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 volume
from/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end
1_dil.nii.$
niiRead(): error opening
file/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end
1_dil.nii.gz
ERROR: Could not
read/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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