[Mne_analysis] Mne_analysis Digest, Vol 96, Issue 19

Thu Jan 21 09:13:31 EST 2016

Hi Alex,

Not sure how we can do it as the file is 3G big. 
Do you have an access to Neurospin server?

T.

On 21 Jan, 2016,at 03:05 PM, mne_analysis-request at nmr.mgh.harvard.edu wrote:

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Today's Topics:

1. reading bem solution (Tadeusz W. Kononowicz)
2. Re: reading bem solution (Alexandre Gramfort)

----------------------------------------------------------------------

Message: 1
Date: Thu, 21 Jan 2016 13:33:52 +0000 (GMT)
From: "Tadeusz W. Kononowicz" <t.w.kononowicz at icloud.com>
Subject: [Mne_analysis] reading bem solution
To: mne_analysis at nmr.mgh.harvard.edu
Message-ID: <0eea2f05-e157-40f6-bd2b-d08d4257c789 at me.com>
Content-Type: text/plain; charset="us-ascii"

Hello Mne Users,

This code works fine:
bem1 = path + '-20480-20480-20480-bem-sol.fif'
surfaces = mne.read_bem_surfaces(bem1)

But when I want to read another solution I got that. Any hints?

bem2 = path + '-5120-5120-5120-bem-sol.fif'
surfaces = mne.read_bem_surfaces(bem2)

---------------------------------------------------------------------------
IOError Traceback (most recent call last)
<ipython-input-10-5b41654e22f2> in <module>()
----> 1 surfaces = mne.read_bem_surfaces(sub_name_bem)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/bem.pyc in read_bem_surfaces(fname, patch_stats, s_id, verbose)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc in verbose(function, *args, **kwargs)
549 finally:
550 set_log_level(old_level)
--> 551 return function(*args, **kwargs)
552
553

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/bem.pyc in read_bem_surfaces(fname, patch_stats, s_id, verbose)
1063 coord_frame = FIFF.FIFFV_COORD_MRI
1064 # Open the file, create directory
-> 1065 f, tree, _ = fiff_open(fname)
1066 with f as fid:
1067 # Find BEM

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/open.pyc in fiff_open(fname, preload, verbose)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc in verbose(function, *args, **kwargs)
549 finally:
550 set_log_level(old_level)
--> 551 return function(*args, **kwargs)
552
553

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/open.pyc in fiff_open(fname, preload, verbose)
144 directory.append(tag)
145
--> 146 tree, _ = make_dir_tree(fid, directory)
147
148 logger.debug('[done]')

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc in make_dir_tree(fid, directory, start, indent, verbose)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc in verbose(function, *args, **kwargs)
549 finally:
550 set_log_level(old_level)
--> 551 return function(*args, **kwargs)
552
553

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc in make_dir_tree(fid, directory, start, indent, verbose)
76 if directory[this].kind == FIFF_BLOCK_START:
77 if this != start:
---> 78 child, this = make_dir_tree(fid, directory, this, indent + 1)
79 tree['nchild'] += 1
80 tree['children'].append(child)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc in make_dir_tree(fid, directory, start, indent, verbose)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc in verbose(function, *args, **kwargs)
549 finally:
550 set_log_level(old_level)
--> 551 return function(*args, **kwargs)
552
553

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc in make_dir_tree(fid, directory, start, indent, verbose)
55
56 if directory[start].kind == FIFF_BLOCK_START:
---> 57 tag = read_tag(fid, directory[start].pos)
58 block = tag.data
59 else:

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tag.pyc in read_tag(fid, pos, shape, rlims)
480 if tag.next != FIFF.FIFFV_NEXT_SEQ:
481 # f.seek(tag.next,0)
--> 482 fid.seek(tag.next, 1) # XXX : fix? pb when tag.next < 0
483
484 return tag

IOError: [Errno 22] Invalid argument

Thank you for your help,

Tadeusz W. Kononowicz
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Message: 2
Date: Thu, 21 Jan 2016 15:05:02 +0100
From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
Subject: Re: [Mne_analysis] reading bem solution
To: Discussion and support forum for the users of MNE Software
   <mne_analysis at nmr.mgh.harvard.edu>
Message-ID:
 <CADeotZohizT9KWWhA5H8zWJ5uQt3=u8ZYKg47XTu5Qtz4L1bwg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

hi Tadeusz,

can you share the problematic file.

Alex

On Thu, Jan 21, 2016 at 2:33 PM, Tadeusz W. Kononowicz <
t.w.kononowicz at icloud.com> wrote:

Hello Mne Users,

This code works fine:

bem1 = path + '-20480-20480-20480-bem-sol.fif'

surfaces = mne.read_bem_surfaces(bem1)

But when I want to read another solution I got that. Any hints?

bem2 = path + '-5120-5120-5120-bem-sol.fif'

surfaces = mne.read_bem_surfaces(bem2)

---------------------------------------------------------------------------

IOError Traceback (most recent call last)

<ipython-input-10-5b41654e22f2> in <module>()

----> 1 surfaces = mne.read_bem_surfaces(sub_name_bem)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/bem.pyc
in read_bem_surfaces(fname, patch_stats, s_id, verbose)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
in verbose(function, *args, **kwargs)

549 finally:

550 set_log_level(old_level)

--> 551 return function(*args, **kwargs)

552

553

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/bem.pyc
in read_bem_surfaces(fname, patch_stats, s_id, verbose)

1063 coord_frame = FIFF.FIFFV_COORD_MRI

1064 # Open the file, create directory

-> 1065 f, tree, _ = fiff_open(fname)

1066 with f as fid:

1067 # Find BEM

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/open.pyc
in fiff_open(fname, preload, verbose)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
in verbose(function, *args, **kwargs)

549 finally:

550 set_log_level(old_level)

--> 551 return function(*args, **kwargs)

552

553

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/open.pyc
in fiff_open(fname, preload, verbose)

144 directory.append(tag)

145

--> 146 tree, _ = make_dir_tree(fid, directory)

147

148 logger.debug('[done]')

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
in make_dir_tree(fid, directory, start, indent, verbose)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
in verbose(function, *args, **kwargs)

549 finally:

550 set_log_level(old_level)

--> 551 return function(*args, **kwargs)

552

553

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
in make_dir_tree(fid, directory, start, indent, verbose)

76 if directory[this].kind == FIFF_BLOCK_START:

77 if this != start:

---> 78 child, this = make_dir_tree(fid, directory, this, indent + 1)

79 tree['nchild'] += 1

80 tree['children'].append(child)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
in make_dir_tree(fid, directory, start, indent, verbose)

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
in verbose(function, *args, **kwargs)

549 finally:

550 set_log_level(old_level)

--> 551 return function(*args, **kwargs)

552

553

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
in make_dir_tree(fid, directory, start, indent, verbose)

55

56 if directory[start].kind == FIFF_BLOCK_START:

---> 57 tag = read_tag(fid, directory[start].pos)

58 block = tag.data

59 else:

/home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tag.pyc
in read_tag(fid, pos, shape, rlims)

480 if tag.next != FIFF.FIFFV_NEXT_SEQ:

481 # f.seek(tag.next,0)

--> 482 fid.seek(tag.next, 1) # XXX : fix? pb when tag.next < 0

483

484 return tag

IOError: [Errno 22] Invalid argument

Thank you for your help,

Tadeusz W. Kononowicz

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