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> 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> 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> 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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