Any further suggestion?
Thanks.
Thanks! it's running...On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp <bakk.hbg@googlemail.com> wrote:Hi Michele,
Don't think there is anything wrong with the attached dmrirc.tutorial file.
You definitely need to add the '-c' flag infront of the path to your configuration file.
Right now it reads the path to your file as a flag, which is of course not what you want.
Best,
Barbara
On 11/09/2014 17:49, Michele Cavallari wrote:
Hi Anastasia,I am probably doing something wrong with the syntax of the dmrirc file.I get this error message
trac-all -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
ERROR: flag /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial unrecognized
-prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial
Could you please check the attached file?
On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:
Thanks, Michele. Hard to tell what's causing this, perhaps a bit of distortion orbitofrontally. You may be able to fix this type of thing by reinitializing the tract reconstruction: Add "set reinit = 1" to your configuration file, set the pathlist to include only the left and right uncinate, and then rerun the -prior and -path steps of trac-all on this subject.
On Wed, 10 Sep 2014, Michele Cavallari wrote:
uploaded (and activated).Thanks!
On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Michele - The anatomical segmentation does look good, but from the
screenshot the DWI data seems to be noisy in the orbitofrontal area, which
may be affecting the uncinate. It's hard to tell just from one slice.
If you upload all the tracula output directories of this subject (dmri,
dmri.bedpostX, dlabel, dpath) for me here, I'll take a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks!
a.y
On Wed, 10 Sep 2014, Michele Cavallari wrote:
Hi Anastasia,I completed the tracula processing.
By looking at the tractography results in the viewer I noticed
that the uncinate
fasciculus is pretty small (see attached screenshot). It
actually appears as a small
blue dot. And the problem is both on the left and right side.
The other tracts look
fine. I played with threshold, but the size didn't increase. So,
I guess that something
wrong happened with the tractography of that particular bundle.
I checked the aparc+aseg
output (attached): it seems right to me, but could you please
double-check?
Let me also know if you have any suggestions, and if you need
more information or output
files.
Best,
Michele
Inline image 1
On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Ludy - If your gradient table is formatted in 3 rows
you need to
either:
1. Convert it to 3 columns so you can use it with the 5.3
version of
tracula, which requires the gradient table to be formatted
in columns
OR
2. Download the tracula update that can use gradient
tables formatted in
rows
Hope this helps,
a.y
On Thu, 4 Sep 2014, lshih@bidmc.harvard.edu wrote:
> Hi,
>
> I was having similar errors as Michele Cavallari
regarding "error reading
/path/to/subject/dmri/dwi_frame," but I'm not sure it's
related to my bvecs
file. I did try reconfiguring my bvecs file into columns
instead of row just
in case, but that didn't solve the problem. It really just
looks like it
can't find the dwi_frame file after the mri_concat
command.
>
> I am attaching my trac-all.log and config file.
>
> Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs
files were
generated after I converted my dicoms to nifti using
dcm2niigui (GE
scanner).
>
> Can anyone tell me how dwi_frame is generated?
>
>
> Ludy
>
> This message is intended for the use of the person(s) to
whom it may be
addressed. It may contain information that is privileged,
confidential, or
otherwise protected from disclosure under applicable law.
If you are not the
intended recipient, any dissemination, distribution,
copying, or use of this
information is prohibited. If you have received this
message in error,
please permanently delete it and immediately notify the
sender. Thank you.
>
_______________________________________________
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.
_______________________________________________
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.
_______________________________________________
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.
_______________________________________________ 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.
_______________________________________________
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.