<div dir="ltr">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.<div>
<div><br></div><div>Jon</div><div><br><div class="gmail_extra"><br>
<br><div class="gmail_quote">On Thu, Jan 24, 2013 at 11:23 AM, Eric Larson <span dir="ltr"><<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Hey Ji Won,<div><br></div><div>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.</div>
<div><br></div><div>Cheers,<br>Eric</div><div><br></div></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jan 24, 2013 at 9:19 AM, Ji Won Bang <span dir="ltr"><<a href="mailto:kirstens03@gmail.com" target="_blank">kirstens03@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hi, MNE users.<div><br></div><div>By the way, I've run </div>
<div>recon-all -autorecon1 -subjid $SUBJECT</div><div>
recon-all -autorecon2 -subjid $SUBJECT</div><div>recon-all -autorecon3 -subjid $SUBJECT</div><div><br></div>
<div>Thanks,</div><div>Ji Won<div><div><br><br><div class="gmail_quote">2013/1/24 dgw <span dir="ltr"><<a href="mailto:dgwakeman@gmail.com" target="_blank">dgwakeman@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi Ji-Won,<br>
<br>
I believe you need to have completed recon-all (i.e. more than just<br>
autorecon1) to use mne_analyze.<br>
<br>
D<br>
<div><div><br>
On Thu, Jan 24, 2013 at 12:07 PM, Ji Won Bang <<a href="mailto:kirstens03@gmail.com" target="_blank">kirstens03@gmail.com</a>> wrote:<br>
> Dear. MNE users.<br>
><br>
> When I mne_analyze to coordinate MEG and MRI and load surface(inflated)<br>
> (file->load surface->inflated), I get this message.<br>
><br>
> "adding talairach transforms failed. Warning: transform file not present in<br>
> these MRI data"<br>
><br>
> I checked that $SUBJECT/mri/transforms/talairach.xfm exists for this<br>
> subject.<br>
><br>
> Is it a fatal problem that I need to fix? And if it is, how can I fix it?<br>
><br>
> Please give me any advice!<br>
><br>
> By the way, if it is related to the reconstruction of mri data, this is the<br>
> command that I've run.<br>
> recon-all -autorecon1 -subjid $SUBJECT<br>
><br>
> Thanks a lot.<br>
><br>
> Best,<br>
> Ji Won<br>
><br>
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