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Hello, I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I put the volume into freesurfer space how can I get it to sample onto a surface when the values are in white matter and not grey matter? To rephrase, how can I pull data from white matter (just below the grey matter) and display it on a surface?
Many thanks, Sara
Hi Sara
you can use a negative projdist in mri_vol2surf
cheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
External Email - Use Caution
Hello,
I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I put the volume into freesurfer space how can I get it to sample onto a surface when the values are in white matter and not grey matter? To rephrase, how can I pull data from white matter (just below the grey matter) and display it on a surface?
Many thanks,
Sara
External Email - Use Caution
Bruce, Thanks! So if I set it to say 4mm would it sample from 0-4mm or just from exactly 4mm and ignore things slightly closer to the surface? My problem would be somethings could be 2mm or 3mm etc. and it's not exactly the same all the way around the brain.
Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu
On 6/26/18, 2:27 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Sara
you can use a negative projdist in mri_vol2surf
cheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
> > External Email - Use Caution > > Hello, > > I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I > put the volume into freesurfer space how can I get it to sample onto a surface when the > values are in white matter and not grey matter? To rephrase, how can I pull data from white > matter (just below the grey matter) and display it on a surface? > > > > Many thanks, > > Sara > > >
Hi Sara check out the help (with --help). For example you could use:
--projdist-avg min max del : average along normal
cheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
External Email - Use CautionBruce, Thanks! So if I set it to say 4mm would it sample from 0-4mm or just from exactly 4mm and ignore things slightly closer to the surface? My problem would be somethings could be 2mm or 3mm etc. and it's not exactly the same all the way around the brain.
Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu
On 6/26/18, 2:27 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Sara
you can use a negative projdist in mri_vol2surf
cheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
External Email - Use CautionHello,
I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I put the volume into freesurfer space how can I get it to sample onto a surface when the values are in white matter and not grey matter? To rephrase, how can I pull data from white matter (just below the grey matter) and display it on a surface?
Many thanks,
Sara
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Bruce, What does "del" mean in the --projdist-avg flag?
Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu
On 6/26/18, 2:49 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Sara check out the help (with --help). For example you could use:
--projdist-avg min max del : average along normal
cheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
> External Email - Use Caution > > Bruce, > Thanks! So if I set it to say 4mm would it sample from 0-4mm or just from exactly 4mm and ignore things slightly closer to the surface? > My problem would be somethings could be 2mm or 3mm etc. and it's not exactly the same all the way around the brain. > > Sara Sims > Graduate Research Fellow > University of Alabama at Birmingham > Department of Psychology > 205-975-4060 > snolin@uab.edu > > On 6/26/18, 2:27 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote: > > Hi Sara > > you can use a negative projdist in mri_vol2surf > > cheers > Bruce > On Tue, 26 Jun 2018, Sims, > Sara A wrote: > > > > > External Email - Use Caution > > > > Hello, > > > > I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I > > put the volume into freesurfer space how can I get it to sample onto a surface when the > > values are in white matter and not grey matter? To rephrase, how can I pull data from white > > matter (just below the grey matter) and display it on a surface? > > > > > > > > Many thanks, > > > > Sara > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
I think it is short for "delta" - how far about the samples are
On Mon, 9 Jul 2018, Sims, Sara A wrote:
External Email - Use CautionBruce, What does "del" mean in the --projdist-avg flag?
Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu
On 6/26/18, 2:49 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Sara check out the help (with --help). For example you could use:
--projdist-avg min max del : average along normalcheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
External Email - Use CautionBruce, Thanks! So if I set it to say 4mm would it sample from 0-4mm or just from exactly 4mm and ignore things slightly closer to the surface? My problem would be somethings could be 2mm or 3mm etc. and it's not exactly the same all the way around the brain.
Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu
On 6/26/18, 2:27 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Sara
you can use a negative projdist in mri_vol2surf
cheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
External Email - Use CautionHello,
I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I put the volume into freesurfer space how can I get it to sample onto a surface when the values are in white matter and not grey matter? To rephrase, how can I pull data from white matter (just below the grey matter) and display it on a surface?
Many thanks,
Sara
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
External Email - Use Caution
Bruce, The help file and wiki don't explain the units of the min, max, and del. I still can't get the data to sample onto the surface correctly and so I'm wondering if it has something to do with my assumptions about how this command flag is working. What unit are these values supposed to be in? Also is the difference between projdist-avg and projdist-max that avg averages all values (including zeros) and max finds the highest value from the points between min and max? Sorry to get into the nitty gritty, I am just trying to understand all the options so I can use them appropriately.
Thanks, Sara Sims
On 7/9/18, 3:15 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
I think it is short for "delta" - how far about the samples are
On Mon, 9 Jul 2018, Sims, Sara A wrote:
> External Email - Use Caution > > Bruce, > What does "del" mean in the --projdist-avg flag? > > Sara Sims > Graduate Research Fellow > University of Alabama at Birmingham > Department of Psychology > 205-975-4060 > snolin@uab.edu > > On 6/26/18, 2:49 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote: > > Hi Sara > check out the help (with --help). For example you could use: > > --projdist-avg min max del : average along normal > > cheers > Bruce > On Tue, 26 Jun > 2018, Sims, Sara A wrote: > > > External Email - Use Caution > > > > Bruce, > > Thanks! So if I set it to say 4mm would it sample from 0-4mm or just from exactly 4mm and ignore things slightly closer to the surface? > > My problem would be somethings could be 2mm or 3mm etc. and it's not exactly the same all the way around the brain. > > > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > snolin@uab.edu > > > > On 6/26/18, 2:27 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote: > > > > Hi Sara > > > > you can use a negative projdist in mri_vol2surf > > > > cheers > > Bruce > > On Tue, 26 Jun 2018, Sims, > > Sara A wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello, > > > > > > I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I > > > put the volume into freesurfer space how can I get it to sample onto a surface when the > > > values are in white matter and not grey matter? To rephrase, how can I pull data from white > > > matter (just below the grey matter) and display it on a surface? > > > > > > > > > > > > Many thanks, > > > > > > Sara > > > > > > > > > > > > > > > _______________________________________________ > > 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 > > >
Hi Sara
no worries. The units are mm, and use -avg averages the values and max takes the max over them (which is a somewhat dicey thing to do if you are going to do stats afterwards).
cheers Bruce
On Wed, 11 Jul 2018, Sims, Sara A wrote:
External Email - Use CautionBruce, The help file and wiki don't explain the units of the min, max, and del. I still can't get the data to sample onto the surface correctly and so I'm wondering if it has something to do with my assumptions about how this command flag is working. What unit are these values supposed to be in? Also is the difference between projdist-avg and projdist-max that avg averages all values (including zeros) and max finds the highest value from the points between min and max? Sorry to get into the nitty gritty, I am just trying to understand all the options so I can use them appropriately.
Thanks, Sara Sims
On 7/9/18, 3:15 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
I think it is short for "delta" - how far about the samples are
On Mon, 9 Jul 2018, Sims, Sara A wrote:
External Email - Use CautionBruce, What does "del" mean in the --projdist-avg flag?
Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu
On 6/26/18, 2:49 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Sara check out the help (with --help). For example you could use:
--projdist-avg min max del : average along normalcheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
External Email - Use CautionBruce, Thanks! So if I set it to say 4mm would it sample from 0-4mm or just from exactly 4mm and ignore things slightly closer to the surface? My problem would be somethings could be 2mm or 3mm etc. and it's not exactly the same all the way around the brain.
Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu
On 6/26/18, 2:27 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Sara
you can use a negative projdist in mri_vol2surf
cheers Bruce On Tue, 26 Jun 2018, Sims, Sara A wrote:
External Email - Use CautionHello,
I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I put the volume into freesurfer space how can I get it to sample onto a surface when the values are in white matter and not grey matter? To rephrase, how can I pull data from white matter (just below the grey matter) and display it on a surface?
Many thanks,
Sara
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 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 -
Sims, Sara A