When you to the parcellations in autorecon3, you get an unknown volume
in middle of the brain. What exactly is in this unknown volume, and why
does it label it as such?
thanks,
dave
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Alright I converted the COR files to mgz fine, and saved the volume as
brainmask.mgz. All looks good. But before I run -autorecon2, am I
going to run into problems because I only have a brainmask.mgz and not a
brainmask.auto.mgz? (I deleted the old brainmask.auto.mgz because it
was the old volum
I just finished my 4 hour manual editing...went to file>save volume
as...then saved it to where it defaulted me, which was the mri folder of
this subject. When i pull up my brainmask, it is giving me the same one
that it had before i made any changes. I hope i didnt do something
wrong and lost al
I am currently in the process of manual editing...just curious though,
what exatly does adding an atlas do to the skullstrip process?
Quoting Nick Schmansky <[EMAIL PROTECTED]>:
> First have a look at the troubleshooting wiki pages at:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tro
I am having trouble with one of my skull strips, and getting very
extreme results. When I re-run the skullstrip using different watershed
values, anything at 56% or below takes 75%+ of the brain out, and as
soon as I jump to 57% or higher, it leaves on almost all of the skull,
except for maybe 5%
Well, I figured out what my problem is. The skull strip only took off
about a quarter of the skull on the top. Any suggestions on how to
correct this?
Quoting Bruce Fischl <[EMAIL PROTECTED]>:
> You must have a number of *huge* defects:
>
> > 163949 ambiguous faces found in tessellation
> > se
I think my fix topology sequence froze...I typed "top" in another
terminal and this is what came up...
ID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND
899 surf 25 0 2169m 1.6g 1984 R 99.1 43.1 1042:33 mris_fix_topolo
18609 root 15 0 457m 196m 8616 S 0.7 5.3
How do I go about finding/getting these tables? Sorry, I am fairly new
to the program.
Quoting Jenni Pacheco <[EMAIL PROTECTED]>:
> In the latest version there is asegstats2table and aparcstats2table
> which
> will do what you want.
>
> Jenni
>
> -Original Message-
> From: [EMAIL PROTE
I ran all three -autorecons and also was able to get my volumetric
statistics. I was wondering if there is a way (make my life easier) to
export all the information given in the anatomical stats directly to a
spreadsheet format without having to copy and paste eveything. I have
OpenOffice.org Cal
my terminal screen has been sitting on this for about an hour...is this
normal or does it look like something is stuck?
pass 1 of 1
setting smoothness coefficient to 0.01
blurring input image with Gaussian with sigma=2.000...
pct change decreased
pct chan
I'm running autorecon2 and i forgot to turn off the setting on my
computer that automatically stalls any processes that are going at the
time and asks for a log-in password when the computer sits idle for a
while. I logged back in and it appears autorecon2 has stalled because
of this. The comman
I'm confused about how to use my license key. It was sent to me, but
there isn't a file names .license in my freesurfer home folder. And
there isn't a license key FILE, only the three lines of text sent to me.
What should I type in the command line to validate the license?
__
I am trying to convert Dicom files to mgz format and I keep getting the
same error even when I try some variations on what I am typing in the
terminal. I have already set my subjects directory to
/home/amc/freesurferstable/subjects, which is where my first data set is
located, /1593-4. First I ch
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