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vim-2 data in Pyrcca missing xfms

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vim-2 data in Pyrcca missing xfms

Posted by Dirk Zomerdijk at February 21. 2017


I am working with the vim-2 data in the pyrcca neuroimaging example. The obtained data are:

Functional data:

Anatomical data:

When i am running the example code i get an error when it tries to obtain the mask.

Mask not found, generating...
Traceback (most recent call last):
  File "/home/c10530274/", line 24, in <module>
    mask = cortex.db.get_mask(subjects[subj], xfms[subj], type = 'thick')
  File "/home/c10530274/pycortex/cortex/", line 526, in get_mask
    mask = get_cortical_mask(subject, xfmname, type)
  File "/home/c10530274/pycortex/cortex/", line 99, in get_cortical_mask
    dist, idx = get_vox_dist(subject, xfmname)
  File "/home/c10530274/pycortex/cortex/", line 133, in get_vox_dist
    xfm = db.get_xfm(subject, xfmname)
  File "/home/c10530274/pycortex/cortex/", line 433, in get_xfm
    xfmdict = json.load(open(fname))
IOError: [Errno 2] No such file or directory: u'/home/c10530274/pycortex/filestore/db/S1/transforms/S1_xfm/matrices.xfm'
[Finished in 1.6s with exit code 1]

It appears that the subjects's corresponding xfm files are needed to succesfully get the mask.

./db/S1 map is  generated during pycortex installation. i tried to delete this to check if the xfm for subject s1 was generated but it did not.
Am i missing something? Is there a way to obtain the xfms file?
I attached the used code.




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