Indeed. It's actually really easy to set up, too. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.htm... http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-...

---

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapereira@gmail.com] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Dear Anastasia and FreeSurfers,

I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc:

INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue "short.q". Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue "long.q". Exiting. Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue "long.q". Exiting.

Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks.

You will get an email at the end of the post-processing stage.

So far no slices have been processed. Does anyone know how to solve it?

Thanks!

---

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.

A. You should overlay the tracts on the subject's FA (see example command line on wiki) B. Check the mailing list archives about reinitializing tracts. That should improve the results here. You don't need to reinitialize the tracts that are already correct (although none of yours look particularly good).

Is this a noisy dataset or something?

________________________________________ From: Joana Braga Pereira [jbragapereira@gmail.com] Sent: Thursday, September 05, 2013 9:32 AM To: Watson, Christopher Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi,

Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the tracts were not properly reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently from the ones proposed on Tracula website?

Any help will be greatly appreciated!

Thanks,

joana

2013/9/2 Watson, Christopher <Christopher.Watson@childrens.harvard.edumailto:Christopher.Watson@childrens.harvard.edu> Indeed. It's actually really easy to set up, too. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edumailto:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.htm... http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-...

---

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapereira@gmail.commailto:jbragapereira@gmail.com] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Dear Anastasia and FreeSurfers,

I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc:

INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue "short.q". Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue "long.q". Exiting. Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue "long.q". Exiting.

Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks.

You will get an email at the end of the post-processing stage.

So far no slices have been processed. Does anyone know how to solve it?

Thanks!

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

Try this: http://www.mail-archive.com/search?q=reinit&l=freesurfer%40nmr.mgh.harva... ________________________________________ From: Joana Braga Pereira [jbragapereira@gmail.com] Sent: Thursday, September 05, 2013 9:51 AM To: Watson, Christopher Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi Christopher,

Thanks a lot for such a prompt reply.

I know I should overlay the tracts of the FA image, but I just wanted to show you how small the reconsctrutions were.

I don't think this is particularly noisy data.

I'm trying to find solutions on the mailing list archives by typing "reinitializing tracts Tracula" but I haven't found much information.

Would you kindly suggest me a few that provide solutions to this problem or make some recommendations yourself?

Thanks again,

joana

2013/9/5 Watson, Christopher <Christopher.Watson@childrens.harvard.edumailto:Christopher.Watson@childrens.harvard.edu> A. You should overlay the tracts on the subject's FA (see example command line on wiki) B. Check the mailing list archives about reinitializing tracts. That should improve the results here. You don't need to reinitialize the tracts that are already correct (although none of yours look particularly good).

Is this a noisy dataset or something?

________________________________________ From: Joana Braga Pereira [jbragapereira@gmail.commailto:jbragapereira@gmail.com] Sent: Thursday, September 05, 2013 9:32 AM To: Watson, Christopher Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi,

Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the tracts were not properly reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently from the ones proposed on Tracula website?

Any help will be greatly appreciated!

Thanks,

joana

2013/9/2 Watson, Christopher <Christopher.Watson@childrens.harvard.edumailto:Christopher.Watson@childrens.harvard.edu<mailto:Christopher.Watson@childrens.harvard.edumailto:Christopher.Watson@childrens.harvard.edu>> Indeed. It's actually really easy to set up, too. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edumailto:ayendiki@nmr.mgh.harvard.edu<mailto:ayendiki@nmr.mgh.harvard.edumailto:ayendiki@nmr.mgh.harvard.edu>] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

This is an FSL problem. You can try the FSL list, and check out some links: https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.htm... http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-...

---

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Joana Braga Pereira [jbragapereira@gmail.commailto:jbragapereira@gmail.com<mailto:jbragapereira@gmail.commailto:jbragapereira@gmail.com>] Sent: Monday, September 02, 2013 9:53 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Dear Anastasia and FreeSurfers,

I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc:

INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue "short.q". Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue "long.q". Exiting. Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue "long.q". Exiting.

Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks.

You will get an email at the end of the post-processing stage.

So far no slices have been processed. Does anyone know how to solve it?

Thanks!

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto: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.

Hi Anastasia,

Thanks! I checked dtifit_FA and did the overlay with V1.

They don't look ok to me (see attached picture). Any suggestions on how to solve this? Perhaps by modifying any of the previous steps?

Thanks!

2013/9/5 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

Hm, this looks uniformly bad. Have you checked that the gradient directions are correct? You can check that by looking at the eigenvectors from the tensor fit that's done as part of the preprocessing. Although tracula doesn't use tensors for tractography, it's a quick way to check that your inputs are correct.

In fslview, overlay dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz, and display dtifit_V1 as lines. Then make sure that the lines follow the basic anatomy e.g. in the corpus callosum (L-R), cingulum (A-P), corticospinal tract (I-S).

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Hi,

...

Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_**bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the tracts were not properly reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently from the ones proposed on Tracula website?

Any help will be greatly appreciated!

Thanks,

joana

2013/9/2 Watson, Christopher <Christopher.Watson@childrens.**harvard.eduChristopher.Watson@childrens.harvard.edu

...

  Indeed. It's actually really easy to set up, too.
  ______________________________**__________
  From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu]
  Sent: Monday, September 02, 2013 3:46 PM
  To: Watson, Christopher
  Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q",

"short.q"

  Thanks for the pointers, Chris. I'd call it an "opportunity for FSL
  customization" rather than an "FSL problem" per se :o)

  On Mon, 2 Sep 2013, Watson, Christopher wrote:

  > This is an FSL problem. You can try the FSL list, and check out

some links: > https://www2.fmrib.ox.ac.uk/**phpwiki/index/FslSgehttps://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge > http://neuro.debian.net/blog/**2012/2012-03-09_parallelize_** fsl_with_condor.htmlhttp://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html > http://chrisfilo.tumblr.com/**post/579493955/how-to-** configure-sun-grid-engine-for-**fsl-under-ubuntuhttp://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu > > ______________________________**__________ > From: freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu[ freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapereira@gmail.com] > Sent: Monday, September 02, 2013 9:53 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q" > > Dear Anastasia and FreeSurfers, > > I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: > > INFO: SUBJECTS_DIR is /data-02/joana/Last > INFO: Diffusion root is /data-02/joana/tracula/ > Actual FREESURFER_HOME /usr/local/freesurfer-5.3 > WARN: Running FSL's bedbost locally - this might take a while > WARN: It is recommended to run this step on a cluster > bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/**dmri > subjectdir is /data-02/joana/tracula/XXX/**dmri > Making bedpostx directory structure > Queuing preprocessing stages > Unable to run job: Job was rejected because job requests unknown queue "short.q". > Exiting. > Queuing parallel processing stage > Unable to run job: Job was rejected because job requests unknown queue "long.q". > Exiting. > Queuing post processing stage > Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) > Job was rejected because job requests unknown queue "long.q". > Exiting. > > Type /data-02/joana/tracula/3119/**dmri.bedpostX/monitor to show progress. > Type /data-02/joana/tracula/3119/**dmri.bedpostX/cancel to terminate all the queued tasks. > > You will get an email at the end of the post-processing stage. > > > So far no slices have been processed. Does anyone know how to solve it? > > Thanks! > > ______________________________**_________________ > 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.

Thanks!

I've uploaded those files as well as dmrirc and bvecs and bvals.

Let me know what you think.

2013/9/5 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

Indeed, they look like they're oriented A-P in the corpus callosum and L-R in the cinglulum, when it should be the opposite obviously. This'd mean you'd have to swap things in the gradient table. It's hard to tell for sure from the screenshot though. If you upload the dtifit_FA and dtifit_V1 volumes for me here, I'll look at them: https://gate.nmr.mgh.harvard.**edu/filedrop2/https://gate.nmr.mgh.harvard.edu/filedrop2/

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Hi Anastasia,

...

Thanks! I checked dtifit_FA and did the overlay with V1.

They don't look ok to me (see attached picture). Any suggestions on how to solve this? Perhaps by modifying any of the previous steps?

Thanks!

2013/9/5 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

  Hm, this looks uniformly bad. Have you checked that the gradient

directions are correct? You can check that by looking at the eigenvectors from the tensor fit that's done as part of the preprocessing. Although tracula doesn't use tensors for tractography, it's a quick way to check that your inputs are correct.

  In fslview, overlay dmri/dtifit_V1.nii.gz on dmri/dtifit_FA.nii.gz,

and display dtifit_V1 as lines. Then make sure that the lines follow the basic anatomy e.g. in the corpus callosum (L-R), cingulum (A-P), corticospinal tract (I-S).

  On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

        Hi,
        Thanks for all the replies, I solved the problem I had before.

        However, after finishing the Tracula pre-processing steps I

tried to visualize the tracts by typing:

        freeview -tv CTR01/dpath/merged_avg33_mni_**bbr.mgz

        And, as you can see in the picture I'm attaching to this

email, it seems the tracts were not properly reconstructed.

        Does anyone know why?

        Should I make some changes and for example set the control

points differently from the ones proposed on Tracula website?

        Any help will be greatly appreciated!

        Thanks,

        joana




        2013/9/2 Watson, Christopher <Christopher.Watson@childrens.**

harvard.edu Christopher.Watson@childrens.harvard.edu> Indeed. It's actually really easy to set up, too. ______________________________**__________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

              Thanks for the pointers, Chris. I'd call it an

"opportunity for FSL customization" rather than an "FSL problem" per se :o)

              On Mon, 2 Sep 2013, Watson, Christopher wrote:

              > This is an FSL problem. You can try the FSL list, and

check out some links: > https://www2.fmrib.ox.ac.uk/**phpwiki/index/FslSgehttps://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge > http://neuro.debian.net/blog/**2012/2012-03-09_parallelize_** fsl_with_condor.htmlhttp://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html >

        http://chrisfilo.tumblr.com/**post/579493955/how-to-**

configure-sun-grid-engine-for-**fsl-under-ubuntuhttp://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu > > ______________________________**__________ > From: freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [jbragapereira@gmail.com] > Sent: Monday, September 02, 2013 9:53 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q" > > Dear Anastasia and FreeSurfers, > > I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: > > INFO: SUBJECTS_DIR is /data-02/joana/Last > INFO: Diffusion root is /data-02/joana/tracula/ > Actual FREESURFER_HOME /usr/local/freesurfer-5.3 > WARN: Running FSL's bedbost locally - this might take a while > WARN: It is recommended to run this step on a cluster > bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/**dmri > subjectdir is /data-02/joana/tracula/XXX/**dmri > Making bedpostx directory structure > Queuing preprocessing stages > Unable to run job: Job was rejected because job requests unknown queue "short.q". > Exiting. > Queuing parallel processing stage > Unable to run job: Job was rejected because job requests unknown queue "long.q". > Exiting. > Queuing post processing stage > Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) > Job was rejected because job requests unknown queue "long.q". > Exiting. > > Type /data-02/joana/tracula/3119/**dmri.bedpostX/monitor to show progress. > Type /data-02/joana/tracula/3119/**dmri.bedpostX/cancel to terminate all the queued tasks. > > You will get an email at the end of the post-processing stage. > > > So far no slices have been processed. Does anyone know how to solve it? > > Thanks! > > ______________________________**_________________ > 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.

Thanks!

I will try that and let you know!

joana

2013/9/5 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

Yes, it does look from the images like the L-R and A-P directions are swapped. So you can switch around the x and y columns of you gradient table and rerun the preprocessing and check the eigenvectors again. It may be some other combination of swaps that needs to be done, but the x and y looks like the most likely to me. For sure the gradient table is wrong.

On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

Thanks!

...

I've uploaded those files as well as dmrirc and bvecs and bvals.

Let me know what you think.

2013/9/5 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

  Indeed, they look like they're oriented A-P in the corpus callosum

and L-R in the cinglulum, when it should be the opposite obviously. This'd mean you'd have to swap things in the gradient table. It's hard to tell for sure from the screenshot though. If you upload the dtifit_FA and dtifit_V1 volumes for me here, I'll look at them: https://gate.nmr.mgh.harvard.**edu/filedrop2/https://gate.nmr.mgh.harvard.edu/filedrop2/

  On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

        Hi Anastasia,
        Thanks! I checked dtifit_FA and did the overlay with V1.

        They don't look ok to me (see attached picture). Any

suggestions on how to solve this? Perhaps by modifying any of the previous steps?

        Thanks!




        2013/9/5 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>

              Hm, this looks uniformly bad. Have you checked that the

gradient directions are correct? You can check that by looking at the eigenvectors from the tensor fit that's done as part of the preprocessing. Although tracula doesn't use tensors for tractography, it's a quick way to check that your inputs are correct.

              In fslview, overlay dmri/dtifit_V1.nii.gz on

dmri/dtifit_FA.nii.gz, and display dtifit_V1 as lines. Then make sure that the lines follow the basic anatomy e.g. in the corpus callosum (L-R), cingulum (A-P), corticospinal tract (I-S).

              On Thu, 5 Sep 2013, Joana Braga Pereira wrote:

                    Hi,
                    Thanks for all the replies, I solved the problem

I had before.

                    However, after finishing the Tracula

pre-processing steps I tried to visualize the tracts by typing:

                    freeview -tv CTR01/dpath/merged_avg33_mni_**

bbr.mgz

                    And, as you can see in the picture I'm attaching

to this email, it seems the tracts were not properly reconstructed.

                    Does anyone know why?

                    Should I make some changes and for example set

the control points differently from the ones proposed on Tracula website?

                    Any help will be greatly appreciated!

                    Thanks,

                    joana




                    2013/9/2 Watson, Christopher <

Christopher.Watson@childrens.**harvard.eduChristopher.Watson@childrens.harvard.edu

...

                          Indeed. It's actually really easy to set

up, too. ______________________________**__________ From: Anastasia Yendiki [ ayendiki@nmr.mgh.harvard.edu] Sent: Monday, September 02, 2013 3:46 PM To: Watson, Christopher Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

                          Thanks for the pointers, Chris. I'd call it

an "opportunity for FSL customization" rather than an "FSL problem" per se :o)

                          On Mon, 2 Sep 2013, Watson, Christopher

wrote:

                          > This is an FSL problem. You can try the

FSL list, and check out some links: > https://www2.fmrib.ox.ac.uk/** phpwiki/index/FslSge https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge >

        http://neuro.debian.net/blog/**2012/2012-03-09_parallelize_**

fsl_with_condor.htmlhttp://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html >

        http://chrisfilo.tumblr.com/**post/579493955/how-to-**

configure-sun-grid-engine-for-**fsl-under-ubuntuhttp://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu > > ______________________________** __________ > From: freesurfer-bounces@nmr.mgh.** harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira [ jbragapereira@gmail.com] > Sent: Monday, September 02, 2013 9:53 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q" > > Dear Anastasia and FreeSurfers, > > I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: > > INFO: SUBJECTS_DIR is /data-02/joana/Last > INFO: Diffusion root is /data-02/joana/tracula/ > Actual FREESURFER_HOME /usr/local/freesurfer-5.3 > WARN: Running FSL's bedbost locally - this might take a while > WARN: It is recommended to run this step on a cluster > bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/**dmri > subjectdir is /data-02/joana/tracula/XXX/ **dmri > Making bedpostx directory structure > Queuing preprocessing stages > Unable to run job: Job was rejected because job requests unknown queue "short.q". > Exiting. > Queuing parallel processing stage > Unable to run job: Job was rejected because job requests unknown queue "long.q". > Exiting. > Queuing post processing stage > Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) > Job was rejected because job requests unknown queue "long.q". > Exiting. > > Type /data-02/joana/tracula/3119/**dmri.bedpostX/monitor to show progress. > Type /data-02/joana/tracula/3119/**dmri.bedpostX/cancel to terminate all the queued tasks. > > You will get an email at the end of the post-processing stage. > > > So far no slices have been processed. Does anyone know how to solve it? > > Thanks! > > ______________________________** _________________ > 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 > > >

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