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
> 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
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> Mne_analysis Info Page
>
>
> 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
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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
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
> 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
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> Mne_analysis Info Page
>
>
> 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
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you
in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu Mne_analysis Info Page
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
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
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.
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
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
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
> 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
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> 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
> e-mail
> contains patient information, please contact the Partners
Compliance it's
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
you in
> error
> but does not contain patient information, please contact the sender
and
> properly
> dispose of the e-mail.
>
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
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
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
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.