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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