[Mne_analysis] Mne_analysis Digest, Vol 96, Issue 24
Tadeusz W. Kononowicz
t.w.kononowicz at icloud.com
Thu Jan 21 16:40:22 EST 2016
Thank you for your help! I will proceed with (ico 4) than.
Tadeusz
> On Jan 21, 2016, at 3:35 PM, mne_analysis-request at nmr.mgh.harvard.edu wrote:
>
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>
> Today's Topics:
>
> 1. Re: Mne_analysis Digest, Vol 96, Issue 21 (dgw)
> 2. Re: Mne_analysis Digest, Vol 96, Issue 21 (Eric Larson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 21 Jan 2016 09:31:10 -0500
> From: dgw <dgwakeman at gmail.com>
> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 96, Issue 21
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CADM2BThacHk7zUtMvG0MSf=TgxUvtqEVb8cXnem3O7hy6=xZ7A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Eric,
>
> What if he calculates it in mne-python on the fly and doesn't write to disk?
>
> d
>
> On Thu, Jan 21, 2016 at 9:26 AM, Eric Larson <larson.eric.d at gmail.com> wrote:
>> I suspect creating a 3-layer BEM solution with 20480 triangles will end up
>> using too much space -- to limit it would mean cutting off some data from
>> the solution, rendering it unusable.
>>
>> Have you tried using 5120 triangles (the default, ico 4)?
>>
>> Eric
>>
>>
>> On Thu, Jan 21, 2016 at 9:22 AM, Tadeusz W. Kononowicz
>> <t.w.kononowicz at icloud.com> wrote:
>>>
>>> Hello,
>>>
>>> Is there a quick fix to that limit that I could use locally?
>>>
>>> T
>>>
>>> On 21 Jan, 2016,at 03:16 PM, mne_analysis-request at nmr.mgh.harvard.edu
>>> wrote:
>>>
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>>> Today's Topics:
>>>
>>> 1. Re: Mne_analysis Digest, Vol 96, Issue 19 (Eric Larson)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Thu, 21 Jan 2016 09:15:58 -0500
>>> From: Eric Larson <larson.eric.d at gmail.com>
>>> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 96, Issue 19
>>> To: Discussion and support forum for the users of MNE Software
>>> <mne_analysis at nmr.mgh.harvard.edu>
>>> Message-ID:
>>> <CAGu2niXcWvm2XfpCuN1h9-EJmJo-nM=NNHTynN2PUstUOkYRmA at mail.gmail.com>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> Ahh, that's likely the problem. There is a 2GB file size limit on FIF
>>> files, so the pointer to the next tag is invalid (probably overflows and
>>> goes negative?). Do you need 20480 triangles instead of 5120?
>>>
>>> Eric
>>>
>>>
>>> On Thu, Jan 21, 2016 at 9:13 AM, Tadeusz W. Kononowicz <
>>> t.w.kononowicz at icloud.com> wrote:
>>>
>>> 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
>>>
>>> -------------- next part --------------
>>>
>>> An HTML attachment was scrubbed...
>>>
>>> URL:
>>>
>>>
>>> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160121/55269845/attachment-0001.html
>>>
>>>
>>> ------------------------------
>>>
>>>
>>> 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
>>>
>>>
>>>
>>> _______________________________________________
>>>
>>>
>>> Mne_analysis mailing list
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> ------------------------------
>
> Message: 2
> Date: Thu, 21 Jan 2016 09:34:41 -0500
> From: Eric Larson <larson.eric.d at gmail.com>
> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 96, Issue 21
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CAGu2niXPeCPUM7WZFHSEggmaFa7oOf+18JpPUbmQxcMHbQf4aQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Actually yeah, you could do that. It could lead to a lot of wasted
> computation time to have to redo such a static, anatomy-(only)-dependent
> step, but it would be doable. I'd still prefer running the 5120 version,
> unless there is a good reason to suspect the 20480 will give better
> results. It will also make forward solution calculation faster.
>
> Eric
>
>
> On Thu, Jan 21, 2016 at 9:31 AM, dgw <dgwakeman at gmail.com> wrote:
>
>> Eric,
>>
>> What if he calculates it in mne-python on the fly and doesn't write to
>> disk?
>>
>> d
>>
>> On Thu, Jan 21, 2016 at 9:26 AM, Eric Larson <larson.eric.d at gmail.com>
>> wrote:
>>> I suspect creating a 3-layer BEM solution with 20480 triangles will end
>> up
>>> using too much space -- to limit it would mean cutting off some data from
>>> the solution, rendering it unusable.
>>>
>>> Have you tried using 5120 triangles (the default, ico 4)?
>>>
>>> Eric
>>>
>>>
>>> On Thu, Jan 21, 2016 at 9:22 AM, Tadeusz W. Kononowicz
>>> <t.w.kononowicz at icloud.com> wrote:
>>>>
>>>> Hello,
>>>>
>>>> Is there a quick fix to that limit that I could use locally?
>>>>
>>>> T
>>>>
>>>> On 21 Jan, 2016,at 03:16 PM, mne_analysis-request at nmr.mgh.harvard.edu
>>>> wrote:
>>>>
>>>> Send Mne_analysis mailing list submissions to
>>>> mne_analysis at nmr.mgh.harvard.edu
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>> or, via email, send a message with subject or body 'help' to
>>>> mne_analysis-request at nmr.mgh.harvard.edu
>>>>
>>>> You can reach the person managing the list at
>>>> mne_analysis-owner at nmr.mgh.harvard.edu
>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of Mne_analysis digest..."
>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. Re: Mne_analysis Digest, Vol 96, Issue 19 (Eric Larson)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Thu, 21 Jan 2016 09:15:58 -0500
>>>> From: Eric Larson <larson.eric.d at gmail.com>
>>>> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 96, Issue 19
>>>> To: Discussion and support forum for the users of MNE Software
>>>> <mne_analysis at nmr.mgh.harvard.edu>
>>>> Message-ID:
>>>> <CAGu2niXcWvm2XfpCuN1h9-EJmJo-nM=
>> NNHTynN2PUstUOkYRmA at mail.gmail.com>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> Ahh, that's likely the problem. There is a 2GB file size limit on FIF
>>>> files, so the pointer to the next tag is invalid (probably overflows and
>>>> goes negative?). Do you need 20480 triangles instead of 5120?
>>>>
>>>> Eric
>>>>
>>>>
>>>> On Thu, Jan 21, 2016 at 9:13 AM, Tadeusz W. Kononowicz <
>>>> t.w.kononowicz at icloud.com> wrote:
>>>>
>>>> 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:
>>>>
>>>>
>>>> Send Mne_analysis mailing list submissions to
>>>>
>>>> mne_analysis at nmr.mgh.harvard.edu
>>>>
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>
>>>> or, via email, send a message with subject or body 'help' to
>>>>
>>>> mne_analysis-request at nmr.mgh.harvard.edu
>>>>
>>>>
>>>> You can reach the person managing the list at
>>>>
>>>> mne_analysis-owner at nmr.mgh.harvard.edu
>>>>
>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>>
>>>> than "Re: Contents of Mne_analysis digest..."
>>>>
>>>>
>>>>
>>>> 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
>>>>
>>>> -------------- next part --------------
>>>>
>>>> An HTML attachment was scrubbed...
>>>>
>>>> URL:
>>>>
>>>>
>>>>
>> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160121/55269845/attachment-0001.html
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>>
>>>> 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
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>>
>>>>
>>>> Mne_analysis mailing list
>>>>
>>>>
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>>>>
>>>>
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>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom
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>>>>
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>>>>
>>>>
>>>> addressed. If you believe this e-mail was sent to you in error and the
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>>>>
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>>>>
>>>>
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>>>>
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>>>>
>>>>
>>>> ------------------------------
>>>>
>>>>
>>>> _______________________________________________
>>>>
>>>> Mne_analysis mailing list
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>>>> End of Mne_analysis Digest, Vol 96, Issue 19
>>>>
>>>> ********************************************
>>>>
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>>>>
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