Hi Jasmin
actually things look pretty reasonble given the degree of motion
corruption. Is it still running? I would expect it to finish ok. I doubt
you can get realiable thickness estimates off this kind of data, but you
should be able to do e.g. fMRI analysis.
There were a bunch of big defects so the topology fixing took a lot longer
than usual, but it did complete
cheers
Bruce
On Thu, 1 Jun 2017, Jasmin Alves wrote:
Hi Bruce,
I uploaded two subjects directories to the FTP site.
Thanks,
Jasmin
On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
you can put it on our ftp site:
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard
.edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7C
Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_oo
LOM&s=SWUWcgct6aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e=
but at that point you might as well tar and gzip the entire
subject dir and upload it
On Wed, 31 May 2017, Jasmin Alves wrote:
Hi Bruce,
Thanks for the reply, below is a couple of sentences
from the recon-all.log
reading initial pial vertex positions from
white.preaparc...
mean border=65.6, 300 (300) missing vertices, mean
dist 2.2 [2.0 (%0.1)->3.2
(%99.9))]
%21 local maxima, %44 large gradients and %29 min
vals, 639 gradients
ignored
perforing initial smooth deformation to move away
from white surface
tol=1.0e-04, sigma=2.0, host=hpc17, nav=16, nbrs=2,
l_surf_repulse=1.000,
l_tspring=1.000, l_nspring=0.500, l_intensity=0.200,
l_curv=1.000
mom=0.00, dt=0.05.
I also attached a screenshot of the log.
Is there a place I should upload the files?
Thanks,
Jasmin
On Wed, May 31, 2017 at 12:28 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Jasmin
typically that means there is a big
topological defect, which
definitely can be caused by motion. What is
the last couple of
lines of the recon-all.log file of one of the
subjects? Can you
upload an image we can look at?
cheers
Bruce
On Wed, 31 May 2017, Jasmin Alves wrote:
Hello,
I have used FS6.0 to do recon-all on
about 57
brains, but for some reason,
recon-all is not working on some brains,
recon-all
is not able to get past
"Automatic topology fixer", after the
command has
been running for 24 hours.
Is it possible there is too much motion
in the
image? Or does FS6.0
possibly take longer to complete for
some brains?
Thanks,
Jasmin
--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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