If your WM volume is not conformed, you will need to conform it with
mri_convert yourwm.mgz --conform wm.mgz


On 12/5/19 4:24 AM, Jordi Huguet wrote:
>
>         External Email - Use Caution
>
> Hi Douglas,
>
> I have followed the suggested approach, however I get an error related
> to the dimensions of the WM volume (see log trace below).
>
>     ...
>
>     Found wm edits: 23448857 deletes, 783317 fills
>
>      cp wm.mgz wm.seg.mgz
>
>
>      mri_segment -keep -mprage brain.mgz wm.seg.mgz
>
>     preserving editing changes in output volume...
>     doing initial intensity segmentation...
>     using local statistics to label ambiguous voxels...
>     computing class statistics for intensity windows...
>     WM (104.0): 105.4 +- 6.0 [79.0 --> 125.0]
>     GM (69.0) : 67.0 +- 10.5 [30.0 --> 95.0]
>     setting bottom of white matter range to 77.5
>     setting top of gray matter range to 88.0
>     doing initial intensity segmentation...
>     using local statistics to label ambiguous voxels...
>     using local geometry to label remaining ambiguous voxels...
>
>     reclassifying voxels using Gaussian border classifier...
>
>     removing voxels with positive offset direction...
>     smoothing T1 volume with sigma = 0.250
>     removing 1-dimensional structures...
>     thickening thin strands....
>     20 segments, 7509 filled
>     8232 bright non-wm voxels segmented.
>     8121 diagonally connected voxels added...
>     white matter segmentation took 2.7 minutes
>     writing output to wm.seg.mgz...
>     *ERROR: mri_segment-MRIcheckVolDims: volume1 width=240 != volume2
>     width=320.*
>
>
> My WM segmentations (as well as the T1w images) are 320 rows x 320
> columns in 240 frames. Seems like FreeSurfer expects them to be cubic,
> correct?
> Would that fix the problem if I add 80 frames of zeroes (or ones) to
> my volumes? Any other ideas of what I might be doing wrong?
>
> Regards,
> Jordi
>
> On Thu, Nov 28, 2019 at 8:47 AM Jordi Huguet <jhuguetn@gmail.com
> <mailto:jhuguetn@gmail.com>> wrote:
>
>     Great, just what I was looking for!
>
>     Thanks Douglas,
>     Jordi
>
>     On Wed, Nov 27, 2019, 19:47 Greve, Douglas N.,Ph.D.
>     <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>
>         It might work if you
>         mkdir -p FOO/mri
>         cp yourwm.mgz FOO/mri/wm.mgz
>         cp inputdata.mgz FOO/mri/orig/001.mgz
>         then run recon-all -s FOO -all
>
>
>         On 11/27/2019 12:39 PM, Jordi Huguet wrote:
>>
>>                 External Email - Use Caution
>>
>>         Hi Bruce,
>>
>>         Many thanks for your reply.
>>
>>         I understand from your answer that it could be done as
>>         follows (I am not an expert in FreeSurfer directives):
>>
>>         a) run full FreeSurfer pipeline
>>         recon-all -s FOO
>>         b) insert pre-existing WM segmentation as wm.mgz (modifying
>>         the intensity values)
>>         c) re-run stages 15-23 and 24-31 (recon-all shall use my
>>         external segmentation as WM "edits")
>>         recon-all -s FOO -autorecon2-wm -autorecon3
>>
>>         Is it possible however to just include the WM segmentation
>>         without executing a full early run of recon-all?
>>
>>         Thanks,
>>         Jordi
>>
>>
>>         On Tue, Nov 26, 2019 at 3:08 PM Bruce Fischl
>>         <fischl@nmr.mgh.harvard.edu
>>         <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
>>
>>             Hi Jordi
>>
>>             yes, this should be possible. You might need to run
>>             recon-all in stages
>>             though. Although if you set the wm.mgz values from SPM to
>>             255 and 1 (not 0)
>>             recon-all should detect them as "edits" and retain them
>>
>>             cheers
>>             Bruce
>>
>>
>>             On Tue, 26 Nov 2019, Jordi Huguet wrote:
>>
>>             >
>>             >         External Email - Use Caution
>>             >
>>             > Hi there,
>>             > I wonder if its somehow possible to feed FreeSurfer's
>>             recon-all with pre-existing segmented maps
>>             > (based on prior segmentation procedure e.g. SPM or
>>             ANTs) to "improve" FreeSurfer results.
>>             >
>>             > For some images I am working with the FreeSurfer's WM
>>             segmentation output is not optimal so I am
>>             > looking for alternatives to improve the final results
>>             on such specific cases without requiring any
>>             > manual intervention.
>>             >
>>             > Any comments, examples or shared reflections on this
>>             regard are kindly welcome.
>>             >
>>             > Thanks in advance,
>>             > Jordi Huguet
>>             >
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