<00:00, 6.90it/s]
Visualizing bundles and tract profiles:#
This would run the script and visualize the bundles using the plotly interactive visualization, which should automatically open in a new browser window.
bundle_html = myafq.export("all_bundles_figure")
plotly.io.show(bundle_html["01"])