On Thu, Jun 1, 2017 at 3:52 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Jasmin

how long did you wait? Is the process still running? The last step in the log is not a very long one. Maybe someone/something killed your job prematurely? I see no reason in the log that it wouldn't have finished

Bruce

On Thu, 1 Jun 2017, Jasmin Alves wrote:

Hi Bruce,
So it does not matter that the recon-all.done script never appeared in the
script folder? Or that the isrunning.lh+rh script is still in the folder?

I plan to run the hippocampal subfield analysis on these folders, so I am
wondering if the subfield analysis can still function without the
recon-all.done script being in the folder.

Thanks,
Jasmin

On Thu, Jun 1, 2017 at 11:15 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
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
<fischl@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
<fischl@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
jalves@usc.edu

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