Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

2019-09-14 Thread Thomas Yeo
External Email - Use Caution

Hi Doug,

In which version of FreeSurfer does this bug appear? And under what
situation does this bug appear?

I swear I have used the command with similar flags, but did not experience
this bug.

Thanks,
Thomas

On Fri, Sep 13, 2019 at 10:58 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> This is a bug. I've fixed it in our development version. You can download
> an update from here
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surf2surf
>
>
> On 9/13/19 8:00 AM, Matthieu VANHOUTTE wrote:
>
>External Email - Use Caution
> Dear FS's experts,
>
> I am trying to downsample some surface data from fsaverage to fsaverage6
> with the following command:
>
>  mri_surf2surf --hemi lh --srcsubject fsaverage --sval
> ./lh.fsaverage.s8mm.mgh  --trgsubject fsaverage6 --tval
> ./lh.fsaverage6.s8mm.mgh --cortex
>
> However, the output surface data is a binary file contrary to the source
> one (please see attached).
>
> Would anyone have an idea of the problem?
>
> Best,
>
> Matthieu
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

2019-09-13 Thread Greve, Douglas N.,Ph.D.
This is a bug. I've fixed it in our development version. You can download an 
update from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surf2surf


On 9/13/19 8:00 AM, Matthieu VANHOUTTE wrote:
   External Email - Use Caution
Dear FS's experts,

I am trying to downsample some surface data from fsaverage to fsaverage6 with 
the following command:

 mri_surf2surf --hemi lh --srcsubject fsaverage --sval ./lh.fsaverage.s8mm.mgh  
--trgsubject fsaverage6 --tval ./lh.fsaverage6.s8mm.mgh --cortex

However, the output surface data is a binary file contrary to the source one 
(please see attached).

Would anyone have an idea of the problem?

Best,

Matthieu




___
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

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

2019-09-13 Thread Bruce Fischl
oh I see. I thought you meant the file format was not binary. Hmmm, not 
sure. Maybe Doug will have some insight, as I didn't think surf2surf would 
binarize by default

Bruce
On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:



External Email - Use Caution

Hi Bruce,

The input file has not only binary values (0 or 1) it is made of float
values, whereas the output mri_surf2surf contains only binary values.

Best,

Matthieu

On 13/09/2019 15:52, Bruce Fischl wrote:
  Hi Matthieu

  sorry, I don't understand. All the files are binary, no? Are you
  getting an error?

  cheers
  Bruce
  On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:

  External Email - Use Caution Dear FS's
experts,

I am trying to downsample some surface data from
fsaverage to fsaverage6 with the following command:

 mri_surf2surf --hemi lh --srcsubject fsaverage
--sval ./lh.fsaverage.s8mm.mgh  --trgsubject
fsaverage6 --tval ./lh.fsaverage6.s8mm.mgh --cortex

However, the output surface data is a binary file
contrary to the source one (please see attached).

Would anyone have an idea of the problem?

Best,

Matthieu




___
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

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

2019-09-13 Thread Matthieu VANHOUTTE
   External Email - Use Caution


Hi Bruce,

The input file has not only binary values (0 or 1) it is made of float 
values, whereas the output mri_surf2surf contains only binary values.


Best,

Matthieu

On 13/09/2019 15:52, Bruce Fischl wrote:

Hi Matthieu

sorry, I don't understand. All the files are binary, no? Are you 
getting an error?


cheers
Bruce
On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:


  External Email - Use Caution Dear FS's experts,

I am trying to downsample some surface data from fsaverage to 
fsaverage6 with the following command:


 mri_surf2surf --hemi lh --srcsubject fsaverage --sval 
./lh.fsaverage.s8mm.mgh  --trgsubject fsaverage6 --tval 
./lh.fsaverage6.s8mm.mgh --cortex


However, the output surface data is a binary file contrary to the 
source one (please see attached).


Would anyone have an idea of the problem?

Best,

Matthieu





___
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

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

2019-09-13 Thread Bruce Fischl

Hi Matthieu

sorry, I don't understand. All the files are binary, no? Are you getting 
an error?


cheers
Bruce
On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:

  External Email - Use Caution 
Dear FS's experts,


I am trying to downsample some surface data from fsaverage to fsaverage6 with 
the following command:


 mri_surf2surf --hemi lh --srcsubject fsaverage --sval 
./lh.fsaverage.s8mm.mgh  --trgsubject fsaverage6 --tval 
./lh.fsaverage6.s8mm.mgh --cortex


However, the output surface data is a binary file contrary to the source one 
(please see attached).


Would anyone have an idea of the problem?

Best,

Matthieu


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