[Mne_analysis] adding talairach transforms failed?

[Jon Houck]

I'm not sure if this is the same issue, but I had some subjects processed
with freesurfer 4.2 for whom the talairach would be saved to orig.mgz but
would not be carried forward into nu.mgz or T1.mgz.  The talairach
registration itself was good.  You might try tkmedit $SUBJECT T1.mgz to see
if the coordinates of the T1 are in volume RAS or Talairach.  If RAS, going
to ${SUBJECTS_DIR}/${SUBJECT}/mri and doing something
like mri_add_xform_to_header transforms/talairach.xfm T1.mgz T1.mgz should
work; afterward both mne_analyze and things like mne_collect_transforms
should detect the transformation.

Jon



On Thu, Jan 24, 2013 at 11:23 AM, Eric Larson <larson.eric.d at gmail.com>wrote:

> Hey Ji Won,
>
> I also get this error on my subjects (made using recon-all). For some
> reason the Talairach transform is not read correctly by MNE. If you want,
> mne-python has functionality to convert vertices to mni coordinates (using
> the MNI transform). Or, you can manually read it in in MATLAB and apply the
> transform yourself (based on the subject's surface coordinates), I've
> attached scripts that I use to do it.
>
> Cheers,
> Eric
>
>
>
> On Thu, Jan 24, 2013 at 9:19 AM, Ji Won Bang <kirstens03 at gmail.com> wrote:
>
>> Hi, MNE users.
>>
>> By the way, I've run
>> recon-all -autorecon1 -subjid $SUBJECT
>> recon-all -autorecon2 -subjid $SUBJECT
>> recon-all -autorecon3 -subjid $SUBJECT
>>
>> Thanks,
>> Ji Won
>>
>>
>> 2013/1/24 dgw <dgwakeman at gmail.com>
>>
>>> Hi Ji-Won,
>>>
>>> I believe you need to have completed recon-all (i.e. more than just
>>> autorecon1) to use mne_analyze.
>>>
>>> D
>>>
>>> On Thu, Jan 24, 2013 at 12:07 PM, Ji Won Bang <kirstens03 at gmail.com>
>>> wrote:
>>> > Dear. MNE users.
>>> >
>>> > When I mne_analyze to coordinate MEG and MRI and load surface(inflated)
>>> > (file->load surface->inflated), I get this message.
>>> >
>>> > "adding talairach transforms failed. Warning: transform file not
>>> present in
>>> > these MRI data"
>>> >
>>> > I checked that $SUBJECT/mri/transforms/talairach.xfm exists for this
>>> > subject.
>>> >
>>> > Is it a fatal problem that I need to fix? And if it is, how can I fix
>>> it?
>>> >
>>> > Please give me any advice!
>>> >
>>> > By the way, if it is related to the reconstruction of mri data, this
>>> is the
>>> > command that I've run.
>>> > recon-all -autorecon1 -subjid $SUBJECT
>>> >
>>> > Thanks a lot.
>>> >
>>> > Best,
>>> > Ji Won
>>> >
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