Anastasia,

Thanks for such a quick reply!

Please find my answers inline...

2012/7/26 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

Hi Sergio - Thank you for your kind words, and also thank you for taking the time to search the archives for answers!

The first problems you had with running bedpostx through trac-all have to do with trac-all assuming an older version of FSL than the current one, and this'll be fixed in the upcoming release of trac-all. Indeed the thing to do in the meantime is to run bedpostx by itself, as you did. I apologize for the inconvenience.

Great! By any chance, do you know when that release will happen?

About the problem you had when you ran bedpostx directly: do you get the other outputs of bedpostx, listed here? Are there any other, temporary files left over as well? http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.htmlhttp://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html

I have all of them, except for nodif_brain. And I only have the ones with i=2 while I should have the ones with i=1 too. Attached you can find two files, the output of ls -Rah on both dmri and dmri.bedpostX directories.

The merged_ph?samples are the orientation angles of the each of the two anisotropic compartments ("sticks", "fibers", whatever you want to call them) that bedpostx fit in each voxel. So "1" is the orientation angle of the largest stick/fiber, and "2" the one of the 2nd largest. If there's a "2", there should be a "1"!

But there are not :(

Also, I looked at your dmrirc file and noticed that you decreased the # of control points b/c you hate waiting :) I just wanted to warn you that decreasing that # might make you wait longer b/c make fitting a spline with fewer control points to initialize the algorithm is sometimes more challenging.

Hehe, thanks! I changed it back to 5 now...

Thanks!

Sergio.

Hope this helps, a.y

On Thu, 26 Jul 2012, Sergio Medina wrote:

Hi!

...

First of all let me thank you for having put at our disposal such great tools as FreeSurfer and Tracula! I am trying to run Tracula on the sample data that is on the website, but I've been running into some issues. I am attaching the configuration file just in case (dmrirc_single_subject-serch).

The first step "trac-all -prep" seems to run fine. The first problem comes with the second step "trac-all -bedp". The complete trace is included in the attached file 1-error-trac-all-bedp.txt After finding this on the FreeSurfer mailing listhttps://mail.nmr.mgh.** harvard.edu/pipermail//**freesurfer/2012-May/024042.**htmlhttp://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042.html

I changed the lines

${BPDIR}/fsl_sub_seychelles

for

${FSL_BIN}/fsl_sub

in the bedpostx_seychelles and I could continue, until the script seems to be stuck

Queuing parallel processing stage /volatile/tracula/results/**Diff001/dmri.bedpostX/monitor 0 slices processed 1 slices processed 1 slices processed 1 slices processed <== this line keeps on repeating

Following a suggestion I found on this other archived email http://www.mail-archive.com/**freesurfer@nmr.mgh.harvard.** edu/msg20815.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html I ran bedpostx on the dmri directory and seemed to succeed. I am attaching the output (2-bedpostx-dmri.txt).

Then I tried to run trac-all -path but it stops with the following error:

niiRead(): error opening file /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_** ph1samples.nii.gz ERROR: Could not read /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_** ph1samples.nii.gz

I searched for that file everywhere but it doesn't exist. The closest I found was

results/Diff001/dmri.bedpostX/**merged_ph2samples.nii.gz

Just in case I tried once again to run trac-all -bedp and this time, after having run bedpostx on the dmri directory, I get the following error (the whole output is in the attached 4-error-trac-all-bedp-2.txt file):

[...] slice 62 has already been processed slice 63 has already been processed wc: /volatile/tracula/results/**Diff001/dmri.bedpostX/**commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 390: No such process

I tried searching for a file named commands.txt but I couldn't find any.

Here is the output of bugr:

FREESURFER_HOME: /i2bm/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.38-14-generic x86_64

and the output of source $FREESURFER_HOME/**SetUpFreeSurfer.sh

-------- freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /i2bm/local/freesurfer FSFAST_HOME /i2bm/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /volatile/tracula/data/**buckner_data/tutorial_subjs/ MNI_DIR /i2bm/local/freesurfer/mni FSL_DIR /usr/share/fsl/4.1

Thanks in advance for your help, any hint would be highly appreciated.

Best,

Sergio.

-- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85

---

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.

What a coincide! Our teams have both chosen the same release cycle strategy :P

I ran bedpostx_postproc and I've got so many errors that makes me think the problem is before this step (see output in attached n1-bedpostx-postproc.txt).

So, I ran again bedpostx on the dmri directory, which the first run *seemed* to finish and didn't throw any error (I attached the output in the first email). This run did finish, and it did throw errors (full output in n2-bedpostx-dmri.txt):

*[...]* *slice 63 has already been processed wc: /volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 276: No such process*

Then I started wondering whether I do have the right data to actually run bedpostx, so I run the script that checks that: bedpostx_datacheck, the output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I would like to assume everything is ok with the input data...

Any idea?

Thanks, once again.

Sergio.

2012/7/27 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

Hi Sergio - As with any imminent new version release, it's happening "soon". I'd say in a month, I'm just not sure a month from when :P

The fact that the temporary files (everything with *slice* in the name) are still in your bedpostx directory means that bedpostx didn't finish running properly. You can try running the last step of bedpostx and see if you get any error messages that give you any clues: bedpostx_postproc.sh /volatile/tracula/results/**Diff001/dmri

Normally this step merges the individual slices into volumes and deletes the temporary files. If all else fails, I'd ask the FSL gurus.

Hope this helps, a.y

On Fri, 27 Jul 2012, Sergio Medina wrote:

Anastasia,

...

Thanks for such a quick reply!

Please find my answers inline...

2012/7/26 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

  Hi Sergio - Thank you for your kind words, and also thank you
  for taking the time to search the archives for answers!


  The first problems you had with running bedpostx through
  trac-all have to do with trac-all assuming an older version of
  FSL than the current one, and this'll be fixed in the upcoming
  release of trac-all. Indeed the thing to do in the meantime is
  to run bedpostx by itself, as you did. I apologize for the
  inconvenience.

Great! By any chance, do you know when that release will happen?

  About the problem you had when you ran bedpostx directly: do you
  get the other outputs of bedpostx, listed here? Are there any
  other, temporary files left over as well?
          http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.html<http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html>

I have all of them, except for nodif_brain. And I only have the ones with i=2 while I should have the ones with i=1 too. Attached you can find two files, the output of ls -Rah on both dmri and dmri.bedpostX directories.

  The merged_ph?samples are the orientation angles of the each of
  the two anisotropic compartments ("sticks", "fibers", whatever
  you want to call them) that bedpostx fit in each voxel. So "1"
  is the orientation angle of the largest stick/fiber, and "2" the
  one of the 2nd largest. If there's a "2", there should be a "1"!

But there are not :(

  Also, I looked at your dmrirc file and noticed that you
  decreased the # of control points b/c you hate waiting :) I just
  wanted to warn you that decreasing that # might make you wait
  longer b/c make fitting a spline with fewer control points to
  initialize the algorithm is sometimes more challenging.

Hehe, thanks! I changed it back to 5 now...

Thanks!

Sergio.

  Hope this helps,
  a.y

  On Thu, 26 Jul 2012, Sergio Medina wrote:

  Hi!

  First of all let me thank you for having put at our
  disposal such great
  tools as FreeSurfer and Tracula!
  I am trying to run Tracula on the sample data that is on
  the website, but
  I've been running into some issues.
  I am attaching the configuration file just in case
  (dmrirc_single_subject-serch).

  The first step "trac-all -prep" seems to run fine.
  The first problem comes with the second step "trac-all
  -bedp". The complete
  trace is included in the attached file
  1-error-trac-all-bedp.txt

After finding this on the FreeSurfer mailinglisthttps://mail.nmr.** mgh.harvard.edu/pipermail//**freesurfer/2012-May/024042http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042 . html I changed the lines

${BPDIR}/fsl_sub_seychelles

for

${FSL_BIN}/fsl_sub

in the bedpostx_seychelles and I could continue, until the script seems to be stuck

Queuing parallel processing stage /volatile/tracula/results/**Diff001/dmri.bedpostX/monitor 0 slices processed 1 slices processed 1 slices processed 1 slices processed <== this line keeps on repeating

Following a suggestion I found on this other archived email http://www.mail-archive.com/**freesurfer@nmr.mgh.harvard.** edu/msg20815.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html I ran bedpostx on the dmri directory and seemed to succeed. I am attaching the output (2-bedpostx-dmri.txt).

Then I tried to run trac-all -path but it stops with the following error:

niiRead(): error opening file /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_** ph1samples.nii.gz ERROR: Could not read /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_** ph1samples.nii.gz

I searched for that file everywhere but it doesn't exist. The closest I found was

results/Diff001/dmri.bedpostX/**merged_ph2samples.nii.gz

Just in case I tried once again to run trac-all -bedp and this time, after having run bedpostx on the dmri directory, I get the following error (the whole output is in the attached 4-error-trac-all-bedp-2.txt file):

[...] slice 62 has already been processed slice 63 has already been processed wc: /volatile/tracula/results/**Diff001/dmri.bedpostX/**commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 390: No such process

I tried searching for a file named commands.txt but I couldn't find any.

Here is the output of bugr:

FREESURFER_HOME: /i2bm/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.38-14-generic x86_64

and the output of source $FREESURFER_HOME/**SetUpFreeSurfer.sh

-------- freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0

Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /i2bm/local/freesurfer FSFAST_HOME /i2bm/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /volatile/tracula/data/**buckner_data/tutorial_subjs/ MNI_DIR /i2bm/local/freesurfer/mni FSL_DIR /usr/share/fsl/4.1

Thanks in advance for your help, any hint would be highly appreciated.

Best,

Sergio.

-- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85

______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.

-- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85

Nope, I have the same files as before :(

2012/7/27 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

The monitoring script that bedpostx runs and tells you if things have or haven't finished properly can't always be trusted. So if that's the only error message you see, I wouldn't worry about it. Have the *ph1* and *th1* files appeared this time?

On Fri, 27 Jul 2012, Sergio Medina wrote:

What a coincide! Our teams have both chosen the same release cycle

...

strategy :P

I ran bedpostx_postproc and I've got so many errors that makes me think the problem is before this step (see output in attached n1-bedpostx-postproc.txt).

So, I ran again bedpostx on the dmri directory, which the first run *seemed* to finish and didn't throw any error (I attached the output in the first email). This run did finish, and it did throw errors (full output in n2-bedpostx-dmri.txt):

[...] slice 63 has already been processed wc: /volatile/tracula/results/**Diff001/dmri.bedpostX/**commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 276: No such process

Then I started wondering whether I do have the right data to actually run bedpostx, so I run the script that checks that: bedpostx_datacheck, the output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I would like to assume everything is ok with the input data...

Any idea?

Thanks, once again.

Sergio.

2012/7/27 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

  Hi Sergio - As with any imminent new version release, it's
  happening "soon". I'd say in a month, I'm just not sure a month
  from when :P

  The fact that the temporary files (everything with *slice* in
  the name) are still in your bedpostx directory means that
  bedpostx didn't finish running properly. You can try running the
  last step of bedpostx and see if you get any error messages that
  give you any clues:
          bedpostx_postproc.sh
  /volatile/tracula/results/**Diff001/dmri

  Normally this step merges the individual slices into volumes and
  deletes the temporary files. If all else fails, I'd ask the FSL
  gurus.

  Hope this helps,
  a.y

  On Fri, 27 Jul 2012, Sergio Medina wrote:

        Anastasia,

        Thanks for such a quick reply!

        Please find my answers inline...

        2012/7/26 Anastasia Yendiki
        <ayendiki@nmr.mgh.harvard.edu>

              Hi Sergio - Thank you for your kind words, and
        also thank you
              for taking the time to search the archives for
        answers!


              The first problems you had with running
        bedpostx through
              trac-all have to do with trac-all assuming an
        older version of
              FSL than the current one, and this'll be fixed
        in the upcoming
              release of trac-all. Indeed the thing to do in
        the meantime is
              to run bedpostx by itself, as you did. I
        apologize for the
              inconvenience.


        Great! By any chance, do you know when that release
        will happen?


              About the problem you had when you ran
        bedpostx directly: do you
              get the other outputs of bedpostx, listed
        here? Are there any
              other, temporary files left over as well?

        http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.html<http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html>



        I have all of them, except for nodif_brain. And I
        only have the ones with
        i=2 while I should have the ones with i=1 too.
        Attached you can find two files, the output of ls
        -Rah on both dmri and
        dmri.bedpostX directories.




              The merged_ph?samples are the orientation
        angles of the each of
              the two anisotropic compartments ("sticks",
        "fibers", whatever
              you want to call them) that bedpostx fit in
        each voxel. So "1"
              is the orientation angle of the largest
        stick/fiber, and "2" the
              one of the 2nd largest. If there's a "2",
        there should be a "1"!


        But there are not :(


              Also, I looked at your dmrirc file and noticed
        that you
              decreased the # of control points b/c you hate
        waiting :) I just
              wanted to warn you that decreasing that #
        might make you wait
              longer b/c make fitting a spline with fewer
        control points to
              initialize the algorithm is sometimes more
        challenging.


        Hehe, thanks! I changed it back to 5 now...

        Thanks!

        Sergio.


              Hope this helps,
              a.y

              On Thu, 26 Jul 2012, Sergio Medina wrote:

              Hi!

              First of all let me thank you for having put
        at our
              disposal such great
              tools as FreeSurfer and Tracula!
              I am trying to run Tracula on the sample data
        that is on
              the website, but
              I've been running into some issues.
              I am attaching the configuration file just in
        case
              (dmrirc_single_subject-serch).

              The first step "trac-all -prep" seems to run
        fine.
              The first problem comes with the second step
        "trac-all
              -bedp". The complete
              trace is included in the attached file
              1-error-trac-all-bedp.txt
        After finding this on the FreeSurfermailinglisthttps://m**

ail.nmr.mgh.harvard.edu/**pipermail//freesurfer/2012-**May/http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/ 024042. html I changed the lines

        ${BPDIR}/fsl_sub_seychelles

        for

        ${FSL_BIN}/fsl_sub

        in the bedpostx_seychelles and I could continue,
        until the
        script seems to
        be stuck

        Queuing parallel processing stage
        /volatile/tracula/results/**Diff001/dmri.bedpostX/monitor
        0 slices processed
        1 slices processed
        1 slices processed
        1 slices processed <== this line keeps on repeating

        Following a suggestion I found on this other
        archived email
        http://www.mail-archive.com/**freesurfer@nmr.mgh.harvard.**

edu/msg20815.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html I ran bedpostx on the dmri directory and seemed to succeed. I am attaching the output (2-bedpostx-dmri.txt).

        Then I tried to run  trac-all -path but it stops
        with the
        following error:

        niiRead(): error opening file
        /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_**

ph1samples.nii.gz ERROR: Could not read /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_** ph1samples.nii.gz

        I searched for that file everywhere but it doesn't
        exist. The
        closest I
        found was

        results/Diff001/dmri.bedpostX/**merged_ph2samples.nii.gz

        Just in case I tried once again to run trac-all
        -bedp and this
        time, after
        having run bedpostx on the dmri directory, I get the
        following
        error (the
        whole output is in the attached
        4-error-trac-all-bedp-2.txt
        file):

        [...]
        slice 62 has already been processed
        slice 63 has already been processed
        wc:
        /volatile/tracula/results/**Diff001/dmri.bedpostX/**

commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 390: No such process

        I tried searching for a file named commands.txt but
        I couldn't
        find any.

        Here is the output of bugr:

        FREESURFER_HOME: /i2bm/local/freesurfer
        Build stamp:
        freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
        Debian version: squeeze/sid
        Kernel info: Linux 2.6.38-14-generic x86_64

        and the output of source
        $FREESURFER_HOME/**SetUpFreeSurfer.sh

        --------
        freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
        --------
        Setting up environment for FreeSurfer/FS-FAST (and
        FSL)
        FREESURFER_HOME   /i2bm/local/freesurfer
        FSFAST_HOME       /i2bm/local/freesurfer/fsfast
        FSF_OUTPUT_FORMAT nii.gz
        SUBJECTS_DIR
        /volatile/tracula/data/**buckner_data/tutorial_subjs/
        MNI_DIR           /i2bm/local/freesurfer/mni
        FSL_DIR           /usr/share/fsl/4.1


        Thanks in advance for your help, any hint would be
        highly
        appreciated.

        Best,

        Sergio.

        --
        Sergio Medina
        Engineer
        INRIA Parietal - Neurospin
        Bât 145, Point Courrier 156
        91191 Gif/Yvette, France
        Tel.: (+33) 1 69 08 80 85



        ______________________________**_________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**

freesurfer 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<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.




        --
        Sergio Medina
        Engineer
        INRIA Parietal - Neurospin
        Bât 145, Point Courrier 156
        91191 Gif/Yvette, France
        Tel.: (+33) 1 69 08 80 85

-- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85

Ok I will. Thanks for your help! :)

Sergio.

2012/7/30 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

Hi Sergio - Sorry, if this occurs independently of trac-all, whenever you run bedpostx directly, you're better off asking for help on the FSL list. We've never run into this problem with bedpostx up till now.

a.y

On Mon, 30 Jul 2012, Sergio Medina wrote:

Nope, I have the same files as before :(

...

2012/7/27 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

  The monitoring script that bedpostx runs and tells you if things
  have or haven't finished properly can't always be trusted. So if
  that's the only error message you see, I wouldn't worry about
  it. Have the *ph1* and *th1* files appeared this time?

  On Fri, 27 Jul 2012, Sergio Medina wrote:

        What a coincide! Our teams have both chosen the same
        release cycle strategy
        :P

        I ran bedpostx_postproc and I've got so many errors
        that makes me think the
        problem is before this step (see output in attached
        n1-bedpostx-postproc.txt).

        So, I ran again bedpostx on the dmri directory,
        which the first run *seemed*
        to finish and didn't throw any error (I attached the
        output in the first
        email).
        This run did finish, and it did throw errors (full
        output in
        n2-bedpostx-dmri.txt):

        [...]
        slice 63 has already been processed
        wc:
        /volatile/tracula/results/**Diff001/dmri.bedpostX/**

commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 276: No such process

        Then I started wondering whether I do have the right
        data to actually run
        bedpostx, so I run the script that checks that:
        bedpostx_datacheck, the
        output (n3-bedpostx-datacheck.txt) doesn't show any
        signs of errors so I
        would like to assume everything is ok with the input
        data...

        Any idea?

        Thanks, once again.

        Sergio.


        2012/7/27 Anastasia Yendiki
        <ayendiki@nmr.mgh.harvard.edu>

              Hi Sergio - As with any imminent new version
        release, it's
              happening "soon". I'd say in a month, I'm just
        not sure a month
              from when :P

              The fact that the temporary files (everything
        with *slice* in
              the name) are still in your bedpostx directory
        means that
              bedpostx didn't finish running properly. You
        can try running the
              last step of bedpostx and see if you get any
        error messages that
              give you any clues:
                      bedpostx_postproc.sh
              /volatile/tracula/results/**Diff001/dmri

              Normally this step merges the individual
        slices into volumes and
              deletes the temporary files. If all else
        fails, I'd ask the FSL
              gurus.

              Hope this helps,
              a.y

              On Fri, 27 Jul 2012, Sergio Medina wrote:

                    Anastasia,

                    Thanks for such a quick reply!

                    Please find my answers inline...

                    2012/7/26 Anastasia Yendiki
                    <ayendiki@nmr.mgh.harvard.edu>

                          Hi Sergio - Thank you for your
        kind words, and
                    also thank you
                          for taking the time to search the
        archives for
                    answers!


                          The first problems you had with
        running
                    bedpostx through
                          trac-all have to do with trac-all
        assuming an
                    older version of
                          FSL than the current one, and
        this'll be fixed
                    in the upcoming
                          release of trac-all. Indeed the
        thing to do in
                    the meantime is
                          to run bedpostx by itself, as you
        did. I
                    apologize for the
                          inconvenience.


                    Great! By any chance, do you know when
        that release
                    will happen?


                          About the problem you had when you
        ran
                    bedpostx directly: do you
                          get the other outputs of bedpostx,
        listed
                    here? Are there any
                          other, temporary files left over
        as well?


        http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.html<http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html>



                    I have all of them, except for
        nodif_brain. And I
                    only have the ones with
                    i=2 while I should have the ones with
        i=1 too.
                    Attached you can find two files, the
        output of ls
                    -Rah on both dmri and
                    dmri.bedpostX directories.




                          The merged_ph?samples are the
        orientation
                    angles of the each of
                          the two anisotropic compartments
        ("sticks",
                    "fibers", whatever
                          you want to call them) that
        bedpostx fit in
                    each voxel. So "1"
                          is the orientation angle of the
        largest
                    stick/fiber, and "2" the
                          one of the 2nd largest. If there's
        a "2",
                    there should be a "1"!


                    But there are not :(


                          Also, I looked at your dmrirc file
        and noticed
                    that you
                          decreased the # of control points
        b/c you hate
                    waiting :) I just
                          wanted to warn you that decreasing
        that #
                    might make you wait
                          longer b/c make fitting a spline
        with fewer
                    control points to
                          initialize the algorithm is
        sometimes more
                    challenging.


                    Hehe, thanks! I changed it back to 5
        now...

                    Thanks!

                    Sergio.


                          Hope this helps,
                          a.y

                          On Thu, 26 Jul 2012, Sergio Medina
        wrote:

                          Hi!

                          First of all let me thank you for
        having put
                    at our
                          disposal such great
                          tools as FreeSurfer and Tracula!
                          I am trying to run Tracula on the
        sample data
                    that is on
                          the website, but
                          I've been running into some
        issues.
                          I am attaching the configuration
        file just in
                    case
                          (dmrirc_single_subject-serch).

                          The first step "trac-all -prep"
        seems to run
                    fine.
                          The first problem comes with the
        second step
                    "trac-all
                          -bedp". The complete
                          trace is included in the attached
        file
                          1-error-trac-all-bedp.txt
                    After finding this on

theFreeSurfermailinglisthttps:**//mail.nmr.mgh.harvard.edu/** pipermail//freesurferhttp://mail.nmr.mgh.harvard.edu/pipermail//freesurfer /2012-May/ 024042. html I changed the lines

                    ${BPDIR}/fsl_sub_seychelles

                    for

                    ${FSL_BIN}/fsl_sub

                    in the bedpostx_seychelles and I could
        continue,
                    until the
                    script seems to
                    be stuck

                    Queuing parallel processing stage

        /volatile/tracula/results/**Diff001/dmri.bedpostX/monitor
                    0 slices processed
                    1 slices processed
                    1 slices processed
                    1 slices processed <== this line keeps
        on repeating

                    Following a suggestion I found on this
        other
                    archived email

        http://www.mail-archive.com/**freesurfer@nmr.mgh.harvard.**

edu/msg20815.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html I ran bedpostx on the dmri directory and seemed to succeed. I am attaching the output (2-bedpostx-dmri.txt).

                    Then I tried to run  trac-all -path but
        it stops
                    with the
                    following error:

                    niiRead(): error opening file

        /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_**

ph1samples.nii.gz ERROR: Could not read

        /volatile/tracula/results/**Diff001/dmri.bedpostX/merged_**

ph1samples.nii.gz

                    I searched for that file everywhere but
        it doesn't
                    exist. The
                    closest I
                    found was


        results/Diff001/dmri.bedpostX/**merged_ph2samples.nii.gz

                    Just in case I tried once again to run
        trac-all
                    -bedp and this
                    time, after
                    having run bedpostx on the dmri
        directory, I get the
                    following
                    error (the
                    whole output is in the attached
                    4-error-trac-all-bedp-2.txt
                    file):

                    [...]
                    slice 62 has already been processed
                    slice 63 has already been processed
                    wc:

        /volatile/tracula/results/**Diff001/dmri.bedpostX/**

commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 390: No such process

                    I tried searching for a file named
        commands.txt but
                    I couldn't
                    find any.

                    Here is the output of bugr:

                    FREESURFER_HOME: /i2bm/local/freesurfer
                    Build stamp:

        freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
                    Debian version: squeeze/sid
                    Kernel info: Linux 2.6.38-14-generic
        x86_64

                    and the output of source
                    $FREESURFER_HOME/**SetUpFreeSurfer.sh

                    --------

        freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
                    --------
                    Setting up environment for
        FreeSurfer/FS-FAST (and
                    FSL)
                    FREESURFER_HOME   /i2bm/local/freesurfer
                    FSFAST_HOME
        /i2bm/local/freesurfer/fsfast
                    FSF_OUTPUT_FORMAT nii.gz
                    SUBJECTS_DIR

        /volatile/tracula/data/**buckner_data/tutorial_subjs/
                    MNI_DIR
        /i2bm/local/freesurfer/mni
                    FSL_DIR           /usr/share/fsl/4.1


                    Thanks in advance for your help, any
        hint would be
                    highly
                    appreciated.

                    Best,

                    Sergio.

                    --
                    Sergio Medina
                    Engineer
                    INRIA Parietal - Neurospin
                    Bât 145, Point Courrier 156
                    91191 Gif/Yvette, France
                    Tel.: (+33) 1 69 08 80 85




        ______________________________**_________________
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                    The information in this e-mail is
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                    it is
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        was sent to
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                    contains patient information, please
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                    --
                    Sergio Medina
                    Engineer
                    INRIA Parietal - Neurospin
                    Bât 145, Point Courrier 156
                    91191 Gif/Yvette, France
                    Tel.: (+33) 1 69 08 80 85





        --
        Sergio Medina
        Engineer
        INRIA Parietal - Neurospin
        Bât 145, Point Courrier 156
        91191 Gif/Yvette, France
        Tel.: (+33) 1 69 08 80 85

-- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85

Well, when the current version of tracula was being developped we had FSL 4.1.5 installed here. But now that the next version (you know, the one that will be available "soon") is being developped we have FSL 4.1.9. So I'd suggest going with the latest version of FSL. The only thing that should give you trouble with the latest version of FSL until the next version of trac-all is released will be the trac-all -bedp step.

On Tue, 31 Jul 2012, Sergio Medina wrote:

Anastasia,

We might try installing FSL + FreeSurfer in another machine, because the one we were using was too slow anyway. Would you mind telling us exactly which versions of FreeSurfer and FSL I need to install? As I will mostly/only use Tracula then I would rather install the version of FSL that you used to develop and test Tracula.

Thanks,

Sergio.

2012/7/31 Sergio Medina sergio.medina@inria.fr Ok I will. Thanks for your help! :)

  Sergio.

2012/7/30 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

  Hi Sergio - Sorry, if this occurs independently of
  trac-all, whenever you run bedpostx directly, you're
  better off asking for help on the FSL list. We've never
  run into this problem with bedpostx up till now.

  a.y

  On Mon, 30 Jul 2012, Sergio Medina wrote:

        Nope, I have the same files as before :(

        2012/7/27 Anastasia Yendiki
        <ayendiki@nmr.mgh.harvard.edu>

              The monitoring script that bedpostx runs
        and tells you if things
              have or haven't finished properly can't
        always be trusted. So if
              that's the only error message you see, I
        wouldn't worry about
              it. Have the *ph1* and *th1* files
        appeared this time?

              On Fri, 27 Jul 2012, Sergio Medina
        wrote:

                    What a coincide! Our teams have
        both chosen the same
                    release cycle strategy
                    :P

                    I ran bedpostx_postproc and I've
        got so many errors
                    that makes me think the
                    problem is before this step (see
        output in attached
                    n1-bedpostx-postproc.txt).

                    So, I ran again bedpostx on the
        dmri directory,
                    which the first run *seemed*
                    to finish and didn't throw any
        error (I attached the
                    output in the first
                    email).
                    This run did finish, and it did
        throw errors (full
                    output in
                    n2-bedpostx-dmri.txt):

                    [...]
                    slice 63 has already been
        processed
                    wc:
                   
        /volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt:
                    No such
                    file or directory
                    Queuing post processing stage
                    64 slices processed
                    For some reason the bedpostX
        process DOES NOT appear
                    to have successfully completed.
        Please examine your
                    results carefully.
                    kill: 276: No such process

                    Then I started wondering whether I
        do have the right
                    data to actually run
                    bedpostx, so I run the script that
        checks that:
                    bedpostx_datacheck, the
                    output (n3-bedpostx-datacheck.txt)
        doesn't show any
                    signs of errors so I
                    would like to assume everything is
        ok with the input
                    data...

                    Any idea?

                    Thanks, once again.

                    Sergio.


                    2012/7/27 Anastasia Yendiki
                    <ayendiki@nmr.mgh.harvard.edu>

                          Hi Sergio - As with any
        imminent new version
                    release, it's
                          happening "soon". I'd say in
        a month, I'm just
                    not sure a month
                          from when :P

                          The fact that the temporary
        files (everything
                    with *slice* in
                          the name) are still in your
        bedpostx directory
                    means that
                          bedpostx didn't finish
        running properly. You
                    can try running the
                          last step of bedpostx and
        see if you get any
                    error messages that
                          give you any clues:
                                  bedpostx_postproc.sh
                         
        /volatile/tracula/results/Diff001/dmri

                          Normally this step merges
        the individual
                    slices into volumes and
                          deletes the temporary files.
        If all else
                    fails, I'd ask the FSL
                          gurus.

                          Hope this helps,
                          a.y

                          On Fri, 27 Jul 2012, Sergio
        Medina wrote:

                                Anastasia,

                                Thanks for such a
        quick reply!

                                Please find my answers
        inline...

                                2012/7/26 Anastasia
        Yendiki
                               
        <ayendiki@nmr.mgh.harvard.edu>

                                      Hi Sergio -
        Thank you for your
                    kind words, and
                                also thank you
                                      for taking the
        time to search the
                    archives for
                                answers!


                                      The first
        problems you had with
                    running
                                bedpostx through
                                      trac-all have to
        do with trac-all
                    assuming an
                                older version of
                                      FSL than the
        current one, and
                    this'll be fixed
                                in the upcoming
                                      release of
        trac-all. Indeed the
                    thing to do in
                                the meantime is
                                      to run bedpostx
        by itself, as you
                    did. I
                                apologize for the
                                      inconvenience.


                                Great! By any chance,
        do you know when
                    that release
                                will happen?
                                 

                                      About the
        problem you had when you
                    ran
                                bedpostx directly: do
        you
                                      get the other
        outputs of bedpostx,
                    listed
                                here? Are there any
                                      other, temporary
        files left over
                    as well?
                                             
                               
                   
        http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html



                                I have all of them,
        except for
                    nodif_brain. And I
                                only have the ones
        with
                                i=2 while I should
        have the ones with
                    i=1 too.
                                Attached you can find
        two files, the
                    output of ls
                                -Rah on both dmri and
                                dmri.bedpostX
        directories.

                                 


                                      The
        merged_ph?samples are the
                    orientation
                                angles of the each of
                                      the two
        anisotropic compartments
                    ("sticks",
                                "fibers", whatever
                                      you want to call
        them) that
                    bedpostx fit in
                                each voxel. So "1"
                                      is the
        orientation angle of the
                    largest
                                stick/fiber, and "2"
        the
                                      one of the 2nd
        largest. If there's
                    a "2",
                                there should be a "1"!


                                But there are not :(
                                 

                                      Also, I looked
        at your dmrirc file
                    and noticed
                                that you
                                      decreased the #
        of control points
                    b/c you hate
                                waiting :) I just
                                      wanted to warn
        you that decreasing
                    that #
                                might make you wait
                                      longer b/c make
        fitting a spline
                    with fewer
                                control points to
                                      initialize the
        algorithm is
                    sometimes more
                                challenging.


                                Hehe, thanks! I
        changed it back to 5
                    now...
                                 
                                Thanks!

                                Sergio.


                                      Hope this helps,
                                      a.y

                                      On Thu, 26 Jul
        2012, Sergio Medina
                    wrote:

                                      Hi!

                                      First of all let
        me thank you for
                    having put
                                at our
                                      disposal such
        great
                                      tools as
        FreeSurfer and Tracula!
                                      I am trying to
        run Tracula on the
                    sample data
                                that is on
                                      the website, but
                                      I've been
        running into some
                    issues.
                                      I am attaching
        the configuration
                    file just in
                                case
                                     
        (dmrirc_single_subject-serch).

                                      The first step
        "trac-all -prep"
                    seems to run
                                fine.
                                      The first
        problem comes with the
                    second step
                                "trac-all
                                      -bedp". The
        complete
                                      trace is
        included in the attached
                    file
                                     
        1-error-trac-all-bedp.txt
                                After finding this ontheFreeSurfermailinglisthttps://mail.nmr.mgh.harvard.edu/pipermail//freesur
        fer
                    /2012-May/
                                024042.
                                html
                                I changed the lines

                               
        ${BPDIR}/fsl_sub_seychelles

                                for

                                ${FSL_BIN}/fsl_sub

                                in the
        bedpostx_seychelles and I could
                    continue,
                                until the
                                script seems to
                                be stuck

                                Queuing parallel
        processing stage
                               
                   
        /volatile/tracula/results/Diff001/dmri.bedpostX/monitor
                                0 slices processed
                                1 slices processed
                                1 slices processed
                                1 slices processed <==
        this line keeps
                    on repeating

                                Following a suggestion
        I found on this
                    other
                                archived email
                               
                   
        http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html
                                I ran bedpostx on the
        dmri directory and
                    seemed to
                                succeed. I am
                                attaching
                                the output
        (2-bedpostx-dmri.txt).

                                Then I tried to run 
        trac-all -path but
                    it stops
                                with the
                                following error:

                                niiRead(): error
        opening file
                               
                   
        /volatile/tracula/results/Diff001/dmri.bedpostX/merged_ph1samples.nii.gz
                                ERROR: Could not read
                               
                   
        /volatile/tracula/results/Diff001/dmri.bedpostX/merged_ph1samples.nii.gz

                                I searched for that
        file everywhere but
                    it doesn't
                                exist. The
                                closest I
                                found was

                               
                   
        results/Diff001/dmri.bedpostX/merged_ph2samples.nii.gz

                                Just in case I tried
        once again to run
                    trac-all
                                -bedp and this
                                time, after
                                having run bedpostx on
        the dmri
                    directory, I get the
                                following
                                error (the
                                whole output is in the
        attached
                               
        4-error-trac-all-bedp-2.txt
                                file):

                                [...]
                                slice 62 has already
        been processed
                                slice 63 has already
        been processed
                                wc:
                               
                   
        /volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt:
                                No
                                such
                                file or directory
                                Queuing post
        processing stage
                                64 slices processed
                                For some reason the
        bedpostX process
                    DOES NOT appear
                                to have successfully
        completed. Please
                    examine your
                                results carefully.
                                kill: 390: No such
        process

                                I tried searching for
        a file named
                    commands.txt but
                                I couldn't
                                find any.

                                Here is the output of
        bugr:

                                FREESURFER_HOME:
        /i2bm/local/freesurfer
                                Build stamp:
                               
                   
        freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
                                Debian version:
        squeeze/sid
                                Kernel info: Linux
        2.6.38-14-generic
                    x86_64

                                and the output of
        source
                               
        $FREESURFER_HOME/SetUpFreeSurfer.sh

                                --------
                               
                   
        freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
                                --------
                                Setting up environment
        for
                    FreeSurfer/FS-FAST (and
                                FSL)
                                FREESURFER_HOME  
        /i2bm/local/freesurfer
                                FSFAST_HOME      
                    /i2bm/local/freesurfer/fsfast
                                FSF_OUTPUT_FORMAT
        nii.gz
                                SUBJECTS_DIR     
                               
                   
        /volatile/tracula/data/buckner_data/tutorial_subjs/
                                MNI_DIR          
                    /i2bm/local/freesurfer/mni
                                FSL_DIR          
        /usr/share/fsl/4.1


                                Thanks in advance for
        your help, any
                    hint would be
                                highly
                                appreciated.

                                Best,

                                Sergio.

                                --
                                Sergio Medina
                                Engineer
                                INRIA Parietal -
        Neurospin
                                Bât 145, Point
        Courrier 156
                                91191 Gif/Yvette,
        France
                                Tel.: (+33) 1 69 08 80
        85



                               
                   
        _______________________________________________
                                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.




                                --
                                Sergio Medina
                                Engineer
                                INRIA Parietal -
        Neurospin
                                Bât 145, Point
        Courrier 156
                                91191 Gif/Yvette,
        France
                                Tel.: (+33) 1 69 08 80
        85





                    --
                    Sergio Medina
                    Engineer
                    INRIA Parietal - Neurospin
                    Bât 145, Point Courrier 156
                    91191 Gif/Yvette, France
                    Tel.: (+33) 1 69 08 80 85





        --
        Sergio Medina
        Engineer
        INRIA Parietal - Neurospin
        Bât 145, Point Courrier 156
        91191 Gif/Yvette, France
        Tel.: (+33) 1 69 08 80 85

-- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85

---

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.

-- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85