talairach transforms failed in COR.fif

✉️ Mailing List Archive (read-only)
1

Dear. MNE users.

I have a question regarding talairach transform failure.

When I run 'mne_setup_mri --subject $SUBJECT --overwrite',
it says adding talairach transforms failed and talairach transforms will
not be included into the output file, which is COR.fif.

In addition, when I run 'mne_analyze' and load surface, it again says
adding talairach transforms failed.

To solve this issue (as MNE users have advised before), I have run,

mri_add_xform_to_header -c \
$SUBJECTS_DIR/$SUBJECT/mri/transforms/talairach.xfm \
$SUBJECTS_DIR/$SUBJECT/mri/T1.mgz \
$SUBJECTS_DIR/$SUBJECT/mri/T1.mgz

This actually solved the failure issue with mne_analyze, but not the
failure issue with mne_setup_mri. (why???)

So I'm now wondering whether the COR.fif which does not include talairach
transforms will be problematic when running mne_watershed_bem and
forward/inverse solution..

If not, I can ignore the talairach transform failure in COR.fif and move on
to the next step with COR-'whoami'*.fif that I made. This COR-'whoami'*.fif
has talairach transforms since I've run the mri_add_xform_to_header...

Is there anyone who can give me some advice?

I appreciate it in advance!

Best,
Ji Won Bang
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20130130/1e665c76/attachment.html

2

Dear. MNE users.

No worries..

Now I got the answer.

Thanks,
Ji Won

2013/1/30 Ji Won Bang <kirstens03 at gmail.com>

Dear. MNE users.

I have a question regarding talairach transform failure.

When I run 'mne_setup_mri --subject $SUBJECT --overwrite',
it says adding talairach transforms failed and talairach transforms will
not be included into the output file, which is COR.fif.

In addition, when I run 'mne_analyze' and load surface, it again says
adding talairach transforms failed.

To solve this issue (as MNE users have advised before), I have run,

mri_add_xform_to_header -c \
$SUBJECTS_DIR/$SUBJECT/mri/transforms/talairach.xfm \
$SUBJECTS_DIR/$SUBJECT/mri/T1.mgz \
$SUBJECTS_DIR/$SUBJECT/mri/T1.mgz

This actually solved the failure issue with mne_analyze, but not the
failure issue with mne_setup_mri. (why???)

So I'm now wondering whether the COR.fif which does not include talairach
transforms will be problematic when running mne_watershed_bem and
forward/inverse solution..

If not, I can ignore the talairach transform failure in COR.fif and move
on to the next step with COR-'whoami'*.fif that I made. This
COR-'whoami'*.fif has talairach transforms since I've run the
mri_add_xform_to_header...

Is there anyone who can give me some advice?

I appreciate it in advance!

Best,
Ji Won Bang

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20130130/a29ae498/attachment.html