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Are you also running a 64bit OS? Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of YonghuiLi Sent: Wednesday, November 04, 2009 7:44 PM To: [log in to unmask] Subject: Re: [FSL] Asking for your help about "probtrackx" Dear Saad, I have 16GB RAM in my computer, so I am confused here why there is still "out of memory". Your help will be highly appreciated. Thanks Yonghui Email: [log in to unmask] 2009-11-05 ======= 2009-11-04 22:23:19 ：======= >In your case roughly 4GB of RAM. > >Internally, probtrackx will use six times 50 volumes, each volume >being 256x256x31*sizeof(float). >(+ more if you specify waypoints/targets etc.) > >Saad. >ps: if you can avoid upsampling the original data, that would save you >a lot of RAM. > > > >On 4 Nov 2009, at 13:26, Yonghui Li wrote: > >> Dear FSL, >> >> I am sure that I set the input directory for probtrackx correctly, >> which should be the output directory of BEDPOSTX (im my case, it is >> bedpostx.bedpostX). So, can I assume that the suggestion of Saad is >> the solution for my problem? More RAM will do the job? How many RAM >> is required to run probtrackx? The dimension of my 4D data is >> 256*256*45*31, voxel size 1*1*3. >> >> Best >> Yonghui >> >> >> Hi Yonghui Li >> This is a RAM problem. You need to run probtrackx on a computer with >> more RAM. >> >> Cheers, >> Saad. >> >> >> >> >> > Hi Yonghui, >> >> > >> >> > The the folder bedpostx.bedpostX seems fine so far. >> >> > >> >> > However when running Probtrackx you need to select the >> bedpostx.bedpostX - >> >> > folder, not the BEDPOSTX folder, as you want to use the OUTPUT from >> >> > bedpostx, not the input in order to execute Probtrackx. >> >> > >> >> > Does this help? >> >> > >> >> > Cheers, >> >> > Markus >> >> > >> >> > >> >> > 2009/11/4 YonghuiLi <[log in to unmask]> >> >> > >> >> > > Dear Markus >> >> > > >> >> > > a) I run the "probtrackx" through the GUI window. I first set >> the BEDPOSTX >> >> > > directory, then I set the X Y Z coordinate to one single voxel I >> am >> >> > > interested in, then I "GO". >> >> > > >> >> > > b) I set the name of input directory for "bedpostx" step is >> "bedpostx", so >> >> > > after it is done, the output directory is "bedpostx.bedpostX". >> When doing >> >> > > "ls bedpostx.bedpostX", it shows the following ifnormation: >> >> > > bvals mean_f2samples.nii.gz >> merged_ph1samples.nii.gz >> >> > > bvecs mean_ph1samples.nii.gz >> merged_ph2samples.nii.gz >> >> > > commands.txt mean_ph2samples.nii.gz >> merged_th1samples.nii.gz >> >> > > dyads1.nii.gz mean_th1samples.nii.gz >> merged_th2samples.nii.gz >> >> > > dyads2.nii.gz mean_th2samples.nii.gz monitor >> >> > > logs merged_f1samples.nii.gz >> nodif_brain_mask.nii.gz >> >> > > mean_f1samples.nii.gz merged_f2samples.nii.gz xfms >> >> > > >> >> > > Thank you very much for your help! >> >> > > Best >> >> > > Yonghui >> >> > > >> >> > > >> >> > > ======== 2009-11-03 18:14:06 您在来信中写道： ======== >> >> > > >> >> > > >> >> > > Hi! >> >> > > >> >> > > In order to help, we need to know more. Can you post >> >> > > a) the probtrackx command you run? >> >> > > b) what you get when doing "ls <your_bedpostx.bedpost>" >> >> > > >> >> > > It is most likely that there is a file missing or has the wrong >> name or the >> >> > > wrong path... >> >> > > >> >> > > Hth, >> >> > > Markus >> >> > > >> >> > > >> >> > > 2009/11/3 YonghuiLi <[log in to unmask]> >> >> > > >> >> > >> Dear FSL, >> >> > >> >> >> > >> I run into some troubles while try to do the probtrackx on >> single voxel. >> >> > >> The "eddycurrent" and "bedpostx" steps are completed. Then I >> continued the >> >> > >> "probtrackx" by enter the coordinate of a single seed voxel. >> Then "GO". But >> >> > >> it stopped very soon, showing an error message: >> >> > >> "Errors: Image Exception: #99 :: Out of memory >> >> > >> terminate called after throwing an instance of >> >> > >> 'RBD_COMMON::BaseException' >> >> > >> Then the whole procedure stopped. >> >> > >> >> >> > >> Your help to my situation here will be highly appreciated. >> >> > >> >> >> > >> All the bests! >> >> > >> >> >> > >> Sincerely, >> >> > >> Yonghui Li >> >> > >> >> >> > >> Email: [log in to unmask] >> >> > >> 2009-11-03 >> >> > >> >> >> > > >> >> > > >> >> > > >> >> > > -- >> >> > > >> >> > > >> >> > > Dr. med. Markus Gschwind, M.D. >> >> > > Laboratory for Neurology and Imaging of Cognition - Dept of >> Neurosciences >> >> > > University Medical Center (CMU) >> >> > > 1, Michel-Servet >> >> > > CH-1211 GENEVA - Switzerland >> >> > > >> >> > > Tel 0041 (0) 22 379 5324 >> >> > > Fax 0041 (0) 22 379 5402 >> >> > > email: [log in to unmask] >> >> > > http://labnic.unige.ch >> >> > > >> >> > > = = = = = = = = = = = = = = = = = = = = = = >> >> > > >> >> > > 致 >> >> > > 礼！ >> >> > > >> >> > > *Yonghui Li,* PhD, PostDoc >> >> > > >> >> > > LIAMA Center for Computational Medicine (CMC) >> >> > > National Laboratory of Pattern Recognition (NLPR) >> >> > > Institute of Automation, Chinese Academy of Sciences (CASIA) >> >> > > 95 Zhong Guan Cun East Road, Hai Dian District, Beijing 100190, >> P.R.China >> >> > > Tel: +86-10-62659278 >> >> > > Fax: +86-10-62551993 >> >> > > >> >> > > National Reserach Center for Intelligent Computing Systems (NCIC) >> >> > > Institute of Computing Technology, Chinese Academy of Sciences >> (ICT) >> >> > > 6 Ke Xue Yuan South Road, Hai Dian District, Beijing 100190, >> P.R.China >> >> > > >> >> > > Email: [log in to unmask] or [log in to unmask] <[log in to unmask] >> > >> >> > > [log in to unmask] >> >> > > 2009-11-04 >> >> > > >> >> > > >> >> > >> >> > >> >> > >> >> > -- >> >> > >> >> > >> >> > Dr. med. Markus Gschwind, M.D. >> >> > Laboratory for Neurology and Imaging of Cognition - Dept of >> Neurosciences >> >> > University Medical Center (CMU) >> >> > 1, Michel-Servet >> >> > CH-1211 GENEVA - Switzerland >> >> > >> >> > Tel 0041 (0) 22 379 5324 >> >> > Fax 0041 (0) 22 379 5402 >> >> > email: [log in to unmask] >> >> > http://labnic.unige.ch >> >> > >> >> >> >> > >-- >Saad Jbabdi >University of Oxford, FMRIB Centre > >JR Hospital, Headington, OX3 9DU, UK >+44 (0) 1865 222523 (fax 717) >www.fmrib.ox.ac.uk/~saad