Hi Anastasia, I am still receiving the following error message when I run a different participant doing, trac-all -path –c dmrirc1_sim.txt:
ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt If you have any ideas for what i can try it would be very appreciated! Thanks! Jasmin On Sun, May 22, 2016 at 9:07 PM, Jasmin Alves <jal...@usc.edu> wrote: > Correct. > > > On Sunday, May 22, 2016, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > wrote: > >> >> No idea, sorry. You used the -c option with the previous steps of >> trac-all and didn't see this error, correct? >> >> On Sun, 22 May 2016, Jasmin Alves wrote: >> >> Hi Anastasia, >>> Perhaps I was asking for advice regarding the wrong step in trac-all, do >>> you >>> have any ideas why I am still receiving the following error: >>> >>> ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt >>> >>> This occurs when I do trac-all -path –c dmrirc1_sim.txt >>> >>> I tried looking at posts from previous mailing lists, and found no match >>> to >>> this problem. >>> >>> >>> Thank you, >>> >>> Jasmin >>> >>> >>> On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu> wrote: >>> >>> Ok, then you can ignore the error that you see when you run the >>> bedpost step. >>> >>> `On Sun, 22 May 2016, Jasmin Alves wrote: >>> >>> Sorry for the mix-up. All of the bedpost output files are >>> generated as well >>> both 1 and 2 of each file. >>> >>> On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu> wrote: >>> >>> These are output files from the -prep step. I'm >>> asking about >>> output files from the bedpost step, since that's >>> where you're >>> encountering the error. >>> >>> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard >>> >>> >>> .edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp&d=DQIDaQ&c=clK7kQUTWt >>> >>> >>> AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7c1gaW5UpDUs-D >>> >>> >>> f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8&s=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA >>> >>> &e= >>> What's in the dmri.bedpostX/ directory? >>> >>> On Sun, 22 May 2016, Jasmin Alves wrote: >>> >>> Output files are being generated, ie. >>> 1. dtifit_FA.nii.gz - Fractional Anisotropy >>> 2. dtifit_MD.nii.gz - Mean Diffusivity >>> 3. dtifit_MO.nii.gz - Mode of the Anisotropy >>> 4. dtifit_S0.nii.gz - Non-Diffusion weighted >>> image >>> 5. dtifit_L1.nii.gz - Primary Eigenvalue >>> 6. dtifit_L2.nii.gz - Secondary Eigenvalue >>> 7. dtifit_L3.nii.gz - Tertiary Eigenvalue >>> 8. dtifit_V1.nii.gz - Primary Eigenvector >>> 9. dtifit_V2.nii.gz - Secondary Eigenvector >>> 10. dtifit_V3.nii.gz - Tertiary Eigenvector >>> But it seems the bedpost process gets cut >>> short and >>> then, the trac-all path >>> step won't work. I have ran it a few times and >>> the >>> bedpost step ends at the >>> same point. >>> >>> >>> On Sun, May 22, 2016 at 3:24 PM, Anastasia >>> Yendiki >>> <ayend...@nmr.mgh.harvard.edu> wrote: >>> >>> But do you see the output files from the >>> previous step? The >>> outputs from each step are described on >>> the >>> wiki. >>> >>> On Sun, 22 May 2016, Jasmin Alves wrote: >>> >>> Hi Anastasia, >>> Thank you for the reply, when I do >>> just >>> let it run, >>> I get the following >>> error when I try to do trac-all >>> -path –c >>> dmrirc1_sim.txt >>> >>> I get the following error: >>> >>> ERROR: flag –c unrecognized >>> >>> -path –c dmrirc1_sim.txt >>> >>> >>> Thanks, >>> >>> Jasmin >>> >>> >>> On Sun, May 22, 2016 at 1:51 AM, >>> Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu> >>> wrote: >>> >>> Hi Jasmin - Check if things >>> are >>> running >>> despite that error. Are >>> output files being >>> generated? >>> >>> a.y >>> >>> On Sat, 21 May 2016, Jasmin >>> Alves >>> wrote: >>> >>> >>> Dear Freesurfer, >>> >>> While doing the >>> bedpost step >>> for >>> TRAC-all ( trac-all >>> -bedp -c >>> dmrirc1_sim.txt) I >>> received >>> the >>> following error: >>> >>> >>> >>> /Applications/freesurfer/bin/bedpostx_mgh: >>> line 345: >>> kill: (51042) - No >>> such >>> process >>> >>> Any ideas? >>> >>> Thank you, >>> Jasmin >>> >>> Jasmin >>> AlvesPredoctoral >>> Student >>> Medical Biology >>> Graduate >>> Program >>> University of Southern >>> California >>> jal...@usc.edu >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e >>> >>> >>> >>> >>> du_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 >>> >>> >>> >>> >>> p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYv >>> >>> >>> >>> >>> >>> >>> Jp8mKI&s=fkP_flwCTRv-7FzQB1kw0eRwApBybsAjJNxNF8VH9RQ&e= >>> >>> >>> The information in this >>> e-mail is >>> intended >>> only for the person >>> to whom it is >>> addressed. 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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. >>> >>> >>> >>> >>> -- >>> Jasmin AlvesPredoctoral Student >>> Medical Biology Graduate Program >>> University of Southern California >>> jal...@usc.edu >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e >>> >>> du_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 >>> >>> p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=YxC44q2aLV1gp16SkW5w2b8JLGYtKy7rkUKMf >>> 9UK4ww&s=XYLOkj5Bplu_-U9W9Z0pTE9oRzb_h0CZo4r2HJwKZwU&e= >>> >>> >>> 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 >>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli >>> >>> anceline&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0 >>> >>> KTyqa6rNRHLug&m=YxC44q2aLV1gp16SkW5w2b8JLGYtKy7rkUKMf9UK4ww&s=fbId_fdsEA7gL >>> VFlRdTREPWVzwXNEOX_ceaqFn6l7rQ&e= . 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. >>> >>> >>> >>> >>> -- >>> Jasmin AlvesPredoctoral Student >>> Medical Biology Graduate Program >>> University of Southern California >>> jal...@usc.edu >>> >>> >>> > > -- > Jasmin Alves > Predoctoral Student > Medical Biology Graduate Program > University of Southern California > jal...@usc.edu > > > -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu
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