Hi Sal - Would it be possible for you to run the bbregister command that
fails (you can find the command line in trac-all.log) using both the 5.1
and 5.2 version of bbregister and see if one of them works on your system?
a.y
On Fri, 29 Mar 2013, Salil Soman wrote:
Hi Anastasia,
Because I did not have a compatible older version of fsl on the SGE, I was not
able to
run tracula with 5.1.
Thank you,
Sal
On Fri, Mar 29, 2013 at 8:32 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>
wrote:
Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out
if it's 5.2-specific.
Thanks,
a.y
On Thu, 28 Mar 2013, Salil Soman wrote:
Thank you for your response.
I tried re-running Tracula using bbr in a subject I had
successfully run using flt.
trac-all prep and bedp worked without an error. Bedpostx sent
me an email confirming
bedpost completed without problem. However, when I try to run
trac-all paths, I get
the following error:
Loading atlas reference
volumefrom/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr
_end
1_dil.nii.$
niiRead(): error
openingfile/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr
_end
1_dil.nii.gz
ERROR: Could
notread/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr
_end
1_dil.nii.gz
recon-all did finish without error.
Best wishes,
-S
On Thu, Mar 28, 2013 at 8:43 AM, Anastasia
Yendiki <ayend...@nmr.mgh.harvard.edu> wrote:
Hi Sal,
1. I have no experience with the sun grid engine,
perhaps someone else on
the list can help with that.
2. The -bedp step needs the outputs from the -corr and
-masks steps. The
-path step needs the outputs from the -bedp step. The
output files from
each part are listed here:
http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles
3. Checking the aparc+aseg should be enough for tracula
purposes as well,
since that's the freesurfer output that tracula uses.
Keep in mind that
DWI resolution is usually lower than T1 resolution,
so tiny changes in
the aparc+aseg might not affect tracula at all.
4. Yes, I do recommend using bbregister. It's not
surprising that it would
give better results since it uses the additional
information of the
surfaces. If I remember correctly, Doug didn't manage
to replicate your
bbregister error, right? I'd check if you get the
same error with the
5.1 version of bbregister.
Hope this helps,
a.y
On Wed, 27 Mar 2013, Salil Soman wrote:
Hi,
I have been able to implement FS 5.2 on our Sun
Grid Engine
Cluster using the CentOS 6
distribution. After modifying the fsl_sub_mgh file
to work
with out cluster queue
names and to modify the email notifications, I am
able to run
the entire processing
pipeline using FLT. (Everytime I try bbr I get
errors. I had
email doug about this but
have not heard any response).
I am submitting the jobs to the cluster as follows
recon-all -i ./*.nii -s WCA_0202_T1_FS
-nuintensitycor-3T
-nocanorm -openmp 50
-hippo-subfields -all
trac-all -prep -no-isrunning -c
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
trac-all -bedp -no-isrunning -c
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
trac-all -path -no-isrunning -c
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
There are a few issues I am trying to sort out:
1) how should one conifigure the openmp flag for
the Sun Grid
Engine? the flag I used
did not change processing time, and each subject
is still
taking ~24 hrs?
2) once the script starts bedpost, bedpost has
controller code
which paralelizes all
of the slices (which has been great going from 12
hrs of
processing to 1.5 hrs).
However, my original script goes on to execute
trace-all -path
... before bepost is
done, generating errors. I have gotten around this
by running
the trace-all -path
command again after bedpost sends me an email
confirming
completion. Is there a way to
more cleanly do this (some kind of hold command I
can do based
on output from
bedpost)?
3) In your experience, how important is quality
control of
freesurfer on tracula
results? We have come to the compromise for
freesurfer output
to manually check the
segmentation of aparc+aseg.mgz using free view,
only
correcting and rerunning steps of
freesurfer when there are specific structures we
want the
volumes of (eg hippocampus).
4) have you found a significant benefit of bbr
over flt? If
so, any suggestions on
things I may need to check to get bbr to work
(given flt
works)?
Best wishes,
Sal
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