[FieldTrip] fieldtrip Digest, Vol 92, Issue 24
Fairs, Amie
Amie.Fairs at mpi.nl
Tue Jul 31 16:11:15 CEST 2018
Hi Zhipeng,
I am quite sure of your issue because any images you send in your email are scrubbed and I can't see them, but I might be able to help. I recently also had some issues following this tutorial.
For me, MNE for python was accidentally downloaded at first. For instance, when I first did a 'which mne' search in my system it said [this is my specific path]:
/usr/local/apps/python-2.7.11/bin/mne
And this mne is not the same MNE suite that is discussed in the tutorial. This mne is 'in' python, so it contains:
ls /usr/local/apps/python-2.7.11/bin/
2to3 folia2html foliatree python rst2html.pyc rst2xetex.pyc
alpino2folia folia2rst foliavalidator python2 rst2latex.py rst2xml.py
build folia2txt idle python2.7 rst2latex.pyc rst2xml.pyc
csv2rdf foliacat mne python2.7-config rst2man.py rstpep2html.py
cygdb foliacorrect nosetests python2-config rst2man.pyc rstpep2html.pyc
cython foliacount nosetests-2.7 python-config rst2odt_prepstyles.py smtpd.py
cythonize foliafreqlist pip rdf2dot rst2odt_prepstyles.pyc tclsh8.5
dcoi2folia foliamerge pip2 rdfgraphisomorphism rst2odt.py virtualenv
easy_install foliaquery pip2.7 rdfpipe rst2odt.pyc wish8.5
easy_install-2.7 foliaquery1 pt2to3 rdfs2dot rst2pseudoxml.py
f2py foliasetdefinition ptdump rst2folia rst2pseudoxml.pyc
folia2annotatedtxt foliaspec ptrepack rst2html5.py rst2s5.py
folia2columns foliaspec2json pttree rst2html5.pyc rst2s5.pyc
folia2dcoi foliatextcontent pydoc rst2html.py rst2xetex.py
[sorry for the formatting]
Maybe your system looks something like this?
MNE suite actually looks something like this [with the path on my system]:
ls /usr/local/apps/MNE/MNE-2.7.0-3106-Linux-x86_64/bin
mne_add_patch_info mne_copy_processing_history mne_list_bem mne_redo_file_nocwd
mne_add_to_meas_info mne_cov2proj mne_list_coil_def mne_remove_platform
mne_add_triggers mne_create_comp_data mne_list_proj mne_rename_channels
mne_analyze mne_ctf2fiff mne_list_source_space mne_sensitivity_map
mne_annot2labels mne_ctf_dig2fiff mne_list_versions mne_sensor_locations
mne_anonymize mne_dacq_annotator mne_make_cor_set mne_setup
mne_average_estimates mne_dicom_essentials mne_make_derivations mne_setup_forward_model
mne_average_forward_solutions mne_dipole_fit mne_make_eeg_layout mne_setup_mri
mne_brain_vision2fiff mne_do_forward_solution mne_make_morph_maps mne_setup_sh
mne_browse_raw mne_do_inverse_operator mne_make_movie mne_setup_source_space
mne_change_baselines mne_edf2fiff mne_make_scalp_surfaces mne_show_environment
mne_change_nave mne_epochs2mat mne_make_source_space mne_show_fiff
mne_check_eeg_locations mne_epochs2mat.bin mne_make_sphere_bem mne_simu
mne_check_surface mne_evoked_data_summary mne_make_uniform_stc mne_simu.bin
mne_collect_transforms mne_eximia2fiff mne_map_data mne_smooth
mne_compensate_data mne_fit_sphere_to_surf mne_mark_bad_channels mne_surf2bem
mne_compute_mne mne_fix_mag_coil_types mne_morph_labels mne_toggle_skips
mne_compute_raw_inverse mne_fix_stim14 mne_opengl_test mne_transform_points
mne_convert_ctf_markers mne_flash_bem mne_organize_dicom mne_tufts2fiff
mne_convert_dig_data mne_forward_solution mne_prepare_bem_model mne_version_test
mne_convert_lspcov mne_insert_4D_comp mne_process_raw mne_view_manual
mne_convert_mne_data mne_install_packages mne_process_stc mne_volume_data2mri
mne_convert_mne_data.bin mne_inverse_operator mne_raw2mat mne_volume_source_space
mne_convert_ncov mne_kit2fiff mne_raw2mat.bin mne_watershed_bem
mne_convert_surface mne_launcher mne_redo_file
Then you can see mne_setup_sh, and mne_setup_source_space - the two things you need.
I hope maybe this is helpful?
Best,
Amie
-----------------------------------------------------
Amie Fairs
PhD candidate
International Max Planck Research School for Language Sciences
Max Planck Institute for Psycholinguistics
PO Box 310 | 6500 AH Nijmegen | The Netherlands
Email: amie.fairs at mpi.nl | Phone: +31(0)243521381
-----Original Message-----
From: fieldtrip [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of fieldtrip-request at science.ru.nl
Sent: dinsdag 31 juli 2018 15:52
To: fieldtrip at science.ru.nl
Subject: fieldtrip Digest, Vol 92, Issue 24
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Today's Topics:
1. Re: Regarding Tutorial: Preprocessing and averaging of
multi-channel NIRS data (Herbert J Gould (hgould))
2. Re: fieldtrip Digest, Vol 92, Issue 21 (zhipeng li)
----------------------------------------------------------------------
Message: 1
Date: Tue, 31 Jul 2018 13:37:06 +0000
From: "Herbert J Gould (hgould)" <hgould at memphis.edu>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and
averaging of multi-channel NIRS data
Message-ID: <0pyb6vhuqo1su9hhxc79wnld.1533044221861 at email.android.com>
Content-Type: text/plain; charset="windows-1252"
Please eliminate me from the mailing list. I have retired.
Thank you.
Sent from my Verizon Wireless 4G LTE smartphone
-------- Original message --------
From: "Jörn M. Horschig"
Date:07/31/2018 2:18 AM (GMT-06:00)
To: 'FieldTrip discussion list'
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data
Hi Sunny,
Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code:
>> cfg = [];
>> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3';
>> cfg.trialdef.eventtype = '?';
>> ft_definetrial(cfg);
The output will be:
Warning: no trialfun was specified, using ft_trialfun_general
In ft_definetrial at line 138
evaluating trialfunction 'ft_trialfun_general'
reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'
reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'
the following events were found in the datafile
event type: 'ADC001'
with event values: 1.5
no trials have been defined yet, see FT_DEFINETRIAL for further help
found 1 events
created 0 trials
the call to "ft_definetrial" took 1 seconds
The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now).
You can still read in the oxy3-data running this code:
>> cfg = [];
>> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3';
>> data = ft_preprocessing(cfg);
The output will be:
processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' }
reading and preprocessing
reading and preprocessing trial 1 from 1
the call to "ft_preprocessing" took 2 seconds
You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events:
>> cfg = [];
>> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3';
>> cfg.trialdef.eventtype = '?';
>> ft_definetrial(cfg);
With the output being:
evaluating trialfunction 'ft_trialfun_general'
reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'
reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'
the following events were found in the datafile
event type: 'ADC001'
with event values: 1.4
event type: 'event'
with event values: 'A' 'B' 'C' 'D'
no trials have been defined yet, see FT_DEFINETRIAL for further help
found 5 events
created 0 trials
the call to "ft_definetrial" took 3 seconds
I am not sure what your events mean, but you are then able to define trials according to these events, e.g.
>> cfg.trialdef.eventtype = 'event';
>> cfg.trialdef.eventvalue = 'B';
>> cfg.trialdef.prestim = 5;
>> cfg.trialdef.prestim = 35;
>> cfg = ft_definetrial(cfg);
This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via:
>> data = ft_preprocessing(cfg);
The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started!
Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout.
With best regards,
Jörn
--
Jörn M. Horschig, PhD, Project Leader & Software Engineer
Artinis Medical Systems<http://www.artinis.com/> | +31 481 350 980
Sign up for our NIRS newsletter<http://artinis.us3.list-manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46>
From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Jörn M. Horschig
Sent: Monday, July 30, 2018 15:42
To: 'FieldTrip discussion list' <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data
Hi Sunny,
The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip).
With best regards,
Jörn
--
Jörn M. Horschig, PhD, Project Leader & Software Engineer
Artinis Medical Systems<http://www.artinis.com/> | +31 481 350 980
Sign up for our NIRS newsletter<http://artinis.us3.list-manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46>
From: Sunny p <sunnypitt1965 at gmail.com<mailto:sunnypitt1965 at gmail.com>>
Sent: Monday, July 30, 2018 15:29
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>; jorn at artinis.com<mailto:jorn at artinis.com>
Cc: Arana, S.L. (Sophie) <S.Arana at donders.ru.nl<mailto:S.Arana at donders.ru.nl>>
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data
Hello Jorn,
Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial.
Thanks for your understanding and support.
Best Regards,
Sunny
On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig <jorn at artinis.com<mailto:jorn at artinis.com>> wrote:
Hi Sunny,
Yes, the FieldTrip NIRS plugin works for all our devices.
With best regards,
Jörn
--
Jörn M. Horschig, PhD, Project Leader & Software Engineer
Artinis Medical Systems<http://www.artinis.com/> | +31 481 350 980
Sign up for our NIRS newsletter<http://artinis.us3.list-manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46>
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Sunny p
Sent: Friday, July 27, 2018 20:41
To: Arana, S.L. (Sophie) <S.Arana at donders.ru.nl<mailto:S.Arana at donders.ru.nl>>
Cc: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data
Hello Sophie,
Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ?
Thanks for your understanding and support.
Best Regards,
Sunny
On Wed, Jul 25, 2018 at 12:35 PM, Sunny p <sunnypitt1965 at gmail.com<mailto:sunnypitt1965 at gmail.com>> wrote:
Hello Sophie,
Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code.
Thanks for your understanding and support.
Best Regards,
Sunny
On Wed, Jul 25, 2018 at 8:22 AM, Sunny p <sunnypitt1965 at gmail.com<mailto:sunnypitt1965 at gmail.com>> wrote:
Hello Sophie,
Thanks a lot for your clarification. This is very useful.
Sunny
On Wednesday, July 25, 2018, Arana, S.L. (Sophie) <S.Arana at donders.ru.nl<mailto:S.Arana at donders.ru.nl>> wrote:
Dear Sunny,
the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered.
The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching.
cfg = [];
cfg.hpfilter = 'yes';
cfg.hpfreq = 0.01;
data_flt = ft_preprocessing(cfg,data_down);
This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on.
Best,
Sophie
________________________________
From: fieldtrip [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Sunny p [sunnypitt1965 at gmail.com<mailto:sunnypitt1965 at gmail.com>]
Sent: Tuesday, July 24, 2018 9:24 PM
To: fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>
Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data
Hello All Good Day,
Hope you are doing fine,
Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue?
Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel
The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis.
[cid:image001.png at 01D428AE.213F63D0]
Thanks for your understanding and support
Best Regards,
Sunny
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------------------------------
Message: 2
Date: Tue, 31 Jul 2018 21:52:11 +0800
From: zhipeng li <lizhipeng3924 at gmail.com>
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 21
Message-ID:
<CAAUszHEBU2UVAsKxkHe5fKV1SPntBSALvVJ_RbLB+nbyvDLyQg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
-
Thank you very much for your reply.@ Alexandre Gramfort
But with your answer, my question remains unsolved . On my computer, I
can't find any files on mne setup, including any of your list.
Following the instructions on the site, I made this step
-
But the setup file can't be found,I hope you can give me further
guidance.
-
Yours,
-
zhipeng
2018-07-30 18:00 GMT+08:00 <fieldtrip-request at science.ru.nl>:
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
> 1. Re: Regarding Tutorial: Preprocessing and averaging of
> multi-channel NIRS data (=?utf-8?Q?J=C3=B6rn_M._Horschig?=)
> 2. Re: fieldtrip Digest, Vol 92, Issue 19 (Alexandre Gramfort)
> 3. Postdoc position to work with human single neurons and LFPs,
> 9 days left to apply! (Simon Hanslmayr)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Jul 2018 08:47:25 +0200
> From: "=?utf-8?Q?J=C3=B6rn_M._Horschig?=" <jorn at artinis.com>
> To: "'FieldTrip discussion list'" <fieldtrip at science.ru.nl>, "'Arana,
> S.L. \(Sophie\)'" <S.Arana at donders.ru.nl>
> Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and
> averaging of multi-channel NIRS data
> Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sunny,
>
>
>
> Yes, the FieldTrip NIRS plugin works for all our devices.
>
>
>
> With best regards,
>
> Jörn
>
>
>
> --
> Jörn M. Horschig, PhD, Project Leader & Software Engineer
> <http://www.artinis.com/> Artinis Medical Systems | +31 481 350 980
>
> Sign up for our NIRS newsletter <http://artinis.us3.list-
> manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46>
>
>
>
> From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Sunny p
> Sent: Friday, July 27, 2018 20:41
> To: Arana, S.L. (Sophie) <S.Arana at donders.ru.nl>
> Cc: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging
> of multi-channel NIRS data
>
>
>
> Hello Sophie,
>
>
>
> Once this tutorial is fully developed, Can we use this for OCTAMON (
> https://www.artinis.com/octamon/) ?
>
>
>
> Thanks for your understanding and support.
>
>
>
> Best Regards,
>
> Sunny
>
>
>
> On Wed, Jul 25, 2018 at 12:35 PM, Sunny p <sunnypitt1965 at gmail.com
> <mailto:sunnypitt1965 at gmail.com> > wrote:
>
> Hello Sophie,
>
>
>
> Thanks a lot for providing this code. I am making some changes that are
> useful. Can you please inform what is the variable 'data_func' in the code
> relates to. This is the last undefined variable in code.
>
>
>
> Thanks for your understanding and support.
>
>
>
> Best Regards,
>
> Sunny
>
>
>
> On Wed, Jul 25, 2018 at 8:22 AM, Sunny p <sunnypitt1965 at gmail.com <mailto:
> sunnypitt1965 at gmail.com> > wrote:
>
> Hello Sophie,
>
>
>
> Thanks a lot for your clarification. This is very useful.
>
>
>
> Sunny
>
>
>
> On Wednesday, July 25, 2018, Arana, S.L. (Sophie) <S.Arana at donders.ru.nl
> <mailto:S.Arana at donders.ru.nl> > wrote:
>
> Dear Sunny,
>
>
>
> the multi-channel NIRS data tutorial is currently under construction and
> will hopefully be fully available in a couple of weeks. Until then, there
> might still be some inconsistencies such as the one you have encountered.
>
>
>
> The variable you refer to is indeed missing. It refers to a filtered
> version of the data, and you can created it by running the following code
> before the epoching.
>
>
>
> cfg = [];
>
> cfg.hpfilter = 'yes';
>
> cfg.hpfreq = 0.01;
>
> data_flt = ft_preprocessing(cfg,data_down);
>
>
>
> This should help you to continue with the tutorial, but please do keep in
> mind that we are currently working on it and you might encounter some other
> inconsistencies still later on.
>
>
>
> Best,
>
> Sophie
>
>
>
>
> _____
>
>
> From: fieldtrip [fieldtrip-bounces at science.ru.nl <mailto:
> fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [
> sunnypitt1965 at gmail.com <mailto:sunnypitt1965 at gmail.com> ]
> Sent: Tuesday, July 24, 2018 9:24 PM
> To: fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of
> multi-channel NIRS data
>
> Hello All Good Day,
>
>
>
> Hope you are doing fine,
>
>
>
> Thanks a lot for providing with fieldtrip which is really useful to
> analyze fNIRS data. I have an issue in the "Preprocessing and averaging of
> multi-channel NIRS data" tutorial. Can you please help me with this issue?
>
>
>
> Issue: In the "Preprocessing and averaging of multi-channel NIRS data"
> tutorial " <http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel>
> http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel
>
>
>
> The "Epoch" section consists of a variable "data_flt.fsample" where
> "data_flt" variable is not defined. Can you please inform what is this
> variable related to? as this is needed to complete my analysis.
>
>
>
>
>
>
>
>
>
> Thanks for your understanding and support
>
>
>
> Best Regards,
> Sunny
>
>
>
>
>
>
>
>
>
>
> <http://www.avg.com/email-signature?utm_medium=email&
> utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
>
> Virus-free. <http://www.avg.com/email-signature?utm_medium=email&
> utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
> www.avg.com
>
>
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 30 Jul 2018 08:49:46 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19
> Message-ID:
> <CADeotZqiKpnpykgvhfTQmoSONaBkEikFf9eyi379chfdzKkntg at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> it's the $MNE_ROOT/bin folder
> after setting the MNE_ROOT env variable to the folder that contains
> the MNE command line tools.
>
> HTH
> Alex
> On Mon, Jul 30, 2018 at 3:52 AM zhipeng li <lizhipeng3924 at gmail.com>
> wrote:
> >
> > External Email - Use Caution
> >
> > First of all, thank you very much for your reply @ Alexandre Gramfort .
> >
> > But none of the files you listed were found in bin
> >
> >
> > This is all the files contained in bin,
> >
> > I need your further help.
> >
> > Yours,
> > zhipeng
> >
> >
> > 2018-07-29 18:00 GMT+08:00 <fieldtrip-request at science.ru.nl>:
> >>
> >> Send fieldtrip mailing list submissions to
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> >> To subscribe or unsubscribe via the World Wide Web, visit
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> >> Today's Topics:
> >>
> >> 1. A question about MEG source reconstruction (zhipeng li)
> >> 2. Re: A question about MEG source reconstruction
> >> (Alexandre Gramfort)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Sun, 29 Jul 2018 10:55:37 +0800
> >> From: zhipeng li <lizhipeng3924 at gmail.com>
> >> To: fieldtrip at science.ru.nl
> >> Subject: [FieldTrip] A question about MEG source reconstruction
> >> Message-ID:
> >> <CAAUszHHfd_jTwxGTnNzrbR=cBNUpremEz=PBhyCDYEhUGe=NQw@
> mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Dear all,
> >> When I was about to create a sourcemodel, I ran into a problem.The
> >> documentary which I refers to is Tutorial documentation>Source
> >> reconstruction of event-related fields using minimum-norm
> >> estimation>Creating a sourcemodel for source-reconstruction of MEG or
> EEG
> >> data.When I installed MNE as their description, I found that the.sh file
> >> doesn't exist.The command I am using is posted below as a
> >> picture.Therefore, the following steps cannot be carried out.
> >> I would appreciate it if you could help me.
> >> Yours,
> >> zhipeng
> >> -------------- next part --------------
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> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Sun, 29 Jul 2018 10:03:59 +0200
> >> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> >> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> >> Subject: Re: [FieldTrip] A question about MEG source reconstruction
> >> Message-ID:
> >> <CADeotZrzo1Z8XREpbHXOqXn3tTDQCLE1B0f0QGjrU4HZWN6x4Q at mail.
> gmail.com>
> >> Content-Type: text/plain; charset="UTF-8"
> >>
> >> hi,
> >>
> >> indeed there is a typo:
> >>
> >> $ cd $MNE_ROOT
> >> $ ls bin/mne_setup*
> >> bin/mne_setup bin/mne_setup_matlab_csh
> >> bin/mne_setup_mri bin/mne_setup_source_space
> >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh
> >>
> >> depending on your shell it can be
> >>
> >> source $MNE_ROOT/bin/mne_setup_sh
> >>
> >> HTH
> >> Alex
> >>
> >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li <lizhipeng3924 at gmail.com>
> wrote:
> >> >
> >> > External Email - Use Caution
> >> >
> >> > Dear all,
> >> > When I was about to create a sourcemodel, I ran into a problem.The
> documentary which I refers to is Tutorial documentation>Source
> reconstruction of event-related fields using minimum-norm
> estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG
> data.When I installed MNE as their description, I found that the.sh file
> doesn't exist.The command I am using is posted below as a
> picture.Therefore, the following steps cannot be carried out.
> >> > I would appreciate it if you could help me.
> >> > Yours,
> >> > zhipeng
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > fieldtrip mailing list
> >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >> > https://doi.org/10.1371/journal.pcbi.1002202
> >> >
> >> >
> >> > The information in this e-mail is intended only for the person to
> whom it is
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> the e-mail
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> >>
> >>
> >>
> >> ------------------------------
> >>
> >> Subject: Digest Footer
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> >> https://doi.org/10.1371/journal.pcbi.1002202
> >>
> >>
> >> ------------------------------
> >>
> >> End of fieldtrip Digest, Vol 92, Issue 19
> >> *****************************************
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > https://doi.org/10.1371/journal.pcbi.1002202
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
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> > contains patient information, please contact the Partners Compliance
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 30 Jul 2018 09:23:31 +0000
> From: Simon Hanslmayr <S.Hanslmayr at bham.ac.uk>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Postdoc position to work with human single
> neurons and LFPs, 9 days left to apply!
> Message-ID:
> <257F6C65A372A04CA41056EACC0DE7CED8783389 at EX12.adf.bham.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Fieldtrippers,
>
> We are pleased to announce an open postdoc position in our group to work
> with human single neurons and LFP recordings in an exciting memory project
> funded by the ERC. The position is initially for 2 years with an option for
> 1 year extension. The negotiable start date is 1st Oct. Preliminary data
> has been collected and is waiting to be analysed. If you have strong
> electrophysiological analytical skills and are interested then please do
> not hesitate to apply here: http://www.memorybham.com/open-positions/
>
> If you have any questions then please do not hesitate to contact me.
>
> Best wishes,
> Dr. Simon Hanslmayr
> Reader in Cognitive Neuroscience
> Royal Society Wolfson Research Merit Award Holder
> School of Psychology
> Hills Building 2.37
> University of Birmingham
> Edgbaston
> Birmingham
> B15 2TT
> UK
>
> Tel +44 121 4146203
> http://www.memorybham.com/people/#/simon-hanslmayr/
> [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif]
>
>
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> ------------------------------
>
> Subject: Digest Footer
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> https://doi.org/10.1371/journal.pcbi.1002202
>
>
> ------------------------------
>
> End of fieldtrip Digest, Vol 92, Issue 21
> *****************************************
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