Re: [Freesurfer] Anterior Temporal Lobe / Pial Reconstruc​tion Troubles - part 1

Hi Las

it's tough to tell from just those images. Can you upload the entire subject directory?

cheers Bruce

On Fri, 18 Jul 2014, Las Blawimo wrote:

Dear dr. Fischl,   I was wondering if you've had any chance to look at our images (image 3 and 4 are attached to a second e-mail with the subject: Anterior Temporal Lobe / Pial Reconstruction Troubles - part 2)?   Sincerely, Las

2014-07-11 16:06 GMT+02:00 Las Blawimo lasblawimo@gmail.com:

  Dear Dr. Fischl,

  Thanks for your quick reply.

  Attached you will find some images (image 1&2) showing the
  issues we're having (I'll send a second e-mail including image
  3&4).

  The images are as follows:

  1.) sagittal_1353_norm2+3T_vs_default -> the v5.3 suggested
  norm2 flags (from the release notes) and the -3T flag vs. the
  default v5.3 pipeline. Blue is the norm2/3T flag pipeline,
  yellow is the default.

  2.) sagittal_1353_wusl_vs_default->v5.3 using the -washu_mprage
  flag, obvious improvement in temporal lobe pial surface. Blue is
  -washu_mprage flag, yellow is the default v5.3 pipeline

  3.) axial_1353_norm2+3T_white -> The white surface, which
  appears OK using v5.3 with the suggested norm2 parameters and
  the -3T flag

  4.) axial_1353_wusl_white_error -> the white surface, with an
  obvious error in the lh_postcentral area, using the
  -washu_mprage flag.

  Let me know if you have any suggestions on other parameters I
  should try to improve the temporal lobe pial surface, without
  compromising the white matter surface reconstruction.

  Sincerely,

  Las