Yes. I did it. Thank you very much. Best, Xiaofu
On Tue, Jun 16, 2015 at 2:34 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > 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 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the >> person to whom >> it is >> addressed. If you believe this e-mail was sent to you in >> error and the >> e-mail >> contains patient information, please contact the Partners >> Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was >> sent to you >> in error >> but does not contain patient information, please contact the >> sender >> and properly >> dispose of the e-mail. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
