Hi Megha
looking at the scan you sent I can tell gray from white over most of the
occipital lobe, so I think control points could recover reasonable
surfaces. I would try leaving a "trail" of them going from the
inferior-most, very dark places heading up.
cheers
Bruce
On Thu, 28 Jun 2018,
Chawla, Megha wrote:
External Email - Use Caution
Hi, I'm just resending this email in case you missed it.
Thanks!
Megha
_____________________________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on
behalf of Chawla, Megha <megha.cha...@yale.edu>
Sent: Wednesday, June 20, 2018 11:11 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Poor occipital signal and low contrast
External Email - Use Caution
Hi,
I have scans for ~60 participants, and for some reason the scans are of visibly
poor quality
when I convert them to .mgz (blurry, very low contrast). The white boundary
also seems to
exclude considerable white matter in the occipital in about half of the scans
(best seen in
sag view). Because of the extremely low contrast, I am unable to manually add
control points
as I cannot visibly tell the difference between wm and gm. I am attaching
orig.mgz for one
participant here.
Acquisition parameters for these scans were: High-resolution T1-weighted
anatomical images (1
× 1 × 1 mm3) were acquired with an MPRAGE pulse sequence (TI=900 ms, sagittal
slices, 256 ×
256 matrix) using a Siemens Allegra 3T head-only scanner.
I tried running more iterations of during the nu_correct (as suggested
here:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-November/008985.html)
using
the following command:
mc2835% recon-all -autorecon1 -nuintensitycor -nuiterations 10 -subjid 30026_FS
but got the following error:
ERROR: Flag -nuiterations unrecognized.
-autorecon1 -nuiterations 10 -subjid 30026_FS
Darwin Ifats-Mac-Pro.med.yale.internal 16.7.0 Darwin Kernel Version 16.7.0: Thu
Jun 15
17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Tue Jun 19 14:56:04 EDT 2018
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Is there any way to salvage this data for analysis?
Any help will be really appreciated.
Thank you!
Megha
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