Re: [Freesurfer] DTI - Tracula question
That was helpful. Thanks Michael. On Fri, Feb 5, 2016 at 5:19 PM, 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: mha...@wustl.edu > > From: on behalf of Alan Francis < > alandarkene...@gmail.com> > Reply-To: Freesurfer support list > Date: Friday, February 5, 2016 at 3:57 PM > To: Anastasia Yendiki > Cc: Freesurfer support list > 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 < > ayend...@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 < >>> ayend...@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 >>> >> > > -- > > 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. > > - ___ 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.
Re: [Freesurfer] DTI - Tracula question
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: mha...@wustl.edu From: on behalf of Alan Francis Reply-To: Freesurfer support list Date: Friday, February 5, 2016 at 3:57 PM To: Anastasia Yendiki Cc: Freesurfer support list 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 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 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 al...@bwh.harvard.edu afran...@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. -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Re: [Freesurfer] DTI - Tracula question
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: mha...@wustl.edu From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <alandarkene...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Friday, February 5, 2016 at 3:57 PM To: Anastasia Yendiki <ayend...@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 <ayend...@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 <ayend...@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 al...@bwh.harvard.edu afran...@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 al...@bwh.harvard.edu afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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 < ayend...@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 < >> ayend...@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 >> al...@bwh.harvard.edu >> afran...@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 >> al...@bwh.harvard.edu >> afran...@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 al...@bwh.harvard.edu afran...@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.
Re: [Freesurfer] DTI - Tracula question
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 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 al...@bwh.harvard.edu afran...@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 al...@bwh.harvard.edu afran...@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.
Re: [Freesurfer] DTI - Tracula question
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 < ayend...@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 >> al...@bwh.harvard.edu >> afran...@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 al...@bwh.harvard.edu afran...@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.
Re: [Freesurfer] DTI - Tracula question
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 al...@bwh.harvard.edu afran...@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.
[Freesurfer] DTI - Tracula question
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 al...@bwh.harvard.edu afran...@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.
