[pymvpa] design matrix identical across sessions
Yaroslav Halchenko
debian at onerussian.com
Tue May 10 01:27:15 UTC 2016
sorry Wolfgang, I have no mental capacity left to parse those outputs...
it kinda looks ok, but you better just h5save sample dataset
(ds[:,0] should be enough) and those events and then accompany with the
code operating on those which would demonstrate the problem. you can
send directly to my email (ml will not allow for large attachments)
That would be the best way to reproduce and understand (tomorrow morning
I guess)
On Mon, 09 May 2016, Wolfgang Pauli wrote:
> Hi,A
> Thank you for the quick response. I did infact have
> condition_attr=['targets', 'chunks'], sorry about the typo. Have been
> trying to debug this for too long ...
> Regarding the even definitions. Please see below the event definitions
> according to.A
> onsets = []
> targets = []
> chunks = []
> for ev in events:
> A A onsets.append(ev['onset'])
> A A targets.append(ev['targets'])
> A A chunks.append(ev['chunks'])
> >>> targets
> ['csA', 'csX_j_1', 'csB', 'csY_n_1', 'csA', 'csX_j_1', 'csB', 'csY_n_1',
> 'csA', 'csX_j_1', 'csB', 'csY_n_1', 'csA', 'csX_j_1', 'csB', 'csY_n_1',
> 'csB', 'csA', 'csX_j_1', 'csB', 'csY_n_1', 'csA', 'csX_j_1', 'csB',\
> A 'csY_n_1', 'csA', 'csX_j_1', 'csB', 'csY_n_1', 'csA', 'csX_j_1', 'csB',
> 'csY_n_1', 'csA', 'csX_j_1', 'csB', 'csB', 'csY_n_1', 'csA', 'csA',
> 'csX_j_1', 'csB', 'csY_n_1', 'csB', 'csA', 'csX_j_1', 'csA', 'csX_j_1',\
> A 'csB', 'csY_n_1', 'csA', 'csB', 'csY_n_1', 'csA', 'csC', 'csX_n_1',
> 'csD', 'csY_j_1', 'csD', 'csY_j_1', 'csC', 'csX_n_1', 'csD', 'csY_j_1',
> 'csC', 'csX_n_1', 'csD', 'csY_j_1', 'csC', 'csX_n_1', 'csD', 'csY_j_1',\
> A 'csC', 'csC', 'csX_n_1', 'csC', 'csX_n_1', 'csD', 'csY_j_1', 'csC',
> 'csX_n_1', 'csC', 'csC', 'csX_n_1', 'csD', 'csD', 'csY_j_1', 'csC',
> 'csX_n_1', 'csD', 'csY_j_1', 'csC', 'csX_n_1', 'csD', 'csY_j_1', 'csD',
> 'cs\
> D', 'csY_j_1', 'csC', 'csX_n_1', 'csD', 'csY_j_1', 'csC', 'csD',
> 'csY_j_1', 'csD', 'csC', 'csX_n_1', 'csE', 'csX_j_2', 'csE', 'csX_j_2',
> 'csE', 'csX_j_2', 'csF', 'csY_n_2', 'csE', 'csX_j_2', 'csF', 'csY_n_2',
> 'cs\
> E', 'csX_j_2', 'csF', 'csY_n_2', 'csE', 'csX_j_2', 'csF', 'csY_n_2',
> 'csF', 'csF', 'csY_n_2', 'csE', 'csX_j_2', 'csF', 'csY_n_2', 'csE', 'csF',
> 'csY_n_2', 'csE', 'csX_j_2', 'csF', 'csY_n_2', 'csE', 'csX_j_2', 'cs\
> F', 'csY_n_2', 'csE', 'csX_j_2', 'csF', 'csY_n_2', 'csE', 'csX_j_2',
> 'csF', 'csY_n_2', 'csE', 'csF', 'csY_n_2', 'csF', 'csE', 'csF', 'csE',
> 'csX_j_2', 'csH', 'csY_j_2', 'csH', 'csY_j_2', 'csH', 'csY_j_2', 'csG', \
> 'csX_n_2', 'csH', 'csY_j_2', 'csG', 'csX_n_2', 'csH', 'csY_j_2', 'csG',
> 'csX_n_2', 'csH', 'csY_j_2', 'csG', 'csX_n_2', 'csH', 'csY_j_2', 'csH',
> 'csH', 'csY_j_2', 'csG', 'csX_n_2', 'csH', 'csY_j_2', 'csG', 'csX_n_\
> 2', 'csG', 'csG', 'csX_n_2', 'csH', 'csG', 'csX_n_2', 'csH', 'csY_j_2',
> 'csG', 'csX_n_2', 'csG', 'csG', 'csX_n_2', 'csH', 'csY_j_2', 'csG',
> 'csX_n_2', 'csH', 'csY_j_2', 'csH', 'csG', 'csX_n_2', 'csG']
> >>> onsets
> [4.2000001668930054, 7.2000002861022949, 20.400000810623169,
> 25.200001001358032, 39.600001573562622, 45.600001811981201,
> 61.800002455711365, 66.600002646446228, 80.40000319480896,
> 84.000003337860107, 94.800003767\
> 01355, 98.400003910064697, 114.000004529953, 117.00000464916229,
> 127.20000505447388, 132.00000524520874, 144.0000057220459,
> 162.00000643730164, 166.20000660419464, 178.80000710487366,
> 184.20000731945038, 199.8000\
> 0793933868, 203.40000808238983, 216.00000858306885, 219.60000872612,
> 230.40000915527344, 235.80000936985016, 249.60000991821289,
> 254.40001010894775, 270.00001072883606, 275.40001094341278,
> 291.00001156330109, 295\
> .20001173019409, 306.00001215934753, 310.8000123500824,
> 327.00001299381256, 346.20001375675201, 351.60001397132874,
> 367.8000146150589, 386.40001535415649, 392.40001559257507,
> 409.80001628398895, 415.2000164985656\
> 7, 432.60001718997955, 451.80001795291901, 456.00001811981201,
> 469.20001864433289, 473.40001881122589, 487.80001938343048,
> 492.60001957416534, 507.00002014636993, 528.00002098083496,
> 532.80002117156982, 548.40002\
> 179145813, 606.60002410411835, 610.80002427101135, 624.00002479553223,
> 628.80002498626709, 640.20002543926239, 644.4000256061554,
> 658.20002615451813, 661.80002629756927, 673.80002677440643,
> 676.80002689361572, 68\
> 8.20002734661102, 693.00002753734589, 703.20002794265747,
> 707.40002810955048, 720.00002861022949, 725.40002882480621,
> 737.40002930164337, 740.40002942085266, 755.40003001689911,
> 777.00003087520599, 781.2000310420\
> 99, 793.20003151893616, 798.60003173351288, 811.20003223419189,
> 815.4000324010849, 828.60003292560577, 834.0000331401825,
> 846.00003361701965, 862.80003428459167, 867.00003445148468,
> 878.40003490447998, 897.000035\
> 64357758, 901.20003581047058, 917.40003645420074, 922.20003664493561,
> 939.60003733634949, 943.80003750324249, 955.20003795623779,
> 958.80003809928894, 972.60003864765167, 976.20003879070282,
> 989.40003931522369, 10\
> 08.0000400543213, 1012.2000402212143, 1025.4000407457352,
> 1030.8000409603119, 1043.4000414609909, 1047.0000416040421,
> 1062.0000422000885, 1083.0000430345535, 1087.8000432252884,
> 1100.4000437259674, 1119.000044465\
> 065, 1122.0000445842743, 1206.6000479459763, 1210.8000481128693,
> 1225.8000487089157, 1230.6000488996506, 1243.2000494003296,
> 1247.4000495672226, 1260.0000500679016, 1266.0000503063202,
> 1279.8000508546829, 1284.00\
> 00510215759, 1299.0000516176224, 1304.4000518321991, 1318.2000523805618,
> 1323.6000525951385, 1335.6000530719757, 1339.2000532150269,
> 1354.2000538110733, 1358.4000539779663, 1369.2000544071198,
> 1374.0000545978546,\
> A 1390.2000552415848, 1407.6000559329987, 1412.4000561237335,
> 1428.0000567436218, 1434.0000569820404, 1448.400057554245,
> 1453.8000577688217, 1470.0000584125519, 1485.0000590085983,
> 1488.0000591278076, 1504.8000597\
> 953796, 1510.8000600337982, 1523.4000605344772, 1527.6000607013702,
> 1543.2000613212585, 1547.4000614881516, 1559.4000619649887,
> 1564.8000621795654, 1579.20006275177, 1584.6000629663467,
> 1600.200063586235, 1603.20\
> 00637054443, 1615.2000641822815, 1618.2000643014908, 1630.8000648021698,
> 1634.4000649452209, 1647.6000654697418, 1662.0000660419464,
> 1666.2000662088394, 1679.4000667333603, 1696.2000674009323,
> 1714.200068116188, \
> 1735.2000689506531, 1741.2000691890717, 1806.6000717878342,
> 1809.6000719070435, 1824.000072479248, 1830.0000727176666,
> 1842.0000731945038, 1848.0000734329224, 1860.0000739097595,
> 1865.4000741243362, 1879.80007469\
> 65408, 1884.6000748872757, 1900.200075507164, 1904.400075674057,
> 1919.4000762701035, 1923.0000764131546, 1937.4000769853592,
> 1943.4000772237778, 1956.0000777244568, 1960.8000779151917,
> 1974.6000784635544, 1977.60\
> 00785827637, 1993.200079202652, 1998.6000794172287, 2011.2000799179077,
> 2026.2000805139542, 2030.4000806808472, 2042.4000811576843,
> 2047.800081372261, 2059.8000818490982, 2065.2000820636749,
> 2077.2000825405121, 2\
> 080.8000826835632, 2092.8000831604004, 2107.8000837564468,
> 2112.6000839471817, 2125.8000844717026, 2140.800085067749,
> 2145.000085234642, 2158.8000857830048, 2164.2000859975815,
> 2176.8000864982605, 2179.8000866174\
> 698, 2195.4000872373581, 2212.2000879049301, 2217.000088095665,
> 2232.6000887155533, 2235.6000888347626, 2250.0000894069672,
> 2254.2000895738602, 2269.8000901937485, 2274.6000903844833,
> 2289.0000909566879, 2306.400\
> 0916481018, 2311.8000918626785, 2322.0000922679901]
> >>> chunksA
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1\
> , 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, \
> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3,
> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,\
> A 3, 3, 3, 3]
> This looks correct, no? I am trying to attach the image plot of the design
> matrix, split into the 4 sessions.A
> Best,
> Wolfganga**
> [IMG]A figure_1.png
> a**
> On Mon, May 9, 2016 at 5:50 PM, Yaroslav Halchenko <debian at onerussian.com>
> wrote:
> On Mon, 09 May 2016, Wolfgang Pauli wrote:
> > Hi,
> > I am trying to perform an mvpa analysis of an experiment in which I
> have 16
> > different trial types and 4 sessions, 4 trial types in each session
> (run).
> > Based on the tutorial, I was getting started by using
> fit_event_hrf_model,
> > like so:
> > evds = fit_event_hrf_model(ds, events, time_attr='time_coords',
> > condition_attr=('onset'), return_model=True)
> > where ds is an openfmri dataset (get_model_bold_dataset).
> > I was trying to figure out why I would always get the warning that the
> > design matrix was singular, and eventually ended up investigating the
> > design matrix of the model.
> > I used matplotlib to plot the design matrix, split it up into the four
> > session, and found that the four parts were IDENTICAL. What could I be
> > doing wrong? Obviously, it shouldn't be the same, because there are
> > different trial types in the four sessions, and the trial order is
> also
> > randomized.
> > Furthermore, the design matrix has 26 regressors. I don't quite
> understand
> > where that number is coming from, as I have 16 unique event types, and
> 4
> > sessions.
> most probably that events definition was was the same in each of the
> chunks... but also note that if you do it in a dataset which has
> multiple chunks, you want to have condition_attr=['onset', 'chunks'] if
> you want to make a model per each onset x chunk pair as was demoed e.g.
> atA http://www.pymvpa.org/tutorial_eventrelated.html#response-modeling
> if you share your data, and ideally your investigation script then we
> could may be look deeper
--
Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik
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