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://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputsfromtrac-all-bedp 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. 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=KiW0HwopUPkuxl00iNmJ-d2_v8Lvm5ziYpz8re5nRJg&s=ncZFIkFGSZn2l eTYeESq0AVS7_txy3i6lPQonGMyZE8&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
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