New subject: problems with tracula pre-processing (bvecs)

16 Sep 2014

      Dear all,
What does this mean? That tracula is more robust when running it seperately
for the tracts I am interested in?
Thanks,
Barbara
On Mon, Sep 15, 2014 at 4:44 PM, Michele Cavallari <
cavallari.michele@gmail.com> wrote:
...
errata corrige: it did work! I had to re-run the whole thing including
only that specific tract...and eventually it worked.
On Fri, Sep 12, 2014 at 11:19 AM, Michele Cavallari <
cavallari.michele@gmail.com> wrote:
...
Tried...unfortunately it didn't improve
On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson <
Christopher.Watson@childrens.harvard.edu> wrote:
...
You can try just re-running "trac-prep -prior" and "trac-paths" for
the L uncinate and no other tracts
On 09/11/2014 02:58 PM, Michele Cavallari wrote:
So, I re-ran the case with the set reinit option. It "half"
worked!...in the sense that the new results show the left uncinate right,
but the right-side one is still a dot (see screenshot of the brain view
from the bottom).
Any further suggestion?
Thanks.
[image: Inline image 2]
On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari <
cavallari.michele@gmail.com> wrote:
...
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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.

Re: [Freesurfer] problems with tracula pre-processing (bvecs)