# (no subject)
**URL:** https://mne.discourse.group/t/no-subject/504
**Category:** Mailing List Archive (read-only)
**Tags:** list-archive
**Created:** [November 6, 2012, 2:12pm UTC](https://mne.discourse.group/t/no-subject/504 "2012-11-06T14:12:55Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [November 6, 2012, 2:12pm UTC](https://mne.discourse.group/t/no-subject/504/1 "2012-11-06T14:12:55Z")
Dear MNE group
I am new to MNE and did not succeed to get things to work yet
at the moment two things hold me:
1. mne\_analyze open in a strange way. it is a narrow window with all the
areas piled one over the other. there is little room to display anything
this way (the surface of the head cannot be enlarged to cover more than
1cm). buttons also seem not to be displayed as meant to. I can however load
and display headshape + MRI and realign. I am running ubutnu Pangolin
64bit. did anyone encountered such a problem?
2. I work on 4D data after conversion to fif (thanks, Denis). after running
freesurfer I align the MRI to the digitized headshape with mne\_analyze and
save MRI set and the transformation matrix. I then follow this pipeline:
mne\_watershed\_bem --atlas
mne\_setup\_source\_space --ico -6 --overwrite
mne\_setup\_forward\_model --homog --surf --ico 4
mne\_do\_forward\_solution --spacing oct-6 mindist --overwrite
--meas 'subject1.fif' --megonly
I get the following message:
mne\_forward\_solution version 2.9 compiled at Jan 6 2011 02:25:30
Source space : /usr/local/freesurfer/
subjects/maor1/bem/maor1-oct-6-src.fif
MRI -\> head transform source : ./maor-trans.fif
Measurement data : maor.fif
BEM model :
/usr/local/freesurfer/subjects/maor1/bem/maor1-5120-bem.fif
Accurate field computations
Do computations in head coordinates.
Free source orientations
Destination for the solution : ./maor-oct-6-fwd.fif
Reading /usr/local/freesurfer/subjects/maor1/bem/maor1-oct-6-src.fif...
Read 2 source spaces a total of 8196 active source locations
Coordinate transformation: MRI (surface RAS) -\> head
0.000000 0.951057 0.309017 18.33 mm
-1.000000 -0.000000 0.000000 -3.00 mm
0.000000 -0.309017 0.951057 43.46 mm
0.000000 0.000000 0.000000 1.00
MEG -\> head coordinate transformation not found.
Forward computation failed (see above)
I found a similar report here:
[https://mail.nmr.mgh.harvard.edu/pipermail//mne\_analysis/2012-April/001003.html](https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2012-April/001003.html)
but I did not see a solution there.
Thanks
Yuval
---
### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [November 7, 2012, 8:56pm UTC](https://mne.discourse.group/t/no-subject/504/2 "2012-11-07T20:56:20Z")
hi Yuval,
> I am new to MNE and did not succeed to get things to work yet
> at the moment two things hold me:
> 1. mne\_analyze open in a strange way. it is a narrow window with all the
> areas piled one over the other. there is little room to display anything
> this way (the surface of the head cannot be enlarged to cover more than
> 1cm). buttons also seem not to be displayed as meant to. I can however load
> and display headshape + MRI and realign. I am running ubutnu Pangolin 64bit.
> did anyone encountered such a problem?
how did you setup MNE?
did you actually source mne\_setup\_sh as explain on the website? or did you
manually set your PATH ?
you should do something like:
export MNE\_ROOT=..
source $MNE\_ROOT/bin/mne\_setup\_sh
at least if you use bash.
> 2. I work on 4D data after conversion to fif (thanks, Denis). after running
> freesurfer I align the MRI to the digitized headshape with mne\_analyze and
> save MRI set and the transformation matrix. I then follow this pipeline:
how did you convert the 4d file? python or the mne C command?
maybe Denis can help you on this.
Alex