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 < ayendiki@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.... What's in the dmri.bedpostX/ directory?
On Sun, 22 May 2016, Jasmin Alves wrote:
Output files are being generated, ie.
- dtifit_FA.nii.gz - Fractional Anisotropy
- dtifit_MD.nii.gz - Mean Diffusivity
- dtifit_MO.nii.gz - Mode of the Anisotropy
- dtifit_S0.nii.gz - Non-Diffusion weighted image
- dtifit_L1.nii.gz - Primary Eigenvalue
- dtifit_L2.nii.gz - Secondary Eigenvalue
- dtifit_L3.nii.gz - Tertiary Eigenvalue
- dtifit_V1.nii.gz - Primary Eigenvector
- dtifit_V2.nii.gz - Secondary Eigenvector
- 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 ayendiki@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 <ayendiki@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 jalves@usc.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e
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