sorry, ignore my previous post. I thought it was mri_segstats. doug

Bruce Fischl wrote:

oops, I just fixed that. If you let us know what software/hardware env you are using we'll give you an updated binary.

Bruce

On Thu, 4 Aug 2011, Christopher Luna wrote:

...

Hello, I'm trying to run mri_segment with some custom values in the optional flags, such as -p for setting the percentage threshold with a float value.

When I run the command though, "mri_segment -p 0.6 brain.mgz wm.seg.mgz"

The command properly sets the threshold to 60%, but also takes the "0.6" to be in the input file name instead of brain.mgz.

Is there another option I'm missing? Or have I unfortunately stumbled upon a small bug?

Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Wil

we can certainly post it if there is enough interest.

cheers Bruce On Fri, 5 Aug 2011, Irwin, William wrote:

Hi Bruce-

Is this fix going to be put on the site as a patch/fix download (e.g., ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/) or distributed on a per-user need?

Thanks, Wil ____________________________________ William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco  CA  94143-1207 wirwin@memory.ucsf.edu | memory.ucsf.edu p: 415.476.1680 | f: 415.476.1816

|-----Original Message----- |From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] |Sent: Thursday, August 04, 2011 12:39 PM |To: Christopher Luna |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] mri_segment optional flags problem | |oops, I just fixed that. If you let us know what software/hardware env you are |using we'll give you an updated binary. | |Bruce | | |On Thu, 4 Aug 2011, Christopher Luna |wrote: | |> Hello, |> I'm trying to run mri_segment with some custom values in the optional |> flags, such as -p for setting the percentage threshold with a float value. |> |> When I run the command though, |> "mri_segment -p 0.6 brain.mgz wm.seg.mgz" |> |> The command properly sets the threshold to 60%, but also takes the "0.6" to |be in the input file name instead of brain.mgz. |> |> Is there another option I'm missing? Or have I unfortunately stumbled upon |a small bug? |> |> Thanks, |> Christopher Luna |> MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern |> Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony |> at MIT |> |> |>

Thanks for your help!

Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

On Fri, Aug 5, 2011 at 3:22 PM, Irwin, William WIrwin@memory.ucsf.eduwrote:

Bruce,

Until it is determined if there is enough interest, how do I obtain it for centos4_x86_64?

Thanks much, Wil

|-----Original Message----- |From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] |Sent: Friday, August 05, 2011 12:10 PM |To: Irwin, William |Cc: Christopher Luna; freesurfer@nmr.mgh.harvard.edu |Subject: RE: [Freesurfer] mri_segment optional flags problem | |Hi Wil | |we can certainly post it if there is enough interest. | |cheers |Bruce |On Fri, 5 Aug 2011, |Irwin, William wrote: | |> Hi Bruce- |> |> Is this fix going to be put on the site as a patch/fix download (e.g., |ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux- |centos4_x86_64/) or distributed on a per-user need? |> |> Thanks, |> Wil |> ____________________________________ |> William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging |> Center |> 350 Parnassus Avenue, Suite 905 |> San Francisco CA 94143-1207 |> wirwin@memory.ucsf.edu | memory.ucsf.edu |> p: 415.476.1680 | f: 415.476.1816 |> |> |> |> |-----Original Message----- |> |From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] |> |Sent: Thursday, August 04, 2011 12:39 PM |> |To: Christopher Luna |> |Cc: freesurfer@nmr.mgh.harvard.edu |> |Subject: Re: [Freesurfer] mri_segment optional flags problem |> | |> |oops, I just fixed that. If you let us know what software/hardware |> |env you are using we'll give you an updated binary. |> | |> |Bruce |> | |> | |> |On Thu, 4 Aug 2011, Christopher Luna |> |wrote: |> | |> |> Hello, |> |> I'm trying to run mri_segment with some custom values in the |> |> optional flags, such as -p for setting the percentage threshold with a float |value. |> |> |> |> When I run the command though, |> |> "mri_segment -p 0.6 brain.mgz wm.seg.mgz" |> |> |> |> The command properly sets the threshold to 60%, but also takes the |> |> "0.6" to |> |be in the input file name instead of brain.mgz. |> |> |> |> Is there another option I'm missing? Or have I unfortunately |> |> stumbled upon |> |a small bug? |> |> |> |> Thanks, |> |> Christopher Luna |> |> MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, |> |> McGovern Institute for Brain Research MIT Archery Club Alpha Kappa |> |> Psi Colony at MIT |> |> |> |> |> |> |> |> |> |> | | |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.