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 <jhugu...@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. < > dgr...@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 <fis...@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 >>> > >>> >_______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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