Re: [Freesurfer] Generating Surfaces from Labels

[Zach Humphrey]

Hello Dr. Fischl,

Thanks for the feedback. Can the flattened patches be "re-inflated" into
surface files again after being flattened?

I am also continuing to run into the issue with the label2vol function
where I end up with a volume that is completely filled. The steps I have
been following to reach this point are
1: Run mri_annotation2label --subject subjectname --hemi lh --outdir out
2: mri_label2vol --label $labelgeneratedfromstep1 --temp rawavg.mgz
--subject subjectname --hemi lh --o outputdirectory --fillthresh .3 --reg
register.dat --proj frac 0 1 .1
Honestly I am not sure what the --proj field actually means and so I have
been just using the 0 1 .1 that I found in examples of mri_label2vol. Could
this be the problem?

Thanks,
Zachary Humphrey

On Tue, Aug 8, 2017 at 3:51 PM, Bruce Fischl 
wrote:

> Hi Zach
>
> I think if you cut and flatten the cortical part of the surfaces, convert
> tha .annot files to separate label files, you can then use label2flat on
> each label to generate a flattened patch that is just taht label. I haven't
> used it in years (decades?), but I think it should work
>
> cheers
> Bruce
>
>  On Tue, 8 Aug 2017, Zach Humphrey wrote:
>
> Hello All,
>> I have been attempting to convert Label files generated using
>> mri_annotation2label into surface files for use in external programs. In
>> order to do this I first need to convert the label files into freesurfer
>> binary. I have attempted to use the mri_label2vol function to generate an
>> mgz file which could then be converted into freesurfer binary but this has
>> resulted in mgz files which depict a solid cube rather than any brain
>> structure. Any ideas as to why this could be?
>>
>> I would also prefer to avoid ever converting the label files to a volume
>> as
>> converting the volume file to a surface file results in a lower quality
>> than
>> if the file has been maintained as a surface file throughout. Is there any
>> way to use the Desikan Atlas to "divide" say the lh.pial surface file and
>> generate a number of .pial files each consisting of one of the regions
>> described by the Desikan Atlas?
>>
>> Thanks,
>> Zachary Humphrey
>>
>>
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Re: [Freesurfer] Generating Surfaces from Labels

[Douglas N Greve]

On 08/08/2017 03:42 PM, Zach Humphrey wrote:
> Hello All,
>
> I have been attempting to convert Label files generated using 
> mri_annotation2label into surface files for use in external programs. 
> In order to do this I first need to convert the label files into 
> freesurfer binary. I have attempted to use the mri_label2vol function 
> to generate an mgz file which could then be converted into freesurfer 
> binary but this has resulted in mgz files which depict a solid cube 
> rather than any brain structure. Any ideas as to why this could be?
I don't understand what this means. Can you elaborate or share a pic?
>
> I would also prefer to avoid ever converting the label files to a 
> volume as converting the volume file to a surface file results in a 
> lower quality than if the file has been maintained as a surface file 
> throughout. Is there any way to use the Desikan Atlas to "divide" say 
> the lh.pial surface file and generate a number of .pial files each 
> consisting of one of the regions described by the Desikan Atlas?
>
> Thanks,
> Zachary Humphrey
>
>
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Re: [Freesurfer] Generating Surfaces from Labels

[Bruce Fischl]

Hi Zach

I think if you cut and flatten the cortical part of the surfaces, convert 
tha .annot files to separate label files, you can then use label2flat on 
each label to generate a flattened patch that is just taht label. I haven't 
used it in years (decades?), but I think it should work


cheers
Bruce
 On Tue, 8 Aug 2017, 
Zach Humphrey wrote:



Hello All, 
I have been attempting to convert Label files generated using
mri_annotation2label into surface files for use in external programs. In
order to do this I first need to convert the label files into freesurfer
binary. I have attempted to use the mri_label2vol function to generate an
mgz file which could then be converted into freesurfer binary but this has
resulted in mgz files which depict a solid cube rather than any brain
structure. Any ideas as to why this could be? 

I would also prefer to avoid ever converting the label files to a volume as
converting the volume file to a surface file results in a lower quality than
if the file has been maintained as a surface file throughout. Is there any
way to use the Desikan Atlas to "divide" say the lh.pial surface file and
generate a number of .pial files each consisting of one of the regions
described by the Desikan Atlas? 

Thanks,
Zachary Humphrey

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[Freesurfer] Generating Surfaces from Labels

[Zach Humphrey]

Hello All,

I have been attempting to convert Label files generated using
mri_annotation2label into surface files for use in external programs. In
order to do this I first need to convert the label files into freesurfer
binary. I have attempted to use the mri_label2vol function to generate an
mgz file which could then be converted into freesurfer binary but this has
resulted in mgz files which depict a solid cube rather than any brain
structure. Any ideas as to why this could be?

I would also prefer to avoid ever converting the label files to a volume as
converting the volume file to a surface file results in a lower quality
than if the file has been maintained as a surface file throughout. Is there
any way to use the Desikan Atlas to "divide" say the lh.pial surface file
and generate a number of .pial files each consisting of one of the regions
described by the Desikan Atlas?

Thanks,
Zachary Humphrey
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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