[Freesurfer] DTI error
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 Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ 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.
Re: [Freesurfer] DTI error
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://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.
Re: [Freesurfer] DTI error
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.edu_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYvJp8mKI&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_complianceline&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYvJp8mKI&s=ZCxo2mqb7_uBlK06A4PzG2Oc3tXOOfY5nkuRQDxr1-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 Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ 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.
Re: [Freesurfer] DTI error
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 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://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.
Re: [Freesurfer] DTI error
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 >> 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.edu_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=KiW0HwopUPkuxl00iNmJ-d2_v8Lvm5ziYpz8re5nRJg&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_complianceline&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=KiW0HwopUPkuxl00iNmJ-d2_v8Lvm5ziYpz8re5nRJg&s=ncZFIkFGSZn2leTYeESq0AVS7_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 Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ 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 He
Re: [Freesurfer] DTI error
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 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 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=KiW0HwopUPkuxl
Re: [Freesurfer] DTI error
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=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7c1gaW5UpDUs-Df4uqLGaiN1YKi8WpD7PUUFUH_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 >> 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 >> 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 lis
Re: [Freesurfer] DTI error
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 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 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 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
Re: [Freesurfer] DTI error
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 >> 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 >> 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 >> 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_f
Re: [Freesurfer] DTI error
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 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 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 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 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
Re: [Freesurfer] DTI error
Correct. On Sunday, May 22, 2016, Anastasia Yendiki 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 >> 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 >>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 >>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 >> >> 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 >>
Re: [Freesurfer] DTI error
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 wrote: > Correct. > > > On Sunday, May 22, 2016, Anastasia Yendiki > 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 >>> 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 >>>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 >>>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 >>> >>> 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
Re: [Freesurfer] DTI error
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 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 >>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 >> 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 >> wrote: >> >> But do you see the output files >> from the >> previous step? The >> outputs from each step are >> described on >> the >> wiki. >>
Re: [Freesurfer] DTI error
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 wrote: Correct. On Sunday, May 22, 2016, Anastasia Yendiki 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 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 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 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