Hi Bruce Thanks. The problem is solved. Pardon my last question: After creating a study specific template, I try to map every thickness map into the template using surf2surf and also zero the medial wall with "--no-cortex". Does it mean that the native surface is firstly transformed to the standard fsaverage to extract the cortex and medial wall annotations, and then mapped to the study specific template? Is it ok, or there exists a better approach?

Cheers, Sourena

On 8/18/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Sourena

the inflated.H is the mean curvature of the inflated surface and can be used to guide initial large-scale alignment. I think it is generated by the

current recon-all, but Nick can correct me if not. You can create them using mris_curvature

cheers Bruce

On Sat, 18 Aug 2012, Sourena Soheilinezhad wrote:

...

Hi experts,

I have tried this syntax for making a surface template: mris_make template ?h sphere subj1 subj2 subj3 my_template.tiff

Output is an error saying "Could not read curvature file: ?h.infalted.H"

But searching in the /surf directory for .H file, I have added "-infname white_avg" to the command and it seems to run smoothly. My question is, what is this .H file? Should I safely ignore the default search for inflated.H and keep on using white_avg.H instead? Also, the make_average_surface command gives the same "missing .H file" error but this time there is no -infname parameter to be manipulated.

Thanks in advance, Sourena _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hi Sourena,

I'm not sure it's worth it, since it lives in the same space as our standard template you can just use it. The alternative would be to manually annotate the subjcets that go into your study-specific template, which takes forever and significant training. An alternative would be to rebuild the atlas from your subjects and ther aparcs I guess, but I doubt that would change much (unless you edited them).

cheers Bruce

On Sun, 19 Aug 2012, Sourena Soheilinezhad wrote:

P.S. I realized the mistake I made in the purpose of --no-cortex flag, being smoothing issues. So, is there a way to transfer freesurfer's standard annotations to study-specific custom templates?   Cheers, Sourena On Sat, Aug 18, 2012 at 8:15 PM, Sourena Soheilinezhad sourena.soheili@gmail.com wrote: Hi Bruce Thanks. The problem is solved. Pardon my last question: After creating a study specific template, I try to map every thickness map into the template using surf2surf and also zero the medial wall with "--no-cortex". Does it mean that the native surface is firstly transformed to the standard fsaverage to extract the cortex and medial wall annotations, and then mapped to the study specific template? Is it ok, or there exists a better approach?

  Cheers,
  Sourena

  On 8/18/12, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
  > Hi Sourena
  >
  > the inflated.H is the mean curvature of the inflated surface
  and can be
  > used to guide initial large-scale alignment. I think it is
  generated by the
  >
  > current recon-all, but Nick can correct me if not. You can
  create them
  > using mris_curvature
  >
  > cheers
  > Bruce
  >
  > On Sat, 18 Aug 2012, Sourena
  > Soheilinezhad wrote:
  >
  >> Hi experts,
  >>
  >> I have tried this syntax for making a surface template:
  >> mris_make template ?h sphere subj1 subj2 subj3
  my_template.tiff
  >>
  >> Output is an error saying "Could not read curvature file:
  ?h.infalted.H"
  >>
  >> But searching in the /surf directory for .H file, I have
  added
  >> "-infname white_avg" to the command and it seems to run
  smoothly.
  >> My question is, what is this .H file? Should I safely ignore
  the
  >> default search for inflated.H and keep on using white_avg.H
  instead?
  >> Also, the make_average_surface command gives the same
  "missing .H
  >> file" error but this time there is no -infname parameter to
  be
  >> manipulated.
  >>
  >> Thanks in advance,
  >> Sourena
  >> _______________________________________________
  >> Freesurfer mailing list
  >> Freesurfer@nmr.mgh.harvard.edu
  >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >>
  >>
  >>
  >
  >
  > 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.
  >
  >