Good call! Thanks Anastasia! It worked! On Wed, May 25, 2016 at 8:46 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote:
> > Hi Jasmin - On my screen the dash "-" symbol before the "c" looks > different than the one before "path". I'd check if you are indeed typing a > plain "-c". > > Best, > a.y > > > On Wed, 25 May 2016, Jasmin Alves wrote: > > 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. 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=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYvJp8mKI&s=ZCxo2mqb7_uBl >> >> >> >> >> K06A4PzG2Oc3tXOOfY5nkuRQDxr1-g&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 >> >> >> >> >> _______________________________________________ >> 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=KiW0HwopUPkuxl00iNmJ-d2_v8Lvm5ziYpz8r >> >> >> >> >> e5nRJg&s=BsW_UFqBiIvAMznFD1XkPkffaeZXmAgRB1Q1k-oulXs&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=7c1gaW5UpDUs-Df4uqLGaiN1YKi8WpD7PUUFU >> >> >> H_Yh_8&s=DesJ0SJkKNz4ZoMWgCEPnpLFQw0H2IrVGrH78Z--ivs&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=7c1gaW5UpDUs-Df4uqLGaiN1YKi8WpD7PUUFUH_Yh_8&s=1iWD5AdeBNaZ6 >> >> VLA8KO2r58SGDHR36K4CloQgbI1adc&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 >> >> >> >> _______________________________________________ >> 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 AlvesPredoctoral Student >> Medical Biology Graduate Program >> University of Southern California >> jal...@usc.edu >> >> >> >> >> >> -- >> 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.edu_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=RRnBnMERP5lBpoqunMJjaZkkV2zG0tOxNXOJFDoCX0s&s=3Tx-PCWhT47b4G8RGb8LHJu9yV-RMfNmT4J5WxOM7M8&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_complianceline&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=RRnBnMERP5lBpoqunMJjaZkkV2zG0tOxNXOJFDoCX0s&s=ldZH7CsB4Bw-GnV38jWZlxCD_liscGb6nAZN61ZgMks&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 Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu
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