Ok so this is where my knowledge might be limited because you did a slightly different thing than me by specifying the output type as "paint" - that is what the .w format is. This is a label, I believe and needs to be loaded as such.

What happens if you try to remove the "output_type" and try to load the result as an overlay?

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <CRAWFOA4@ccf.org> wrote:
Thank you! So good news, that worked and created wmparcSlh.w

I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay."

Thank you,
Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca]
Sent: Friday, September 30, 2016 12:51 PM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

My apologies, I meant "--regheader subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <CRAWFOA4@ccf.org> wrote:
Yeah, I get Error: Option unknown for --regmethod

Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca]
Sent: Friday, September 30, 2016 12:41 PM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

hmmm, yup not sure there. Did you try "--regmethod subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <CRAWFOA4@ccf.org> wrote:
Just to make sure I am actually doing what you are suggesting my input and output is below.

Thanks,
Anna

mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --hemi lh --surf white --out_type paint
INFO: output format is paint
srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): Success
Error reading inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca]
Sent: Friday, September 30, 2016 12:08 PM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Did you try --regmethod subjid? or --reg sphere.reg ?

If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <CRAWFOA4@ccf.org> wrote:
I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before.

Thanks,
Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca]
Sent: Friday, September 30, 2016 11:04 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation.

Maybe try that?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <CRAWFOA4@ccf.org> wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.

Thank you,
Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca]
Sent: Friday, September 30, 2016 10:48 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Sorry - always helps to read the whole question :D

So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.

Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <CRAWFOA4@ccf.org> wrote:
I already ran recall-all. I am trying to create a different surface not created using recon-all.

Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca]
Sent: Friday, September 30, 2016 10:40 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

You have to run recon-all to get the surfaces of a volume.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <CRAWFOA4@ccf.org> wrote:
Hello,

I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file?

Thank you,
Anna

mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint
INFO: output format is paint
srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): Success
Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat

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