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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