[pymvpa] hyperalignment inquiry
David Soto
d.soto.b at gmail.com
Thu Aug 4 10:50:04 UTC 2016
Thanks very much Swaroop, the code still gives an error, please see below
-also final comment at the bottom of the email
---------------------------------------------------------------------------AttributeError
Traceback (most recent call
last)<ipython-input-52-8bb0dc44f9a7> in <module>() 63 #
Searchlight Hyperalignment returns a list of mappers corresponding to
64 # subjects in the same order as the list of datasets we
passed in.---> 65 slhypmaps = slhyper(ds_train) 66 67
# Applying hyperalignment parameters is similar to applying any mapper
in
/usr/local/lib/python2.7/site-packages/mvpa2/algorithms/searchlight_hyperalignment.pyc
in __call__(self, datasets) 554 # alignment, i.e. the SL
ROIs cover roughly the same area 555 queryengines =
self._get_trained_queryengines(--> 556 datasets,
params.queryengine, params.radius, params.ref_ds) 557 # For
surface nodes to voxels queryengines, roi_seed hardly makes sense
558 if isinstance(queryengines[params.ref_ds],
SurfaceVerticesQueryEngine):
/usr/local/lib/python2.7/site-packages/mvpa2/algorithms/searchlight_hyperalignment.pyc
in _get_trained_queryengines(self, datasets, queryengine, radius,
ref_ds) 666 _shpaldebug("Training provided query
engines") 667 for qe, ds in zip(queryengines,
datasets):--> 668 qe.train(ds) 669
else: 670 queryengine.train(datasets[ref_ds])
AttributeError: 'function' object has no attribute 'train'
_____
%reset
from mvpa2.suite import *
path0='/Users/dsoto/Dropbox/4hyperal'
attr = SampleAttributes(os.path.join(path0, 'attrs_cv_singlsubj2chunk.txt'))
d=[]
qe=[]
num=-1
for subj in range(1,5):
num=num+1
print(subj)
datapath='/Users/dsoto/Dropbox/4hyperal/subj%d' %(int(subj))
d.append(fmri_dataset(samples=os.path.join(datapath, 'reg4mm.nii.gz'),
targets=attr.targets, chunks=attr.chunks,
mask=os.path.join(path0, 'mni4mm.nii.gz')))
d[num]=remove_invariant_features(d[num])
testqe=IndexQueryEngine(voxel_indices=Sphere(3))
testqe.train(d[num])
qe.append(testqe.query_byid)
qe_merged = [qe[0],qe[1],qe[2],qe[3]]
ds_merged = [d[0],d[1],d[2],d[3]]
_ = [zscore(ds) for ds in ds_merged]
for i, sd in enumerate(ds_merged):
sd.sa['subject'] = np.repeat(i, len(sd))
nsubjs = 4
ncats = 2
nruns = 2
bsc_slhyper_results = []
clf = LinearCSVMC()
cv = CrossValidation(clf, NFoldPartitioner(attr='subject'),
errorfx=mean_match_accuracy)
for test_run in range(nruns):
ds_train = [sd[sd.sa.chunks != test_run, :] for sd in ds_merged]
ds_test = [sd[sd.sa.chunks == test_run, :] for sd in ds_merged]
slhyper = SearchlightHyperalignment(queryengine=qe_merged)
slhypmaps = slhyper(ds_train)
ds_hyper = [h.forward(sd) for h, sd in zip(slhypmaps, ds_test)]
ds_hyper = vstack(ds_hyper)
zscore(ds_hyper, chunks_attr='subject')
res_cv = cv(ds_hyper)
bsc_slhyper_results.append(res_cv)
bsc_slhyper_results = hstack(bsc_slhyper_results)
However, as you know it is likely that searchlighhyperaligment wont work
well if each dataset has different number of features....so perhaps would
be worth to compare any result with the second analyses option you
suggested, that is once I remove invariant features from each subjects
dataset, I could derive an intersection mask with valid features across all
subjects and then use this mask when I load the data with
fmri_dataset......however could you let me know how can this intersection
mask be derived?
best
david
[image: ][image: ][image: ]
___________
On 3 August 2016 at 18:33, Swaroop Guntupalli <swaroopgj at gmail.com> wrote:
> Hi David,
>
> You have to train the queryengine, here is a little modified version of
> what you pasted.
> However, remember that the datasets should be approximately similar in
> coverage. I noticed that your first subject has ~80,000 non-invariant
> features and some other subjects have ~30,000. That's a huge margin.
>
> I am not sure how hyperalignment performs with so many missing regions.
> Swaroop
>
> d[num]=remove_invariant_features(d[num])
>
> # You don't need this line below
> #voxel_indices=d[num].fa.voxel_indices
>
> testqe=IndexQueryEngine(voxel_indices=Sphere(3))
> # Train the testqe with that dataset
> testqe.train(d[num])
>
> qe.append(testqe.query_byid)
>
> On Tue, Aug 2, 2016 at 6:30 AM, David Soto <d.soto.b at gmail.com> wrote:
>
>> Hi Swaroop, thanks for looking into it...
>>
>> There does not seem be a clear documentation on how to get the query
>> engines ..from what I have seen this is what I did:
>>
>> d=[]
>> qe=[]
>> num=-1
>> for subj in range(1,5):
>> num=num+1
>> print(subj)
>> datapath='/Users/dsoto/Dropbox/4hyperal/subj%d' %(int(subj))
>> d.append(fmri_dataset(samples=os.path.join(datapath,
>> 'reg4mm.nii.gz'),
>> targets=attr.targets, chunks=attr.chunks,
>> mask=os.path.join(path0, 'mni4mm.nii.gz')))
>>
>> d[num]=remove_invariant_features(d[num])
>>
>> voxel_indices=d[num].fa.voxel_indices
>>
>> testqe=IndexQueryEngine(voxel_indices=Sphere(3))
>>
>> qe.append(testqe.query_byid)
>>
>> qe_merged = [qe[0],qe[1],qe[2],qe[3]]
>>
>> ds_merged = [d[0],d[1],d[2],d[3]]
>>
>> which I then was hoping to pass later onto
>> slhyper = SearchlightHyperalignment(queryengine=qe_merged)
>>
>> however there does not appear to be an output for each of the 'qe' above,
>> even though I can see the voxel_ids...
>>
>> any tips would be very useful!
>>
>> thanks!
>>
>>
>> [image: ][image: ][image: ]
>> -------------------
>>
>> On 1 August 2016 at 19:02, Swaroop Guntupalli <swaroopgj at gmail.com>
>> wrote:
>>
>>> Hi David,
>>>
>>> Thanks for the data. The issue is that when using searchlight
>>> hyperalignment without supplying queryengines but providing radius (as in
>>> your case), we compute a single spherical volume queryengine on the
>>> reference subject, which means all the datasets need to be aligned and have
>>> exact same number of features. The issue in your script is that you remove
>>> invariance features separately for each subject, which results in different
>>> numbers of features for each subject.
>>>
>>> There are two ways to resolve it:
>>> 1) after removing invariant features, supply list of spherical volume
>>> queryengines corresponding to subjects, or
>>> 2) find the union of invariant features in all subjects, and then remove
>>> the same set of features from all subjects, and proceed with hyperalignment
>>> as you have currently.
>>>
>>> Hope that helps.
>>> Best,
>>> Swaroop
>>>
>>> On Mon, Aug 1, 2016 at 6:30 AM, David Soto <d.soto.b at gmail.com> wrote:
>>>
>>>> Hi Swaroop, I have run the analyses using the individual copes that
>>>> were co-registered in FSL to the individual T1 (using BBR) and then to
>>>> MNI2mm template using a 12 DOF. The problem persists even after doing
>>>> remove_invariant_features().
>>>> I get a similar 'Indexerror: index 226822 is out of bounds for axis 1
>>>> with size 198603'
>>>>
>>>> I have uploaded all the datafiles which you can find in the link below,
>>>> just in case you could have a look. If you open the zip then you will find
>>>> all the relevant files, including the pymvpa script that I use to run the
>>>> analyses ('hyperalscript.py'), the individual data within a folder and also
>>>> the attributes file and the MNI brain mask
>>>> https://drive.google.com/open?id=0B7-qbWx3g9KfUU1jOFVpQ05oRWM
>>>>
>>>> any help would be much appreciated...
>>>>
>>>> thanks!
>>>> david
>>>>
>>>> On 29 July 2016 at 18:28, Swaroop Guntupalli <swaroopgj at gmail.com>
>>>> wrote:
>>>>
>>>>> That is correct. But the searchlight centers across subjects are
>>>>> assumed to be aligned.
>>>>>
>>>>>
>>>>> On Fri, Jul 29, 2016 at 8:24 AM, David Soto <d.soto.b at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi, thanks I will try that, I understand therefore that the number
>>>>>> of features per subject need not be equal across subjects for searchlight
>>>>>> hyperalignment - but please correct me if am wrong.
>>>>>> best
>>>>>> david
>>>>>>
>>>>>> On 29 July 2016 at 16:17, Swaroop Guntupalli <swaroopgj at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi David,
>>>>>>>
>>>>>>> If you are using searchlight hyperalignment, it is advisable to
>>>>>>> align the data across subjects using anatomy first. Simplest would be to be
>>>>>>> align them to an MNI template and then run the searchlight hyperalignment.
>>>>>>> Our tutorial dataset is affine aligned to MNI template.
>>>>>>>
>>>>>>> Best,
>>>>>>> Swaroop
>>>>>>>
>>>>>>> On Thu, Jul 28, 2016 at 10:51 AM, David Soto <d.soto.b at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Thanks Swaroop, I managed to get the dataset in the right format as
>>>>>>>> per the hyperaligmentsearchlight tutorial
>>>>>>>> however when I run the hyperaligment I get the following error (IndexError:
>>>>>>>> index 46268 is out of bounds for axis 1 with size 43506, see
>>>>>>>> further below)...to recap the dataset is a concatenation of each subject
>>>>>>>> data, each in individual native space, so number of features are different
>>>>>>>> across subjects...
>>>>>>>> The code I use is the same as in the tutorial, namely, any feedback
>>>>>>>> would be great, thanks, david
>>>>>>>> cv = CrossValidation(clf, NFoldPartitioner(attr='subject'),
>>>>>>>> errorfx=mean_match_accuracy)
>>>>>>>>
>>>>>>>> for test_run in range(nruns):
>>>>>>>> ds_train = [sd[sd.sa.chunks != test_run, :] for sd in ds_all]
>>>>>>>> ds_test = [sd[sd.sa.chunks == test_run, :] for sd in ds_all]
>>>>>>>>
>>>>>>>> slhyper = SearchlightHyperalignment(radius=3, featsel=0.4,
>>>>>>>> sparse_radius=3)
>>>>>>>> slhypmaps = slhyper(ds_train)
>>>>>>>> ds_hyper = [h.forward(sd) for h, sd in zip(slhypmaps, ds_test)]
>>>>>>>>
>>>>>>>> ds_hyper = vstack(ds_hyper)
>>>>>>>> zscore(ds_hyper, chunks_attr='subject')
>>>>>>>> res_cv = cv(ds_hyper)
>>>>>>>> bsc_slhyper_results.append(res_cv)
>>>>>>>>
>>>>>>>> OUTPUT MESSAGE.........
>>>>>>>> Performing classification analyses...
>>>>>>>> between-subject (searchlight hyperaligned)...
>>>>>>>>
>>>>>>>> ------------------------------------------------------------
>>>>>>>> ---------------
>>>>>>>> IndexError Traceback (most recent
>>>>>>>> call last)
>>>>>>>> <ipython-input-191-85bdb873d4f1> in <module>()
>>>>>>>> 24 # Searchlight Hyperalignment returns a list of mappers
>>>>>>>> corresponding to
>>>>>>>> 25 # subjects in the same order as the list of datasets we
>>>>>>>> passed in.
>>>>>>>> ---> 26 slhypmaps = slhyper(ds_train)
>>>>>>>> 27
>>>>>>>> 28 # Applying hyperalignment parameters is similar to
>>>>>>>> applying any mapper in
>>>>>>>>
>>>>>>>> /usr/local/lib/python2.7/site-packages/mvpa2/algorithms/searchlight_hyperalignment.pyc
>>>>>>>> in __call__(self, datasets)
>>>>>>>> 626 node_blocks = np.array_split(roi_ids,
>>>>>>>> params.nblocks)
>>>>>>>> 627 p_results = [self._proc_block(block, datasets,
>>>>>>>> hmeasure, queryengines)
>>>>>>>> --> 628 for block in node_blocks]
>>>>>>>> 629 results_ds = self.__handle_all_results(p_results)
>>>>>>>> 630 # Dummy iterator for, you know, iteration
>>>>>>>>
>>>>>>>> /usr/local/lib/python2.7/site-packages/mvpa2/algorithms/searchlight_hyperalignment.pyc
>>>>>>>> in _proc_block(self, block, datasets, featselhyper, queryengines, seed,
>>>>>>>> iblock)
>>>>>>>> 387 continue
>>>>>>>> 388 # selecting neighborhood for all subject for
>>>>>>>> hyperalignment
>>>>>>>> --> 389 ds_temp = [sd[:, ids] for sd, ids in
>>>>>>>> zip(datasets, roi_feature_ids_all)]
>>>>>>>> 390 if self.force_roi_seed:
>>>>>>>> 391 roi_seed = np.array(roi_feature_ids_all[self.params.ref_ds])
>>>>>>>> == node_id
>>>>>>>>
>>>>>>>> /usr/local/lib/python2.7/site-packages/mvpa2/datasets/base.pyc in
>>>>>>>> __getitem__(self, args)
>>>>>>>> 139
>>>>>>>> 140 # let the base do the work
>>>>>>>> --> 141 ds = super(Dataset, self).__getitem__(args)
>>>>>>>> 142
>>>>>>>> 143 # and adjusting the mapper (if any)
>>>>>>>>
>>>>>>>> /usr/local/lib/python2.7/site-packages/mvpa2/base/dataset.pyc in
>>>>>>>> __getitem__(self, args)
>>>>>>>> 445 if isinstance(self.samples, np.ndarray):
>>>>>>>> 446 if np.any([isinstance(a, slice) for a in args]):
>>>>>>>> --> 447 samples = self.samples[args[0], args[1]]
>>>>>>>> 448 else:
>>>>>>>> 449 # works even with bool masks (although
>>>>>>>> without
>>>>>>>>
>>>>>>>> IndexError: index 46268 is out of bounds for axis 1 with size 43506
>>>>>>>>
>>>>>>>> On 28 July 2016 at 00:25, Swaroop Guntupalli <swaroopgj at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi David,
>>>>>>>>>
>>>>>>>>> If you have limited data, you can use a part of it (however you
>>>>>>>>> split the data for training and testing)
>>>>>>>>> to train hyperalignment, and also use the same part to train the
>>>>>>>>> classifier and then apply hyperalignment and test classifier on the
>>>>>>>>> left-out part. Yes, you can artificially create 2 chunks (or more if you
>>>>>>>>> prefer).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Jul 27, 2016 at 3:17 PM, David Soto <d.soto.b at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> sounds great thanks, a further thing is that I have seen that in
>>>>>>>>>> order to preclude circularity issues, hyperalinment is implemented on a
>>>>>>>>>> subset of training chunks and then the transformation is applied to the
>>>>>>>>>> full datasets prior to classification analyses. Given that I have no
>>>>>>>>>> proper chunks/runs here, but only 56 betas across trials, would it be okay
>>>>>>>>>> to train hyperaligment just on half of the 56 betas, eg artificially split
>>>>>>>>>> the data set in 2 chunks each containing 14 betas of class A and 14 of
>>>>>>>>>> class B? Or would it be just OK to train hyperaligment on the 56 betas in
>>>>>>>>>> the first instance?
>>>>>>>>>> thanks!
>>>>>>>>>> david
>>>>>>>>>>
>>>>>>>>>> On 28 July 2016 at 00:00, Swaroop Guntupalli <swaroopgj at gmail.com
>>>>>>>>>> > wrote:
>>>>>>>>>>
>>>>>>>>>>> The hyperalignment example on PyMVPA uses one beta map for each
>>>>>>>>>>> category per run.
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Jul 27, 2016 at 2:57 PM, Swaroop Guntupalli <
>>>>>>>>>>> swaroopgj at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi David,
>>>>>>>>>>>>
>>>>>>>>>>>> Beta maps should work fine for hyperalignment. The more maps
>>>>>>>>>>>> (or TRs) there are, better the estimate.
>>>>>>>>>>>> We used within-subject hyperalignment in Haxby et al. 2011,
>>>>>>>>>>>> which uses maps from 6 categories (we used 3 successive betas per condition
>>>>>>>>>>>> I think).
>>>>>>>>>>>>
>>>>>>>>>>>> vstack() merges multiple datasets into a single dataset, and if
>>>>>>>>>>>> there is any voxel count (nfeatures) mismatch across subjects, it won't
>>>>>>>>>>>> work (as evidenced by the error).
>>>>>>>>>>>> Hyperalignment takes in a list of datasets, one per each
>>>>>>>>>>>> subject.
>>>>>>>>>>>> So, you can make that a list as
>>>>>>>>>>>> ds_all =[ds1, ds2, ...., ds16]
>>>>>>>>>>>> and use for Hyperalignment()
>>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>> Swaroop
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Jul 27, 2016 at 2:28 PM, David Soto <d.soto.b at gmail.com
>>>>>>>>>>>> > wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>> in my experiment I have 28 betas in condition A and 28
>>>>>>>>>>>>> parameter estimate images and 28 in condition B for each subject (N=16 in
>>>>>>>>>>>>> total).
>>>>>>>>>>>>>
>>>>>>>>>>>>> i have performed across-subjects SVM-based searchlight
>>>>>>>>>>>>> classification using MNI-registered individual beta images and I would like
>>>>>>>>>>>>> to repeat and confirm my results using searchlight based on hyperaligned
>>>>>>>>>>>>> data.
>>>>>>>>>>>>>
>>>>>>>>>>>>> i am not aware of any paper using hyperaligment on beta
>>>>>>>>>>>>> images but I think this should be possible, any advise please would be nice
>>>>>>>>>>>>>
>>>>>>>>>>>>> i've created individual datasets concatenating the 28 betas in
>>>>>>>>>>>>> condition A and the 28 in condition (in the actual experiment condition A
>>>>>>>>>>>>> and B can appear randomly on each trial). I have 16 nifti datasets, one per
>>>>>>>>>>>>> subject, with each in individual native anatomical space. In trying to get
>>>>>>>>>>>>> a dataset in the same format as in the hyperlignment tutorial I use
>>>>>>>>>>>>> fmri_dataset on each individual wholebrain 48 betas and then try to merged
>>>>>>>>>>>>> then all i.e. ds_merged = vstack((d1, d2, d3, d4, d5, d6, d7,
>>>>>>>>>>>>> d8, d9, d10, d11, d12, d13, d14, d15,d16)) but this gives the following
>>>>>>>>>>>>> error pasted at the end,
>>>>>>>>>>>>> which I think it is becos the number of voxels is different
>>>>>>>>>>>>> across subjects. This is one issue.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Another is that the function vstack does appear to produce the
>>>>>>>>>>>>> list of individual datasets that is in the hyperligment tutorial dataset,
>>>>>>>>>>>>> but a list of individual betas, I would be grateful to receive some tips.
>>>>>>>>>>>>>
>>>>>>>>>>>>> thanks!
>>>>>>>>>>>>> david
>>>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>>>> ---------------
>>>>>>>>>>>>> ValueError Traceback (most
>>>>>>>>>>>>> recent call last)
>>>>>>>>>>>>> <ipython-input-64-2fef46542bfc> in <module>()
>>>>>>>>>>>>> 19 h5save('/home/dsoto/dsoto/fmri/wmlearning/h5.hdf5',
>>>>>>>>>>>>> [d1,d2])
>>>>>>>>>>>>> 20 #ds_merged = vstack((d1, d2, d3, d4, d5, d6, d7,d8,d9,
>>>>>>>>>>>>> d10, d11, d12, d13, d14, d15, d16))
>>>>>>>>>>>>> ---> 21 ds_merged = vstack((d1, d2))
>>>>>>>>>>>>>
>>>>>>>>>>>>> /usr/local/lib/python2.7/site-packages/mvpa2/base/dataset.pyc
>>>>>>>>>>>>> in vstack(datasets, a)
>>>>>>>>>>>>> 687 "datasets have varying
>>>>>>>>>>>>> attributes.")
>>>>>>>>>>>>> 688 # will puke if not equal number of features
>>>>>>>>>>>>> --> 689 stacked_samp = np.concatenate([ds.samples for ds
>>>>>>>>>>>>> in datasets], axis=0)
>>>>>>>>>>>>> 690
>>>>>>>>>>>>> 691 stacked_sa = {}
>>>>>>>>>>>>>
>>>>>>>>>>>>> ValueError: all the input array dimensions except for the
>>>>>>>>>>>>> concatenation axis must match exactly
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/
>>>>>>>>>>>>> pkg-exppsy-pymvpa
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>>>>>>
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