Everything looks to be running fine. Wether I look at the merged file with freeview or fslview, I still have only one tract. Here's an extract of the outputs :
Input files: lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz lh.unc_AS_avg33_mni_flt/path.pd.nii.gz rh.ccg_PP_avg33_mni_flt/path.pd.nii.gz rh.unc_AS_avg33_mni_flt/path.pd.nii.gz Lower threshold for display: 0.150000 Merging volume 1 of 4... Threshold: 111 Name: Left Cingulum - Cingulate Gyrus Merging volume 2 of 4... Threshold: 74.85 Name: Left Uncinate Fasciculus Merging volume 3 of 4... Threshold: 87.9 Name: Right Cingulum - Cingulate Gyrus Merging volume 4 of 4... Threshold: 57.6 Name: Right Uncinate Fasciculus Done in 0.621 sec. dmri_mergepaths done It remains the same if I take a very low threshold (0.001). David Am 24.08.2011 um 16:49 schrieb ayend...@nmr.mgh.harvard.edu: > Yes, it should be a concatenation of all existing pathway reconstructions > under dpath/... If you open it with trackvis --tv, you should be able to > see a 3d view of all the pathways. Sometimes the default threshold might > be too high for some pathways and you might need to adjust it individually > in freeview to be able to see them. > > Does the output of dmri_mergepaths show you that it's found multiple > pathways or just ccg? > >> Yes, there are no more malloc issues, thanks for the update. >> >> However I still have aays question, related to the merged_avg33_mni > file. It >> still only contains the first path that was passed as an input to >> dmri_mergepaths. If I understand correctly I should see all generated >> paths, thresholded and merged into this file ? >> >> David >> >> Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki: >> >>> >>> Hi David - Thanks for catching this. There was something wrong with the >>> new snow leopard build of dmri_mergepaths. (The original from the 5.1 >>> distribution didn't have this problem). Sorry about that! >>> >>> I've now updated the snow leopard tar file, so if you download it again >>> you should not get this error any more. >>> >>> As before it's here: >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz >>> >>> Let me know how it goes, >>> a.y >>> >>> On Tue, 23 Aug 2011, David Coynel wrote: >>> >>>> Hi Anastasia, >>>> >>>> Thanks for your answer. Unfortunately I overwrote the executables (I >>>> could still retrieve them from the website distribution ?). >>>> Interestingly this message does not show up when selecting only a >>>> subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), >>>> however the merged_avg33_mni file only appears to contain the first >>>> pathway (lh.ccg). >>>> >>>> David >>>> >>>> Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki: >>>> >>>>> >>>>> Hi David - Glad to hear things are working! I can look into >>>>> dmri_mergepaths and see if something is wrong with the snow leopard >>>>> build. >>>>> Have you by any chance kept the original leopard build of it? If you >>>>> haven't overwritten it, it'd be useful to run the same thing with that >>>>> version and see if it works. Thanks! >>>>> >>>>> a.y >>>>> >>>>> On Tue, 23 Aug 2011, David Coynel wrote: >>>>> >>>>>> Dear Anastasia, >>>>>> >>>>>> Thanks a lot for the upload. The procedure now runs perfectly, except >>>>>> for that last message at the end of trac-all -path : >>>>>> >>>>>> >>>>>> Merging volume 18 of 18... >>>>>> Threshold: 68.1 Name: Right Uncinate Fasciculus >>>>>> dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) >>>>>> failed (error code=12) >>>>>> *** error: can't allocate region >>>>>> *** set a breakpoint in malloc_error_break to debug >>>>>> Done in 2.433 sec. >>>>>> dmri_mergepaths done >>>>>> #------------------------------------- >>>>>> trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST >>>>>> >>>>>> >>>>>> This however does not seem to affect the pipeline, as all the >>>>>> expected outputs seem to be present and valid. >>>>>> >>>>>> Dr. David Coynel >>>>>> Division of Cognitive Neuroscience >>>>>> >>>>>> University of Basel >>>>>> Birmannsgasse 8 >>>>>> 4055 Basel - Switzerland >>>>>> >>>>>> david.coy...@unibas.ch >>>>>> tel: +41(0)612.670.240 >>>>>> >>>>>> Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki: >>>>>> >>>>>>> >>>>>>> Hi all - By popular demand we've posted the dmri_* executables >>>>>>> compiled on >>>>>>> snow leopard here: >>>>>>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz >>>>>>> >>>>>>> This is not the entire FS distribution, just the commands that are >>>>>>> called >>>>>>> by trac-all. If you are a mac user with snow leopard and have been >>>>>>> running >>>>>>> into memory issues with the leopard version, you can download this, >>>>>>> copy >>>>>>> the new files into your $FREESURFER_HOME/bin, and try rerunning the >>>>>>> part >>>>>>> of the analysis that had errored out. >>>>>>> >>>>>>> Let us know if there are any problems, >>>>>>> a.y >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
