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
Ok, then you can ignore the error that you see when you run the bedpost step.
`On Sun, 22 May 2016, Jasmin Alves wrote:
KTyqa6rNRHLug&m=7c1gaW5UpDUs-Df4uqLGaiN1YKi8WpD7PUUFUH_Yh_8&s=1iWD5AdeBNaZ6Sorry 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
.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
<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
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