Re: [caret-users] Using caret_stats for TFCE
Yes, it works fine at 1000 iterations. I am trying to run 5000. It seems to get really slow after 1000, but continues on to about 2600 until it crashes. On Wed, Jan 22, 2014 at 2:13 PM, Donna Dierker wrote: > How many iterations did you specify? Have you tried it with 1000 > iterations? > > > On Jan 22, 2014, at 3:09 PM, Eshita Shah wrote: > > > Hi Donna, > > > > I have been trying to allocate more memory to caret_stats so it can run > java properly without crashing. However, this has not worked. I just > downloaded the JRE you provided, and it is actually the same one that I am > using. > > > > Do you think there is another source of this problem? > > > > Thank you, > > Eshita > > > > > > On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker < > donna.dier...@sbcglobal.net> wrote: > > At the end of the TFCE processing, you should get a text file named > something like *report.txt, along with a *ignif*metric. If you don't, then > it's not finishing normally. > > > > How many iterations are you using? If it doesn't finish overnight with > 5k iterations, then it might be your java runtime engine. Before I started > using this one, my java runtime engine just hung or grinded to a near halt > after a few thousand iterations: > > > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > > login pub > > password download > > > > You can use others; just be aware that the JRE can be an obstacle. > > > > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > > > > > Hi Donna, > > > > > > I am running a script you sent me a while ago, which uses caret_stats > to run ANOVA and then TFCE for significant cluster analysis. I am noticing > that the output files generated after running the script do not match up to > the expected outputs. I am seeing files such as ".metric.data1", > ".metric.data2", etc. I'm not sure where they are coming from - my hunch is > that the script is being aborted at some point (because I am not getting > any of the TFCE outputs), but I'm not exactly sure why these files would be > generated or what they are. > > > > > > Please let me know if you have any ideas. > > > > > > Thank you, > > > Eshita > > > > > > -- > > > Eshita Shah > > > University of California, Los Angeles | 2014 > > > B.S. Neuroscience > > > eshs...@ucla.edu > > > > > > > > > ___ > > > caret-users mailing list > > > caret-users@brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > -- Eshita Shah University of California, Los Angeles | 2014 B.S. Neuroscience eshs...@ucla.edu ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Using caret_stats for TFCE
How many iterations did you specify? Have you tried it with 1000 iterations? On Jan 22, 2014, at 3:09 PM, Eshita Shah wrote: > Hi Donna, > > I have been trying to allocate more memory to caret_stats so it can run java > properly without crashing. However, this has not worked. I just downloaded > the JRE you provided, and it is actually the same one that I am using. > > Do you think there is another source of this problem? > > Thank you, > Eshita > > > On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker > wrote: > At the end of the TFCE processing, you should get a text file named something > like *report.txt, along with a *ignif*metric. If you don't, then it's not > finishing normally. > > How many iterations are you using? If it doesn't finish overnight with 5k > iterations, then it might be your java runtime engine. Before I started > using this one, my java runtime engine just hung or grinded to a near halt > after a few thousand iterations: > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > login pub > password download > > You can use others; just be aware that the JRE can be an obstacle. > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > > > Hi Donna, > > > > I am running a script you sent me a while ago, which uses caret_stats to > > run ANOVA and then TFCE for significant cluster analysis. I am noticing > > that the output files generated after running the script do not match up to > > the expected outputs. I am seeing files such as ".metric.data1", > > ".metric.data2", etc. I'm not sure where they are coming from - my hunch is > > that the script is being aborted at some point (because I am not getting > > any of the TFCE outputs), but I'm not exactly sure why these files would be > > generated or what they are. > > > > Please let me know if you have any ideas. > > > > Thank you, > > Eshita > > > > -- > > Eshita Shah > > University of California, Los Angeles | 2014 > > B.S. Neuroscience > > eshs...@ucla.edu > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Using caret_stats for TFCE
Hi Donna, I have been trying to allocate more memory to caret_stats so it can run java properly without crashing. However, this has not worked. I just downloaded the JRE you provided, and it is actually the same one that I am using. Do you think there is another source of this problem? Thank you, Eshita On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker wrote: > At the end of the TFCE processing, you should get a text file named > something like *report.txt, along with a *ignif*metric. If you don't, then > it's not finishing normally. > > How many iterations are you using? If it doesn't finish overnight with 5k > iterations, then it might be your java runtime engine. Before I started > using this one, my java runtime engine just hung or grinded to a near halt > after a few thousand iterations: > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > login pub > password download > > You can use others; just be aware that the JRE can be an obstacle. > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > > > Hi Donna, > > > > I am running a script you sent me a while ago, which uses caret_stats to > run ANOVA and then TFCE for significant cluster analysis. I am noticing > that the output files generated after running the script do not match up to > the expected outputs. I am seeing files such as ".metric.data1", > ".metric.data2", etc. I'm not sure where they are coming from - my hunch is > that the script is being aborted at some point (because I am not getting > any of the TFCE outputs), but I'm not exactly sure why these files would be > generated or what they are. > > > > Please let me know if you have any ideas. > > > > Thank you, > > Eshita > > > > -- > > Eshita Shah > > University of California, Los Angeles | 2014 > > B.S. Neuroscience > > eshs...@ucla.edu > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
