Hi Anastasia:
I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file?
Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS?
thank you so much,
best regards,
Alan
Hi Alan - A nifti file with the gradient tables and b-values embedded? All freesurfer programs can handle nifti volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and b-value table as separate files.
Run "mri_convert --help" to see all image file formats that we can handle.
Hope this helps, a.y
On Wed, 3 Feb 2016, Alan Francis wrote:
Hi Anastasia:
I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file?
Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS?
thank you so much,
best regards,
Alan
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Thanks Anastasia - that was very helpful. I have another question : I am working on a DTI dataset of around 70 subjects. This dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been acquired on the same scanner?
thanks,
Alan
On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Alan - A nifti file with the gradient tables and b-values embedded? All freesurfer programs can handle nifti volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and b-value table as separate files.
Run "mri_convert --help" to see all image file formats that we can handle.
Hope this helps, a.y
On Wed, 3 Feb 2016, Alan Francis wrote:
Hi Anastasia:
I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file?
Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS?
thank you so much,
best regards,
Alan
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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.
Hi Alan - Yes, you can give a single file for all data sets if they're all acquired with the same gradient table and slice prescription. As a test, you can extract the gradient tables from a couple of your data set's dicom headers and see how different they are. If there are only very small differences, using a single table for all will not make a difference.
Hope this helps,
a.y
On Fri, 5 Feb 2016, Alan Francis wrote:
Thanks Anastasia - that was very helpful. I have another question : I am working on a DTI dataset of around 70 subjects. This dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been acquired on the same scanner?
thanks,
Alan
On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Alan - A nifti file with the gradient tables and b-values embedded? All freesurfer programs can handle nifti volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and b-value table as separate files. Run "mri_convert --help" to see all image file formats that we can handle. Hope this helps, a.y On Wed, 3 Feb 2016, Alan Francis wrote: Hi Anastasia: I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file? Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS? thank you so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Hi Anastasia:
Thank you so much. Yes that is very helpful.
best,
Alan
On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Alan - Yes, you can give a single file for all data sets if they're all acquired with the same gradient table and slice prescription. As a test, you can extract the gradient tables from a couple of your data set's dicom headers and see how different they are. If there are only very small differences, using a single table for all will not make a difference.
Hope this helps,
a.y
On Fri, 5 Feb 2016, Alan Francis wrote:
Thanks Anastasia - that was very helpful. I have another question : I am
working on a DTI dataset of around 70 subjects. This dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been acquired on the same scanner?
thanks,
Alan
On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Alan - A nifti file with the gradient tables and b-valuesembedded? All freesurfer programs can handle nifti volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and b-value table as separate files.
Run "mri_convert --help" to see all image file formats that we canhandle.
Hope this helps, a.y On Wed, 3 Feb 2016, Alan Francis wrote: Hi Anastasia: I am working on a set of DTI data that were obtained at theMartinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file?
Should I convert the nii.gz file into Analyze to get at theBVECS/ BVALS?
thank you so much, best regards, Alan --|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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.
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
As an add-on to the add-on, starting in 6.0 we'll be able to figure it out from the dicom header, so hopefully people won't have to worry about any of this in the future.
On Fri, 5 Feb 2016, Harms, Michael wrote:
As an add-on to this, note that using a single table for all subjects is probably only appropriate if the DWI was acquired with a fixed orientation relative to the scanner gradient axes (e.g., strictly axial) for all subjects. If the orientation was customized individually for each subject (e.g., to align the imaging plane with the AC/PC), then it is unlikely that using a single table for all subjects is appropriate.
cheers, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alan Francis alandarkenergy@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, February 5, 2016 at 3:57 PM To: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] DTI - Tracula question
Hi Anastasia:
Thank you so much. Yes that is very helpful.
best,
Alan
On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Alan - Yes, you can give a single file for all data sets if they're all acquired with the same gradient table and slice prescription. As a test, you can extract the gradient tables from a couple of your data set's dicom headers and see how different they are. If there are only very small differences, using a single table for all will not make a difference. Hope this helps, a.y On Fri, 5 Feb 2016, Alan Francis wrote: Thanks Anastasia - that was very helpful. I have another question : I am working on a DTI dataset of around 70 subjects. This dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been acquired on the same scanner? thanks, Alan On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Alan - A nifti file with the gradient tables and b-values embedded? All freesurfer programs can handle nifti volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and b-value table as separate files. Run "mri_convert --help" to see all image file formats that we can handle. Hope this helps, a.y On Wed, 3 Feb 2016, Alan Francis wrote: Hi Anastasia: I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file? Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS? thank you so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| _______________________________________________ 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. -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
That was helpful. Thanks Michael.
On Fri, Feb 5, 2016 at 5:19 PM, Harms, Michael mharms@wustl.edu wrote:
As an add-on to this, note that using a single table for all subjects is probably only appropriate if the DWI was acquired with a fixed orientation relative to the scanner gradient axes (e.g., strictly axial) for all subjects. If the orientation was customized individually for each subject (e.g., to align the imaging plane with the AC/PC), then it is unlikely that using a single table for all subjects is appropriate.
cheers, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alan Francis < alandarkenergy@gmail.com> Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, February 5, 2016 at 3:57 PM To: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] DTI - Tracula question
Hi Anastasia:
Thank you so much. Yes that is very helpful.
best,
Alan
On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Alan - Yes, you can give a single file for all data sets if they're all acquired with the same gradient table and slice prescription. As a test, you can extract the gradient tables from a couple of your data set's dicom headers and see how different they are. If there are only very small differences, using a single table for all will not make a difference.
Hope this helps,
a.y
On Fri, 5 Feb 2016, Alan Francis wrote:
Thanks Anastasia - that was very helpful. I have another question : I am
working on a DTI dataset of around 70 subjects. This dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been acquired on the same scanner?
thanks,
Alan
On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Alan - A nifti file with the gradient tables and b-valuesembedded? All freesurfer programs can handle nifti volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and b-value table as separate files.
Run "mri_convert --help" to see all image file formats that we canhandle.
Hope this helps, a.y On Wed, 3 Feb 2016, Alan Francis wrote: Hi Anastasia: I am working on a set of DTI data that were obtained at theMartinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file?
Should I convert the nii.gz file into Analyze to get at theBVECS/ BVALS?
thank you so much, best regards, Alan
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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freesurfer@nmr.mgh.harvard.edu
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Alan Francis -
Anastasia Yendiki -
Harms, Michael