[Mne_analysis] adding talairach transforms failed?

[Jon Houck]

Great! Glad it worked for you.

Best,

Jon


On Thu, Jan 24, 2013 at 12:52 PM, Ji Won Bang <kirstens03 at gmail.com> wrote:

> 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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