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
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