[Mne_analysis] adding talairach transforms failed?

Ji Won Bang kirstens03 at gmail.com
Thu Jan 24 14:52:01 EST 2013
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Hi, Jon

I've tried it and it worked all fine.

Thanks a lot!

Best,
Ji Won

2013/1/24 Jon Houck <jhouck at mrn.org>

> 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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>>>
>>>
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