Hi Nick,

Thanks for the tool. I am getting output of 0 with

mris_wm_volume con_2304 lh

0

This follows the usage as I see it. Am I using this wrong?

Cheers,

-Morgan

Nick Schmansky wrote:

Morgan,

I've posted mris_wm_volume for the various platforms at this location:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev

Nick

On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote:

...

Would it be possible to post binaries of mris_wm_volume again? I believe this is the preferred tool to calculate the total white matter volume over the current aseg output. Thanks in advance.

Cheers,

-Morgan

---

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

Hi Bruce,

I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps?

Cheers,

-Morgan

Bruce Fischl wrote:

that looks like the correct usage. Can you send the entire screen output? On Fri, 20 Jul 2007, Morgan Hough wrote:

...

Hi Nick,

Thanks for the tool. I am getting output of 0 with

...

mris_wm_volume con_2304 lh

0

This follows the usage as I see it. Am I using this wrong?

Cheers,

-Morgan

Nick Schmansky wrote:

...

Morgan,

I've posted mris_wm_volume for the various platforms at this location:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev

Nick

On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote:

...

Would it be possible to post binaries of mris_wm_volume again? I believe this is the preferred tool to calculate the total white matter volume over the current aseg output. Thanks in advance.

Cheers,

-Morgan

---

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

Morning Bruce,

I just checked this on a subject you already have there. I get the same result at NMR with this subject using the dev version of mris_wm_volume from /usr/local/freesurfer/dev/bin/mris_wm_volume which I think is the best match for the binary I have.

The subject is located at NMR at /autofs/homes/010/morgan/con_2878.

Cheers,

-Morgan

Bruce Fischl wrote:

works for me. Can you drop the subjects on our site? On Tue, 24 Jul 2007, Morgan Hough wrote:

...

Hi Bruce,

I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps?

Cheers,

-Morgan

Bruce Fischl wrote:

...

that looks like the correct usage. Can you send the entire screen output? On Fri, 20 Jul 2007, Morgan Hough wrote:

...

Hi Nick,

Thanks for the tool. I am getting output of 0 with

...

mris_wm_volume con_2304 lh

0

This follows the usage as I see it. Am I using this wrong?

Cheers,

-Morgan

Nick Schmansky wrote:

...

Morgan,

I've posted mris_wm_volume for the various platforms at this location:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev

Nick

On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote:

...

Would it be possible to post binaries of mris_wm_volume again? I believe this is the preferred tool to calculate the total white matter volume over the current aseg output. Thanks in advance.

Cheers,

-Morgan

---

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 Bruce,

I try this in $subject/mri but I get the following:

mri_convert --in_center --in_center 0 0 0 aseg.mgz aseg_test.mgz

mri_convert: error converting "--in_center" to a float for --in_center flag

type mri_convert -u for usage

Do I need to set the output datatype with -odt uchar or something like that?

Cheers,

-Morgan

Bruce Fischl wrote:

okay, I think I know what's happing. Try this and see if it fixes it:

from the subject's mri dir

mri_convert --in_center --in_center 0 0 0 aseg.mg aseg_test.mgz

then run

mris_wm_volume -aseg aseg_test.mgz $subject $hemi

On Tue, 24 Jul 2007, Morgan Hough wrote:

...

Morning Bruce,

I just checked this on a subject you already have there. I get the same result at NMR with this subject using the dev version of mris_wm_volume from /usr/local/freesurfer/dev/bin/mris_wm_volume which I think is the best match for the binary I have.

The subject is located at NMR at /autofs/homes/010/morgan/con_2878.

Cheers,

-Morgan

Bruce Fischl wrote:

...

works for me. Can you drop the subjects on our site? On Tue, 24 Jul 2007, Morgan Hough wrote:

...

Hi Bruce,

I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps?

Cheers,

-Morgan

Bruce Fischl wrote:

...

that looks like the correct usage. Can you send the entire screen output? On Fri, 20 Jul 2007, Morgan Hough wrote:

...

Hi Nick,

Thanks for the tool. I am getting output of 0 with

> mris_wm_volume con_2304 lh 0

This follows the usage as I see it. Am I using this wrong?

Cheers,

-Morgan

Nick Schmansky wrote: > Morgan, > > I've posted mris_wm_volume for the various platforms at this > location: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev > > Nick > > On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote: > >> Would it be possible to post binaries of mris_wm_volume again? >> I believe this is the preferred tool to calculate the total >> white matter volume over the current aseg output. Thanks in >> advance. >> >> Cheers, >> >> -Morgan >> >> _______________________________________________ >> 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 Bruce,

That did it. Great. The output is mm^3? Thanks again.

Cheers,

-Morgan

Bruce Fischl wrote:

oops, there should only be one --in_center on the cmd line (followed by 0 0 0 ) On Tue, 24 Jul 2007, Morgan Hough wrote:

...

Hi Bruce,

I try this in $subject/mri but I get the following:

mri_convert --in_center --in_center 0 0 0 aseg.mgz aseg_test.mgz

mri_convert: error converting "--in_center" to a float for --in_center flag

type mri_convert -u for usage

Do I need to set the output datatype with -odt uchar or something like that?

Cheers,

-Morgan

Bruce Fischl wrote:

...

okay, I think I know what's happing. Try this and see if it fixes it:

from the subject's mri dir

mri_convert --in_center --in_center 0 0 0 aseg.mg aseg_test.mgz

then run

mris_wm_volume -aseg aseg_test.mgz $subject $hemi

On Tue, 24 Jul 2007, Morgan Hough wrote:

...

Morning Bruce,

I just checked this on a subject you already have there. I get the same result at NMR with this subject using the dev version of mris_wm_volume from /usr/local/freesurfer/dev/bin/mris_wm_volume which I think is the best match for the binary I have.

The subject is located at NMR at /autofs/homes/010/morgan/con_2878.

Cheers,

-Morgan

Bruce Fischl wrote:

...

works for me. Can you drop the subjects on our site? On Tue, 24 Jul 2007, Morgan Hough wrote:

...

Hi Bruce,

I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps?

Cheers,

-Morgan

Bruce Fischl wrote: > that looks like the correct usage. Can you send the entire > screen output? > On Fri, 20 Jul 2007, Morgan Hough wrote: > >> Hi Nick, >> >> Thanks for the tool. I am getting output of 0 with >> >>> mris_wm_volume con_2304 lh >> 0 >> >> This follows the usage as I see it. Am I using this wrong? >> >> Cheers, >> >> -Morgan >> >> Nick Schmansky wrote: >>> Morgan, >>> >>> I've posted mris_wm_volume for the various platforms at this >>> location: >>> >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev >>> >>> >>> Nick >>> >>> On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote: >>> >>>> Would it be possible to post binaries of mris_wm_volume >>>> again? I believe this is the preferred tool to calculate the >>>> total white matter volume over the current aseg output. >>>> Thanks in advance. >>>> >>>> Cheers, >>>> >>>> -Morgan >>>> >>>> _______________________________________________ >>>> 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 >> >> >>

p.s. future versions of mris_wm_volume won't need this On Tue, 24 Jul 2007, Morgan Hough wrote:

Hi Bruce,

That did it. Great. The output is mm^3? Thanks again.

Cheers,

-Morgan

Bruce Fischl wrote:

...

oops, there should only be one --in_center on the cmd line (followed by 0 0 0 ) On Tue, 24 Jul 2007, Morgan Hough wrote:

...

Hi Bruce,

I try this in $subject/mri but I get the following:

mri_convert --in_center --in_center 0 0 0 aseg.mgz aseg_test.mgz

mri_convert: error converting "--in_center" to a float for --in_center flag

type mri_convert -u for usage

Do I need to set the output datatype with -odt uchar or something like that?

Cheers,

-Morgan

Bruce Fischl wrote:

...

okay, I think I know what's happing. Try this and see if it fixes it:

from the subject's mri dir

mri_convert --in_center --in_center 0 0 0 aseg.mg aseg_test.mgz

then run

mris_wm_volume -aseg aseg_test.mgz $subject $hemi

On Tue, 24 Jul 2007, Morgan Hough wrote:

...

Morning Bruce,

I just checked this on a subject you already have there. I get the same result at NMR with this subject using the dev version of mris_wm_volume from /usr/local/freesurfer/dev/bin/mris_wm_volume which I think is the best match for the binary I have.

The subject is located at NMR at /autofs/homes/010/morgan/con_2878.

Cheers,

-Morgan

Bruce Fischl wrote:

...

works for me. Can you drop the subjects on our site? On Tue, 24 Jul 2007, Morgan Hough wrote:

> Hi Bruce, > > I am afraid the zero is all the output I get. Do I need an updated > mris_volume as well perhaps? > > Cheers, > > -Morgan > > Bruce Fischl wrote: >> that looks like the correct usage. Can you send the entire screen >> output? >> On Fri, 20 Jul 2007, Morgan Hough wrote: >> >>> Hi Nick, >>> >>> Thanks for the tool. I am getting output of 0 with >>> >>>> mris_wm_volume con_2304 lh >>> 0 >>> >>> This follows the usage as I see it. Am I using this wrong? >>> >>> Cheers, >>> >>> -Morgan >>> >>> Nick Schmansky wrote: >>>> Morgan, >>>> >>>> I've posted mris_wm_volume for the various platforms at this >>>> location: >>>> >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev >>>> >>>> Nick >>>> >>>> On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote: >>>> >>>>> Would it be possible to post binaries of mris_wm_volume again? I >>>>> believe this is the preferred tool to calculate the total white >>>>> matter volume over the current aseg output. Thanks in advance. >>>>> >>>>> Cheers, >>>>> >>>>> -Morgan >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> > > >