Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help!
Best, Panos
Hi Panos
why not just write a matlab script to do it? It would be easy enough. I don't think we have a binary that will quite do what you want Bruce On Mon, 25 Jan 2016, pfotiad@nmr.mgh.harvard.edu wrote:
Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help!
Best, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't think there is a single command line to do it, but if you can get the centroid voxel from somewhere else (eg, fsl), then you can run mri_volsynth --template template.nii.gz --pdf delta -delta-crsf col row slice 0 where col row and slice are the voxel coordinates
On 01/25/2016 03:49 PM, pfotiad@nmr.mgh.harvard.edu wrote:
Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help!
Best, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce and Doug,
Both methods sound great. Thank you both for your help!
Best, Panos
I don't think there is a single command line to do it, but if you can get the centroid voxel from somewhere else (eg, fsl), then you can run mri_volsynth --template template.nii.gz --pdf delta -delta-crsf col row slice 0 where col row and slice are the voxel coordinates
On 01/25/2016 03:49 PM, pfotiad@nmr.mgh.harvard.edu wrote:
Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help!
Best, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sure, but I think Doug wins this round (curse you Greve!)
Bruce
On Mon, 25 Jan 2016, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Bruce and Doug,
Both methods sound great. Thank you both for your help!
Best, Panos
I don't think there is a single command line to do it, but if you can get the centroid voxel from somewhere else (eg, fsl), then you can run mri_volsynth --template template.nii.gz --pdf delta -delta-crsf col row slice 0 where col row and slice are the voxel coordinates
On 01/25/2016 03:49 PM, pfotiad@nmr.mgh.harvard.edu wrote:
Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help!
Best, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
pfotiad＠nmr.mgh.harvard.edu