Hi Xiaofu - Right now your only option is to have a different
configuration file for each set of subjects that was scanned with a
different protocol.
Best,
a.y
On Fri, 12 Jun 2015, Xiaofu wrote:
Hi Anastasia, Yes. I tried to run bedpostx on a stand-alone computer but it
is very slow although it can work well.
Regarding the b-values, we do have some subjects which were scanned in
different protocols a few years ago. If it is possible, please
add the option to the new version of Tracula, or it's even better to let me
know how can I change the script by myself.
I have updated the new version of freesurfer, so, I don't need to use nb0
variable anymore. Thanks for your reminder.
Best,
Xiaofu
Best,
Xiaofu
On Wed, May 27, 2015 at 12:20 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Xiaofu - As I said earlier, it is impossible for us to troubleshoot
problems with every single type of cluster, especially
a type we don't have. You'll have to troubleshoot it with your cluster
admin, or try to run bedpostx on a stand-alone
computer. About your other questions:
1. Currently there is no option to have a different set of b-values for
each subject. Are you using a different scanning
protocol for different subjects?
2. The fact that you mention the nb0 variable tells me that you don't
have the latest version of freesurfer. It is highly
recommended that you run tracula from the 5.3 version of freesurfer,
after also downloading the tracula update posted here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
In the newer version, there is no nb0 variable, the program figures it
out from the b-value file. But again, it is not ideal
to have a different number of b=0 images for each subject.
Best,
a.y
On Tue, 26 May 2015, Xiaofu wrote:
Dear Anastasia,
Thanks for your answer. I tried to replace 'bedpostx_mgh' with
'bedpostx'
in the shell file 'tract-all' in order to run Tracula in the C2B2
server
(Titan cluster). But it failed as well. Is there anyway to run
Tracula,
i.e., by pass the running error of bedpostx_mgh?
Besides, I have two more questions when I set up a configuration
file.
1) In the step9 of Tracula tutorial
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula),
i.e.,
Specify the b-value table, I can only set bvalfile to specify the
location
of the b-value table. Can I specify a different b value file for
each of the
scans in the study (with bvallist,for example) besides a single b
value file
for all scans in the study (with bvalfile).
2) About the number of low-b images.
Since I will use 4D nifty images instead of raw DICOMs, I need
to set
the number of low-b images in the configuration file, i.e., set
nb0. Can I
specify a different nb0 value for each of the scans in the study
(with
nb0list,for example) besides a single nb0 value for all scans in
the study.
Best,
Xiaofu
On Fri, May 22, 2015 at 1:35 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Xiaofu - The bedpostx program is not configured to run on
any
type of cluster with any type of queueing software. It was
originally written to be run on an SGE cluster with specific
queue names. The bedpostx_mgh is a modified version that also
works on our PBS cluster. Making it work on additional
clusters
would require additional tweaks, and it's impossible for us to
make it work on everyone's cluster.
In a future version, I'd like to give the option to simply
print
out all the necessary commands, and then it would be up to the
user to figure out how to submit them as jobs on their own
cluster. This is not implemented yet.
a.y
On Tue, 19 May 2015, Xiaofu wrote:
Dear Sir/Madam, I tried to run Tracula in the C2B2
server at Columbia University. However, I got the
following error message
after submitted my job using qsub to the sever. I'd
greatly appreciate it if you could help me resolve
this problem.
WARN: Running FSL's bedbost locally - this might
take a while
WARN: It is recommended to run this step on a
cluster
bedpostx_mgh -n 2 /DTIdata/Tracula/3789/dmri
subjectdir is /DTIdata/Tracula/3789/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Unable to run job: Job was rejected because job
requests unknown queue "short.q".
Exiting.
Queuing parallel processing stage
Unable to run job: Job was rejected because job
requests unknown queue "long.q".
Exiting.
Queuing post processing stage
Unable to run job: Job was rejected because job
requests unknown queue "long.q".
Exiting.
Looking forward to hearing from you. Thank you very
much.
Best,
Xiaofu
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