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

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lshih＠bidmc.harvard.edu

4 Sep 2014 4 Sep '14

9:48 p.m.

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.

Attachments:

trac-all.log (application/octet-stream — 45.6 KB)
dti.config (application/octet-stream — 827 bytes)

Show replies by date

Anastasia Yendiki

4 Sep 4 Sep

11:55 p.m.

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

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

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.

Michele Cavallari

10 Sep 10 Sep

12:06 p.m.

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

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

[image: 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:

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

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.

Anastasia Yendiki

1:14 p.m.

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

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.

Michele Cavallari

1:28 p.m.

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

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.

Anastasia Yendiki

1:51 p.m.

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

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.

Michele Cavallari

11 Sep 11 Sep

12:49 p.m.

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

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.

Barbara Kreilkamp

1:31 p.m.

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

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 mailto: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
    <mailto: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
    <mailto: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
    <mailto: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
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Michele Cavallari

1:36 p.m.

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

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.

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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.

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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.

Michele Cavallari

2:58 p.m.

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

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.

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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.

Chris Watson

4:56 p.m.

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

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:

...

Inline image 2

On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari <cavallari.michele@gmail.com mailto:cavallari.michele@gmail.com> wrote:

Thanks! it's running...

On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp
<bakk.hbg@googlemail.com <mailto: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
    <mailto: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
            <mailto: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
            <mailto: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
            <mailto: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.
                              >
            _______________________________________________
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                        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
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                        contains patient information, please
            contact the Partners
                        Compliance HelpLine at
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            please contact the
                        sender and properly
                        dispose of the e-mail.




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Michele Cavallari

12 Sep 12 Sep

11:19 a.m.

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

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
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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.

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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.
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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.

Michele Cavallari

15 Sep 15 Sep

11:44 a.m.

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

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.

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participants (5)

Anastasia Yendiki
Barbara Kreilkamp
Chris Watson
lshih＠bidmc.harvard.edu
Michele Cavallari