Using tract querier to dissect HCP tracking

[ghost]

Hi, I am using tract_querier to dissect a tractogram obtained from a human connectome project Q3 dataset. To dissect the tractogram I am using the freesurfer_queries.qry file included in tract_querier but I get incomplete results. For example, out of the seven queries to extract the individual parts of the corpus callosum (cc_1 to cc_7) number 5 and 6 are missing (see attached screenshot). I created a parcellation of the dataset using freesurfer (aparc+aseg.nii.gz). This should be the correct atlas to use with the freesurfer_queries.qry file, right? I also used the parcellation that is directly included in the HCP download (wmparc.nii.gz), which is apparently based on a different atlas. The results look different but are still incomplete. Do you have any ideas what might go wrong here? Maybe the queries are simply not correct. The fibers are there by the way. If I extract the complete corpus callosum with one query it works fine ("CC_full = (frontal.left and frontal.right) or (parietal.left and parietal.right) or (occipital.left and occipital.right) or (cingular.left and cingular.right) not in brain_stem")

Thanks for your help!

[demianw]

Hi!

You are using everything right. The only issue is that you should use the wmparc.nii.gz file as it has the parcellated white matter.

Let me know if it works

Happy to help Demian

On Jun 6, 2014, at 14:14, pneher notifications@github.com wrote:

Hi, I am using tract_querier to dissect a tractogram obtained from a human connectome project Q3 dataset. To dissect the tractogram I am using the freesurfer_queries.qry file included in tract_querier but I get incomplete results. For example, out of the seven queries to extract the individual parts of the corpus callosum (cc_1 to cc_7) number 5 and 6 are missing (see attached screenshot). I created a parcellation of the dataset using freesurfer (aparc+aseg.nii.gz). This should be the correct atlas to use with the freesurfer_queries.qry file, right? Do you have any ideas what might go wrong here? Maybe the queries are simply not correct.

Thanks for your help!

— Reply to this email directly or view it on GitHub.

[ghost]

Hi Demian,

thanks for your fast reply! I also used the wmparc.nii.gz file, but there are still the same parts missing (screenshot attached).

Peter

On 06/06/2014 03:29 PM, Demian Wassermann wrote:

Hi!

You are using everything right. The only issue is that you should use the wmparc.nii.gz file as it has the parcellated white matter.

Let me know if it works

Happy to help Demian

On Jun 6, 2014, at 14:14, pneher notifications@github.com wrote:

Hi, I am using tract_querier to dissect a tractogram obtained from a human connectome project Q3 dataset. To dissect the tractogram I am using the freesurfer_queries.qry file included in tract_querier but I get incomplete results. For example, out of the seven queries to extract the individual parts of the corpus callosum (cc_1 to cc_7) number 5 and 6 are missing (see attached screenshot). I created a parcellation of the dataset using freesurfer (aparc+aseg.nii.gz). This should be the correct atlas to use with the freesurfer_queries.qry file, right? Do you have any ideas what might go wrong here? Maybe the queries are simply not correct.

Thanks for your help!

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/demianw/tract_querier/issues/11#issuecomment-45336261.

Dr. sc. hum. Peter F. Neher Division Medical and Biological Informatics

German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3552 fax: +49 6221 42-2345

p.neher@dkfz.de http://www.dkfz.de/de/mbi/people/Peter_Neher.html

Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited.

[demianw]

Hi again Peter.

I have had success in doing this with the q3 release.

1. Are you sure that these tracts connecting the parietal lobes of both hemispheres are in your tractography?

I will not be able to answer further today but if you send the tractography or how to reproduce it I will gladly assist you more during the weekend or Monday

Demian

On Jun 6, 2014, at 15:53, pneher notifications@github.com wrote:

Hi Demian,

thanks for your fast reply! I also used the wmparc.nii.gz file, but there are still the same parts missing (screenshot attached).

Peter

On 06/06/2014 03:29 PM, Demian Wassermann wrote:

Hi!

You are using everything right. The only issue is that you should use the wmparc.nii.gz file as it has the parcellated white matter.

Let me know if it works

Happy to help Demian

On Jun 6, 2014, at 14:14, pneher notifications@github.com wrote:

Hi, I am using tract_querier to dissect a tractogram obtained from a human connectome project Q3 dataset. To dissect the tractogram I am using the freesurfer_queries.qry file included in tract_querier but I get incomplete results. For example, out of the seven queries to extract the individual parts of the corpus callosum (cc_1 to cc_7) number 5 and 6 are missing (see attached screenshot). I created a parcellation of the dataset using freesurfer (aparc+aseg.nii.gz). This should be the correct atlas to use with the freesurfer_queries.qry file, right? Do you have any ideas what might go wrong here? Maybe the queries are simply not correct.

Thanks for your help!

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/demianw/tract_querier/issues/11#issuecomment-45336261.

Dr. sc. hum. Peter F. Neher Division Medical and Biological Informatics

German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3552 fax: +49 6221 42-2345

p.neher@dkfz.de http://www.dkfz.de/de/mbi/people/Peter_Neher.html

Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited. — Reply to this email directly or view it on GitHub.

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[demianw]

Mmmm I just re read your first mail and if you get the whole cc with a query I need to double check CC 5 and 6. Will get back to you by Monday

Best D

[demianw]

Hello Peter,

I got to the bottom of the issue. In CC_5 and CC_6 I’m using the "corpuscallosum” regions to make the query a bit cleaner. However, I found out that these regions sometimes are not precisely segmented

Probably removing the use of these regions in the queries will work for you:

cc_5 = ( endpoints_in(postcentral.left or posteriorcingulate.left or paracentral.left) and endpoints_in(postcentral.right or posteriorcingulate.right or paracentral.right) )

cc_6 = ( endpoints_in( precuneus.left or supramarginal.left or superiorparietal.left or inferiorparietal.left or superiortemporal.left or middletemporal.left or bankssts.left or transversetemporal.left or isthmuscingulate.left ) and endpoints_in( precuneus.right or supramarginal.right or superiorparietal.right or inferiorparietal.right or superiortemporal.right or middletemporal.right or bankssts.right or transversetemporal.right or isthmuscingulate.right ) )

Please let me know if it works for you

Best Demian

Demian Wassermann, PhD demian.wassermann@inria.fr Research Scientist Athena Project Team INRIA Sophia Antipolis - Méditerranée 2004 route des lucioles - FR-06902

On 06 Jun 2014, at 15:53, pneher notifications@github.com wrote:

Hi Demian,

thanks for your fast reply! I also used the wmparc.nii.gz file, but there are still the same parts missing (screenshot attached).

Peter

On 06/06/2014 03:29 PM, Demian Wassermann wrote:

Hi!

You are using everything right. The only issue is that you should use the wmparc.nii.gz file as it has the parcellated white matter.

Let me know if it works

Happy to help Demian

On Jun 6, 2014, at 14:14, pneher notifications@github.com wrote:

Hi, I am using tract_querier to dissect a tractogram obtained from a human connectome project Q3 dataset. To dissect the tractogram I am using the freesurfer_queries.qry file included in tract_querier but I get incomplete results. For example, out of the seven queries to extract the individual parts of the corpus callosum (cc_1 to cc_7) number 5 and 6 are missing (see attached screenshot). I created a parcellation of the dataset using freesurfer (aparc+aseg.nii.gz). This should be the correct atlas to use with the freesurfer_queries.qry file, right? Do you have any ideas what might go wrong here? Maybe the queries are simply not correct.

Thanks for your help!

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/demianw/tract_querier/issues/11#issuecomment-45336261.

Dr. sc. hum. Peter F. Neher Division Medical and Biological Informatics

German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3552 fax: +49 6221 42-2345

p.neher@dkfz.de http://www.dkfz.de/de/mbi/people/Peter_Neher.html

Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited. — Reply to this email directly or view it on GitHub.

[ghost]

Hi Demian,

sorry for my late reply, we had a long weekend. Take the corpuscallosum label out of the query seems to do the trick, thank you! I will go over all the queries we are interested in with our radiologist. Lets hope everything looks good, otherwise I will get back to you :) If we add further queries, are you interested in including them in you repository?

Best, Peter

On 06/09/2014 05:40 PM, Demian Wassermann wrote:

Hello Peter,

I got to the bottom of the issue. In CC_5 and CC_6 I’m using the "corpuscallosum” regions to make the query a bit cleaner. However, I found out that these regions sometimes are not precisely segmented

Probably removing the use of these regions in the queries will work for you:

cc_5 = ( endpoints_in(postcentral.left or posteriorcingulate.left or paracentral.left) and endpoints_in(postcentral.right or posteriorcingulate.right or paracentral.right) )

cc_6 = ( endpoints_in( precuneus.left or supramarginal.left or superiorparietal.left or inferiorparietal.left or superiortemporal.left or middletemporal.left or bankssts.left or transversetemporal.left or isthmuscingulate.left ) and endpoints_in( precuneus.right or supramarginal.right or superiorparietal.right or inferiorparietal.right or superiortemporal.right or middletemporal.right or bankssts.right or transversetemporal.right or isthmuscingulate.right ) )

Please let me know if it works for you

Best Demian

Demian Wassermann, PhD demian.wassermann@inria.fr Research Scientist Athena Project Team INRIA Sophia Antipolis - Méditerranée 2004 route des lucioles - FR-06902

On 06 Jun 2014, at 15:53, pneher notifications@github.com wrote:

Hi Demian,

thanks for your fast reply! I also used the wmparc.nii.gz file, but there are still the same parts missing (screenshot attached).

Peter

On 06/06/2014 03:29 PM, Demian Wassermann wrote:

Hi!

You are using everything right. The only issue is that you should use the wmparc.nii.gz file as it has the parcellated white matter.

Let me know if it works

Happy to help Demian

On Jun 6, 2014, at 14:14, pneher notifications@github.com wrote:

Hi, I am using tract_querier to dissect a tractogram obtained from a human connectome project Q3 dataset. To dissect the tractogram I am using the freesurfer_queries.qry file included in tract_querier but I get incomplete results. For example, out of the seven queries to extract the individual parts of the corpus callosum (cc_1 to cc_7) number 5 and 6 are missing (see attached screenshot). I created a parcellation of the dataset using freesurfer (aparc+aseg.nii.gz). This should be the correct atlas to use with the freesurfer_queries.qry file, right? Do you have any ideas what might go wrong here? Maybe the queries are simply not correct.

Thanks for your help!

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub

https://github.com/demianw/tract_querier/issues/11#issuecomment-45336261.

Dr. sc. hum. Peter F. Neher Division Medical and Biological Informatics

German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3552 fax: +49 6221 42-2345

p.neher@dkfz.de http://www.dkfz.de/de/mbi/people/Peter_Neher.html

Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited. — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/demianw/tract_querier/issues/11#issuecomment-45505248.

Dr. sc. hum. Peter F. Neher Division Medical and Biological Informatics

German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3552 fax: +49 6221 42-2345

p.neher@dkfz.de http://www.dkfz.de/de/mbi/people/Peter_Neher.html

Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited.

[demianw]

Hello Peter,

Yes it will be great to include them. Probably not in the same file though, to keep things clean and organised.

One more thing is that there is a tool, which I have to document a bit better, which allows you to perform operations on tracts.

It is include in the package and you can invoke it through the command-line “tract_math”. It is in experimental state but it will allow you to perform operations on tracts

Best and happy to help Demian

Demian Wassermann, PhD demian@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/

On 10 Jun 2014, at 14:26, pneher notifications@github.com wrote:

Hi Demian,

sorry for my late reply, we had a long weekend. Take the corpuscallosum label out of the query seems to do the trick, thank you! I will go over all the queries we are interested in with our radiologist. Lets hope everything looks good, otherwise I will get back to you :) If we add further queries, are you interested in including them in you repository?

Best, Peter

On 06/09/2014 05:40 PM, Demian Wassermann wrote:

Hello Peter,

I got to the bottom of the issue. In CC_5 and CC_6 I’m using the "corpuscallosum” regions to make the query a bit cleaner. However, I found out that these regions sometimes are not precisely segmented

Probably removing the use of these regions in the queries will work for you:

cc_5 = ( endpoints_in(postcentral.left or posteriorcingulate.left or paracentral.left) and endpoints_in(postcentral.right or posteriorcingulate.right or paracentral.right) )

cc_6 = ( endpoints_in( precuneus.left or supramarginal.left or superiorparietal.left or inferiorparietal.left or superiortemporal.left or middletemporal.left or bankssts.left or transversetemporal.left or isthmuscingulate.left ) and endpoints_in( precuneus.right or supramarginal.right or superiorparietal.right or inferiorparietal.right or superiortemporal.right or middletemporal.right or bankssts.right or transversetemporal.right or isthmuscingulate.right ) )

Please let me know if it works for you

Best Demian

Demian Wassermann, PhD demian.wassermann@inria.fr Research Scientist Athena Project Team INRIA Sophia Antipolis - Méditerranée 2004 route des lucioles - FR-06902

On 06 Jun 2014, at 15:53, pneher notifications@github.com wrote:

Hi Demian,

thanks for your fast reply! I also used the wmparc.nii.gz file, but there are still the same parts missing (screenshot attached).

Peter

On 06/06/2014 03:29 PM, Demian Wassermann wrote:

Hi!

You are using everything right. The only issue is that you should use the wmparc.nii.gz file as it has the parcellated white matter.

Let me know if it works

Happy to help Demian

On Jun 6, 2014, at 14:14, pneher notifications@github.com wrote:

Hi, I am using tract_querier to dissect a tractogram obtained from a human connectome project Q3 dataset. To dissect the tractogram I am using the freesurfer_queries.qry file included in tract_querier but I get incomplete results. For example, out of the seven queries to extract the individual parts of the corpus callosum (cc_1 to cc_7) number 5 and 6 are missing (see attached screenshot). I created a parcellation of the dataset using freesurfer (aparc+aseg.nii.gz). This should be the correct atlas to use with the freesurfer_queries.qry file, right? Do you have any ideas what might go wrong here? Maybe the queries are simply not correct.

Thanks for your help!

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub

https://github.com/demianw/tract_querier/issues/11#issuecomment-45336261.

Dr. sc. hum. Peter F. Neher Division Medical and Biological Informatics

German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3552 fax: +49 6221 42-2345

p.neher@dkfz.de http://www.dkfz.de/de/mbi/people/Peter_Neher.html

Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited. — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/demianw/tract_querier/issues/11#issuecomment-45505248.

Dr. sc. hum. Peter F. Neher Division Medical and Biological Informatics

German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3552 fax: +49 6221 42-2345

p.neher@dkfz.de http://www.dkfz.de/de/mbi/people/Peter_Neher.html

Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited. — Reply to this email directly or view it on GitHub.