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 <jhugu...@gmail.com > <mailto: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 <mailto: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 >> <mailto: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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
