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
_______________________________________________
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.
