The input needs to be the diffusion-weighted images, not the FA, MD, etc.
There should be as many volumes in this input nifti as there are b-values
in bval file and gradient vectors in the bvec file. The image
registration, tractography, etc etc is performed on the diffusion-weighted
images, not on the FA, MD, etc. The FA, MD, etc are used only in the very
end, to extract FA, MD, etc for each tract. But to get the tracts in the
first place, you need the images.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Yes, each nifti contains one volume. I have different nifti’s for the
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?
On 5/31/16, 9:26 PM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu>
wrote:
Some of the errors make me suspect that your input DWI files contain only
one volume. Could this be the case?
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Hmm, weird, as I put a # in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi
On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:
Hi Heidi - It knows where to find the freesurfer recons of the T1's
from
SUBJECTS_DIR (see example config file). Based on your log file, it
looks
like you haven't turned off the eddy current compensation, because it's
trying to run it. If you attach your config file, I'll take a look.
Best,
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Thanks! I tried to adapt the configuration file and it got a bit
further,
but then crashes again. Not sure why? I have added the log file, so
that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi
On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
ayend...@nmr.mgh.harvard.edu> wrote:
No, it should be pointed to the DWI data, which can be corrected
niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to
be
there for the registration.
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear Anastasia,
Thanks for the feedback. So, does this mean that the dcm root should
be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in
a
different folder.
Enclosed is the log file (of one subject) and the configuration
file.
You
will see that I tried the inter and intra option, because I thought
that
for the inter it would not need anything else than the MNI template
and
the DTI images.
Thanks
Best
Heidi
On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
behalf
of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
ayend...@nmr.mgh.harvard.edu> wrote:
Hi Heidi - The intra-subject registration step that you're trying
to
run
registers your subject's DWI and T1 images. It expects to find
those
images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can
you
please send that file and your configuration file? Thanks!
a.y
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Dear FreeSurfers,
The data I have is preprocessed, so I have the all the metrics
(FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.
I have organized the data as mentioned on the wiki:
For example:
<subjID>/<dmri> dtifit_FA.nii.gz
I have also filled in the configuration file, canceling out the
things
I don¹t need and then I tried to run:
Trac-all intra c <configuration file>
Unfortunately, it does not work, it says: dcmlist: subscript out
of
range
I do not have the original filesŠ is there a way that I can get
the
script working?
Many thanks.
Heidi
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