External Email - Use Caution
Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work?
Best, Daniel Callow
Yes. Please check out the instructions in the tutorial on how to specify your input DWIs and let us know if you have any questions:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com Sent: Friday, September 27, 2019 10:31:19 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA - input Nifti instead of DICOM?
External Email - Use Caution
Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work?
Best, Daniel Callow -- Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298
External Email - Use Caution
Gotcha. I was wondering if it would be possible to extract the bvecs and bval files directly from the Nifti file, however, it seems like based on the documentation that this is not possible and I will have to specify the bvals and bvecs and make sure they are formatted correctly for TRACULA.
Thanks for the reply! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Fri, Sep 27, 2019 at 11:26 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Yes. Please check out the instructions in the tutorial on how to specify your input DWIs and let us know if you have any questions:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow < ddcc2442@gmail.com> *Sent:* Friday, September 27, 2019 10:31:19 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] TRACULA - input Nifti instead of DICOM?
External Email - Use CautionHello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work?
Best, Daniel Callow -- *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nifti files don't store that info. You'd have to get the gradient table and b-values either from the dicom header or from the scanner. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com Sent: Friday, September 27, 2019 11:32 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?
External Email - Use Caution
Gotcha. I was wondering if it would be possible to extract the bvecs and bval files directly from the Nifti file, however, it seems like based on the documentation that this is not possible and I will have to specify the bvals and bvecs and make sure they are formatted correctly for TRACULA.
Thanks for the reply! Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298
On Fri, Sep 27, 2019 at 11:26 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Yes. Please check out the instructions in the tutorial on how to specify your input DWIs and let us know if you have any questions:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula ________________________________ 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 Daniel Callow <ddcc2442@gmail.commailto:ddcc2442@gmail.com> Sent: Friday, September 27, 2019 10:31:19 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA - input Nifti instead of DICOM?
External Email - Use Caution
Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work?
Best, Daniel Callow -- Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Daniel Callow -
Yendiki, Anastasia