Hi Cecilioyou need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this
cheers BruceOn Fri, 1 May 2015, Cecilio C Baro Perez wrote:
Oh thank you, that makes things much more clear! So prefessor, that means
that there is any way possible to speed up the freesurfer processing? I have
30 patients and for each of the it takes like 25 h.
Best regards; Cecilio.
2015-04-30 23:33 GMT+08:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
no, you need to run each subject separately. What I was saying
is that you don't need to separate out the importing into two
steps. You can run:
recon-all -s Pat1 \
-i <path_to_dicoms>/95555-2-1.dcm \
-all
for each subject
cheers
Bruce
On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote:
Hi!
Thank you for quick response! Yes, Pat1 and Pat2,
etc are already imported
into the freesurfer directory. So what I want to do
do the further
processing. Sorry, but I'm kind of confuse, I
following the online
tutorials:
(1)
recon-all -s Pat1 \
-i <path_to_dicoms>/95555-2-1.dcm recon-all -s
Pat2 \
-i <path_to_dicoms>/95555-2-1.dcm
and so on....
(2)
recon-all -s <subjid> -all
Part (1) is completed for all my patients and I
would like to do part (2) fo
r
all my patients at the same time. Isn't the right
way to procede by typing i
n the terminal as below?
recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all
Once again thank you for all your help!
Best regards; Cecilio.
2015-04-30 22:35 GMT+08:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Cecilio
are Pat1 and Pat2 etc... different patients?
If so, they need to
be run separately. e.g.
recon-all -s Pat1 -i <path to dicoms for
patient 1) -all
recon-all -s Pat2 -i <path to dicoms for
patient 2) -all
.
.
.
cheers
Bruce
p.s. for the tcsh bug you should just get your
sysadmin to
update the version of tcsh you are using.
On Thu, 30 Apr 2015, Cecilio C Baro Perez
wrote:
Dear professor Bruce!
Sorry for bothering again, well I did
exatly as you
told before in order to
process different subject at the same
time:
recon-all -s Pat1 -i Pat2 -i Pat3 -i
Pat5 -all
there Pat 1 (and the rest) are subjid.
thought I got
this error message:
ARNING: tcsh v6.17.06 has an exit code
bug! Please
update tcsh!
ERROR: cannot find Pat2
Linux cecilio-N73SV 3.8.0-44-generic
#66~precise1-Ubuntu SMP Tue Jul 15
04:01:04 UTC 2014 x86_64 x86_64 x86_64
GNU/Linux
recon-all -s Pat1 exited with ERRORS at
Thu Apr 30
22:17:19 CST 2015
For more details, see the log file
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Could that be an bug in the program?
Once again! Thank you for your help!
Best regards; Cecilio.
2015-04-29 1:09 GMT+08:00 Cecilio C Baro
Perez
<cecilio.c.b...@gmail.com>:
Thank you so much for your quick
and helpful
response!Best
regards, Cecilio.
2015-04-26 20:27 GMT+08:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
sorry Cecilio, it is pretty
compute intensive.
If you have
multiple cores you can use -openmp
to speed
things up a
bit, or just run more than one
recon-all at a
time. Note
that you don't need to invoke it
twice - just
run:
recon-all -s ----- -i --- -all
cheers
Bruce
On Sun, 26 Apr 2015, Cecilio C
Baro Perez
wrote:
Dear professor Bruce!
Thank you so much for your
help, it help
me a
lot! I have a silly
question,
sorry for that, I'm using
the Freesurfer
to
extract the hippocampal
volume
of two different groups.
Right using
this two
commands:
"recon-all -s ----- -i
followed
by"recon-all
-s ------all"
Is taking like a day of
processing for
just
one patient. Is there any
faster
way as I'm only interested
on the
hippocampal
volume?
Once again thank you for
your help!
Best regards; Cecilio.
2015-04-25 22:10 GMT+08:00
Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Cecilio
what do you mean "224
scans"? I
assume
you mean 224 slices in
each scan? And do you
have two
different
runs of the same scan
type (e.g. mprage) for
each
subject? You
can try:
mri_info
/home/cecilio/Desktop/freesurfer/Test/Pat1/81334010
and
freeview
/home/cecilio/Desktop/freesurfer/Test/Pat1/81334010
to find out the scan
parameters
and also
visualize it.
cheers
Bruce
On Sat, 25 Apr 2015,
Cecilio C
Baro
Perez wrote:
Hi Bruce!
Thank you for
your quick
replay! I
appreciate that!
Well my data is
T1 dicom
images. And For
every
subject I
have 224 scans.
Though as I'm
using
freesurfer I'm
trying by
only
using 2 of 224 scans.
Please correct
me if I'm
wrong:
File name: Pat1
Number of scans
in Pat1: 2
(81334010 and 81334011)
On terminal:
Input command:
1. recon-all
-s Patient1
-i
/home/cecilio/Desktop/freesurfer/Test/Pat1/81334010
(this is
executed free
from errors)
2. recon-all
-s Patient1
-all
My error
becomes:
#@# Talairach
Failure
Detection
Сб. апр. 25 18:25:07
CST 2015
recon-all -s
Patient1 exited
with
ERRORS at Сб. апр.
25 18:25:32 CST
2015
Besides if I try
to use the
tkmedit I get this
following:
Tkmedit
couldn't read the
volume
you specified.
This could be
because the
image
format wasn't
recognized,
or it couldn't
find the
proper
header,
or the file(s)
were
unreadable,
or it was the
wrong size.
Please do you
possibly know
how to
go around this
problem.
Thank you in
advance!
Best regards;
Cecilio.
2015-04-24 21:20
GMT+08:00
Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Cecilio
this means
that the
automatic checking
determined that
the
Talairach
transform to
be
very unlikely and
probably a
failure.
What was
your input
data? If
you bring it up
in tkmedit or
freeview
do the
directions
on the screen
correspond to
true
anatomical
ones (e.g.
is A
really anterior)?
cheers
Bruce
On Fri, 24
Apr 2015,
Cecilio
C Baro Perez
wrote:
Hi!
My
name is
Cecilio!
I'm using the
freesurfer 5.3
and
I'm
having some
issues
that
I hope you
could
help me with. When
I perform:
recon-all -s
patienttesta -all
I
get this
error:
recon-all -s
patienttesta exited with
ERRORS
ERROR:
talairach_afd: Talairach
Transform:
transforms/talairach.xfm
After reading on
the
internet I even try
this
command:
recon-all -s
patienttesta -all
-use-mritotal
But
it stills
give me
the same error
Could you please
tell
me what the
problem could
be?
Thank you in
advance!
Best
regards,
Cecilio.
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http://www.partners.org/complianceline . If the
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The information in this e-mail is intended only for the person to whom
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