You should use aparc+aseg.mgz and set the --projfrac 0.5. This should 
produce something with the same information as the ?h.aparc.annot 
(though the color scale will be different)


On 09/30/2016 03:51 PM, Crawford, Anna wrote:
> I was just using the wmparc as an example to get a volume overlay onto the 
> surface. I chose that one just to see the parcellated surface similar to the 
> volume.
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, September 30, 2016 3:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Volume to Surface
>
> I can't tell from that image if it is right. Why are you mapping the
> wmparc to the surface? The wmparc will have segmentation boundaries
> right at the surface, so the actual value there will be unpredicatable.
>
>
> On 09/30/2016 03:31 PM, Crawford, Anna wrote:
>> Thank you everyone for your help! I do have a follow up question. I believe 
>> this did what I wanted and is what I will want to do for PET data for 
>> example. When I did the wmparc to the surface, I was expecting to  see the 
>> different areas mapped out similar to the volume. I have attached a screen 
>> capture of what it looks like. Can someone confirm that this seems to be 
>> correct and I was just expecting the wrong thing? I suspect this is the case 
>> since to see the different areas in the volume you use the look up table for 
>> the color map and that is not an option for the surface overlay.
>>
>> Thank you all again for your feedback!
>>
>> Anna
>> ________________________________________
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, September 30, 2016 2:42 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Volume to Surface
>>
>> Anna, try removing --out_type paint and instead specify the output file
>> as wmparcSlh.mgh
>>
>> Trisanna, thanks so much for chipping in!
>>
>>
>>
>> On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
>>> 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 <crawf...@ccf.org
>>> <mailto:crawf...@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-boun...@nmr.mgh.harvard.edu
>>>       <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>>       [freesurfer-boun...@nmr.mgh.harvard.edu
>>>       <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>>>       Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>>>       <mailto:trisanna.sprung-m...@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 <crawf...@ccf.org
>>>       <mailto:crawf...@ccf.org>> wrote:
>>>
>>>           Yeah, I get Error: Option unknown for --regmethod
>>>
>>>           Anna
>>>           
>>> ------------------------------------------------------------------------
>>>           *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>           <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>>           [freesurfer-boun...@nmr.mgh.harvard.edu
>>>           <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>>>           Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>>>           <mailto:trisanna.sprung-m...@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
>>>           <crawf...@ccf.org <mailto:crawf...@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-boun...@nmr.mgh.harvard.edu
>>>               <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>>               [freesurfer-boun...@nmr.mgh.harvard.edu
>>>               <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf
>>>               of Trisanna Sprung-Much
>>>               [trisanna.sprung-m...@mail.mcgill.ca
>>>               <mailto:trisanna.sprung-m...@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
>>>               <crawf...@ccf.org <mailto:crawf...@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-boun...@nmr.mgh.harvard.edu
>>>                   <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>>                   [freesurfer-boun...@nmr.mgh.harvard.edu
>>>                   <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on
>>>                   behalf of Trisanna Sprung-Much
>>>                   [trisanna.sprung-m...@mail.mcgill.ca
>>>                   <mailto:trisanna.sprung-m...@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
>>>                   <crawf...@ccf.org <mailto:crawf...@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-boun...@nmr.mgh.harvard.edu
>>>                       <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>>                       [freesurfer-boun...@nmr.mgh.harvard.edu
>>>                       <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>>>                       on behalf of Trisanna Sprung-Much
>>>                       [trisanna.sprung-m...@mail.mcgill.ca
>>>                       <mailto:trisanna.sprung-m...@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
>>>                       <crawf...@ccf.org <mailto:crawf...@ccf.org>> wrote:
>>>
>>>                           I already ran recall-all. I am trying to
>>>                           create a different surface not created using
>>>                           recon-all.
>>>
>>>                           Anna
>>>                           
>>> ------------------------------------------------------------------------
>>>                           *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>                           <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>>                           [freesurfer-boun...@nmr.mgh.harvard.edu
>>>                           <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>>>                           on behalf of Trisanna Sprung-Much
>>>                           [trisanna.sprung-m...@mail.mcgill.ca
>>>                           <mailto:trisanna.sprung-m...@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 <crawf...@ccf.org
>>>                           <mailto:crawf...@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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>>>               Cleveland Clinic is ranked as one of the top hospitals in
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>>>               Note: This message is intended for use only by the
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>>>           ===================================
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>>>           Please consider the environment before printing this e-mail
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>>>           Cleveland Clinic is ranked as one of the top hospitals in
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>>>           http://www.clevelandclinic.org for a complete listing of our
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>>>           message is intended for use only by the individual or entity
>>>           to which it is addressed and may contain information that is
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>>>           https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>           <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>
>>>
>>>           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
>>>           <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.
>>>
>>>
>>>       ===================================
>>>
>>>       Please consider the environment before printing this e-mail
>>>
>>>       Cleveland Clinic is ranked as one of the top hospitals in America
>>>       by U.S.News & World Report (2015). Visit us online at
>>>       http://www.clevelandclinic.org for a complete listing of our
>>>       services, staff and locations. Confidentiality Note: This message
>>>       is intended for use only by the individual or entity to which it
>>>       is addressed and may contain information that is privileged,
>>>       confidential, and exempt from disclosure under applicable law. If
>>>       the reader of this message is not the intended recipient or the
>>>       employee or agent responsible for delivering the message to the
>>>       intended recipient, you are hereby notified that any
>>>       dissemination, distribution or copying of this communication is
>>>       strictly prohibited. If you have received this communication in
>>>       error, please contact the sender immediately and destroy the
>>>       material in its entirety, whether electronic or hard copy. Thank you.
>>>
>>>       _______________________________________________
>>>       Freesurfer mailing list
>>>       Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>       <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>
>>>
>>>       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
>>>       <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.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ===================================
>>
>>
>>    Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>> U.S.News & World Report (2015).
>> Visit us online at http://www.clevelandclinic.org for a complete listing of 
>> our services, staff and locations.
>>
>>
>> Confidentiality Note:  This message is intended for use only by the 
>> individual or entity to which it is addressed and may contain information 
>> that is privileged, confidential, and exempt from disclosure under 
>> applicable law.  If the reader of this message is not the intended recipient 
>> or the employee or agent responsible for delivering the message to the 
>> intended recipient, you are hereby notified that any dissemination, 
>> distribution or copying of this communication is strictly prohibited.  If 
>> you have received this communication in error,  please contact the sender 
>> immediately and destroy the material in its entirety, whether electronic or 
>> hard copy.
>>
>> Thank you.
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ===================================
>
>
>   Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News 
> & World Report (2015).
> Visit us online at http://www.clevelandclinic.org for a complete listing of 
> our services, staff and locations.
>
>
> Confidentiality Note:  This message is intended for use only by the 
> individual or entity to which it is addressed and may contain information 
> that is privileged, confidential, and exempt from disclosure under applicable 
> law.  If the reader of this message is not the intended recipient or the 
> employee or agent responsible for delivering the message to the intended 
> recipient, you are hereby notified that any dissemination, distribution or 
> copying of this communication is strictly prohibited.  If you have received 
> this communication in error,  please contact the sender immediately and 
> destroy the material in its entirety, whether electronic or hard copy.
>
> Thank you.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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