Dear Anastasia,

Thanks very much. I have already downloaded the file. The wiki page was also down a few hours ago, but it's ok now.

And I am interested in the tracula group stat. How could I use mri_glmfit on the text file? And can I use the QDEC (or the contrast generated by QDEC) to do the glm?

Thanks Clive

On Mon, Feb 10, 2014 at 6:13 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Clive - Yes, you can use the recent tracula update on top your already processed data. The new update only adds new functionality to trac-all, without changing any of the existing functionality in 5.3.

Did you try downloading the update from here? http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

a.y

On Sun, 9 Feb 2014, Clive Wong wrote:

Hi,

...

I just want to confirm, is that I can use the new trac-all with the data processed in the original FS5.3 trac-all?

And, I just want to download the new trac-all, but I have problem to connect to the ftp server. I can login to the server, but it does not response to any command. Please advise.

Best, Clive

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.

Thanks Anastasia. I ask that because in the tracula stat page, it saids *"Measures can be extracted from these files to be analyzed further, e.g., for tract-based group analysis. Specifically, the text files can be converted into a table using the command tractstats2table and then used for doing GLM analyses with mri_glmfit or any other statistical software (SPSS, Excel, Statview etc.)"*. So I think I may reuse the GLM matrix.

Best, Clive

On Tue, Feb 11, 2014 at 8:29 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Clive - These are not stats in the volume or on the surface, so mri_glmfit doesn't apply. If you want to do group analyses along a tract on a table produced by trac-all -stat, you should import the table in any software that you use for statistics (matlab, SPSS, etc).

Best, a.y

On Mon, 10 Feb 2014, Clive Wong wrote:

Dear Anastasia,

...

Thanks very much. I have already downloaded the file. The wiki page was also down a few hours ago, but it's ok now.

And I am interested in the tracula group stat. How could I use mri_glmfit on the text file? And can I use the QDEC (or the contrast generated by QDEC) to do the glm?

Thanks Clive

On Mon, Feb 10, 2014 at 6:13 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

  Hi Clive - Yes, you can use the recent tracula update on top your

already processed data. The new update only adds new functionality to trac-all, without changing any of the existing functionality in 5.3.

  Did you try downloading the update from here?
  http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

  a.y

  On Sun, 9 Feb 2014, Clive Wong wrote:

        Hi,
        I just want to confirm, is that I can use the new trac-all

with the data processed in the original FS5.3 trac-all?

        And, I just want to download the new trac-all, but I have

problem to connect to the ftp server. I can login to the server, but it does not response to any command. Please advise.

        Best,
        Clive

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.

Dear Anastasia,

Thank you very much for the clarification.

Best, Clive

On Thu, Feb 13, 2014 at 8:52 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Clive - So you are talking about the overall tract stats, averaged over the whole tract (and not the stats by position on the tract that trac-all -stat outputs). That phrase in the tutorial is not very clear - these could be used as a covariate in mri_glmfit, but the main input of mri_glmfit is on a surface or volume. These stats (e.g., average FA of the uncinate fasciculus) are only one value per subject.

Hope this helps, a.y

On Tue, 11 Feb 2014, Clive Wong wrote:

Thanks Anastasia. I ask that because in the tracula stat page, it saids

...

"Measures can be extracted from these files to be analyzed further, e.g., for tract-based group analysis. Specifically, the text files can be converted into a table using the command tractstats2table and then used for doing GLM analyses with mri_glmfit or any other statistical software (SPSS, Excel, Statview etc.)". So I think I may reuse the GLM matrix. Best, Clive

On Tue, Feb 11, 2014 at 8:29 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

  Hi Clive - These are not stats in the volume or on the surface, so

mri_glmfit doesn't apply. If you want to do group analyses along a tract on a table produced by trac-all -stat, you should import the table in any software that you use for statistics (matlab, SPSS, etc).

  Best,
  a.y

  On Mon, 10 Feb 2014, Clive Wong wrote:

        Dear Anastasia,
        Thanks very much. I have already downloaded the file. The

wiki page was also down a few hours ago, but it's ok now.

        And I am interested in the tracula group stat. How could I

use mri_glmfit on the text file? And can I use the QDEC (or the contrast generated by QDEC) to do the glm?

        Thanks
        Clive


        On Mon, Feb 10, 2014 at 6:13 AM, Anastasia Yendiki <

ayendiki@nmr.mgh.harvard.edu> wrote:

              Hi Clive - Yes, you can use the recent tracula update

on top your already processed data. The new update only adds new functionality to trac-all, without changing any of the existing functionality in 5.3.

              Did you try downloading the update from here?
              http://surfer.nmr.mgh.harvard.

edu/fswiki/Tracula#Updates

              a.y

              On Sun, 9 Feb 2014, Clive Wong wrote:

                    Hi,
                    I just want to confirm, is that I can use the new

trac-all with the data processed in the original FS5.3 trac-all?

                    And, I just want to download the new trac-all,

but I have problem to connect to the ftp server. I can login to the server, but it does not response to any command. Please advise.

                    Best,
                    Clive




        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.