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 <fis...@nmr.mgh.harvard.edu>
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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