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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The information in this e-mail is intended only for the person to whom
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The information in this e-mail is intended only for the person to whom it is
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