Hi, at long last we have an official release of 7.3. See the release
notes can be found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes and also copied
below. Thanks to all who tested the beta version.
best
doug
* Bug fix when converting diffusion tensor data with a negative
determinant from DICOM. There was a bug in the old code that made
the bvecs incorrect in this case. The bvecs will now be correct
regardless of whether you use the old code or the new -dcm2niix
option (see below)
* Bug fix: ability to fill in underlabeled ventricles. This is not
done by default yet. To implement, add "-vent-fix -1 7000 1" to the
mri_ca_label command line. This can be incorporated into recon-all
by an expert options file with the line "mri_ca_label -vent-fix -1
7000 1".
* Bug fix: ability to force white matter (WM) between putamen and
cortex. This is not done by default yet. To implement, add
"-insert-wm-bet-putctx 1" to the mri_ca_label command line. This can
be incorporated into recon-all by an expert options file with the
line "mri_ca_label -insert-wm-bet-putctx 1". If you want to use both
the ventricle fix and the WM insertion, then create a line
"mri_ca_label -vent-fix -1 7000 1 -insert-wm-bet-putctx 1" to the
expert options files
*
Bug fix: improve surface placement in inferior frontal area near
putamen. There are some cases where the white surface is not placed
well in these areas because of the close proximity of putamen to
cortex; it is probably the case that the surface is not well-defined
in this region anyway, but the placement can be improved by creating
an expert options file with the line "WhitePreAparc --rip-bg-no-annot"
* Bug fix/New: ability to automatically edit the filled.mgz to remove
voxels from amygdala and parts of hippocampus. These voxels can
often cause topological defects that are not fixed properly. This is
not done by default yet. To implement, create an expert options file
with the line "mri_edit_wm_with_aseg -fix-scm-ha 1".
*
Bug fix: cross hemisphere analysis (xhemi
<https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>). In previous
versions, the surface registration (surfreg) would use the
annotation during the registration procedure which caused some
misalignment. Now surfreg will require that you specify either
--annot (old behavior) or --no-annot (new recommended). The errors
are small, so, if you have an ongoing analysis, you can stick with
the old behavior.
* Global Expert options file. If you have a file called
global-expert-options.txt in your $SUBJECTS_DIR, recon-all will
automatically read in this file as an expert options file
* Defect labels will now only encompass actual cortical areas. Before,
they would also include vertices on the medial wall, which was not
very useful
* New: Conversion from DICOM can now be done with dcm2niix as a
backend using -dcm2niix with either dcmunpack or mri_convert. This
should give the same result as when using the old code except it
will be much faster and can now handle all cases that dcm2niix can
handle, including enhanced dicom. At some point, this will become
the default method. Thanks to Chris Rorden and Yujing Huang for
getting this working.
* New: Gradient unwarping. There is a new program called
mri_gradunwarp; you still have to supply the gradient unwarping
spherical harmonics tables.
*
New: Minimally Invasive Defacing tool (MiDeFace
<https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace>).
*
New: segment_subfields
<https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation>
beta version new software to run subfield segmentation (hippocampus,
amygdala, thalamic). The old software required matlab. The new tool
is written in python but will not give exactly the same result but
will be extremely close. Does not work with T2 yet.
*
New: SynthStrip <https://surfer.nmr.mgh.harvard.edu/docs/synthstrip>
deep learning tool to strip skulls
*
New: ScLimbic <https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic>
subcortical limbic deep learning segmentation tool
*
New: HypothalamicSubunits
<https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits>
deep learning segmentation of hypothalamic subunits
*
New: SynthSeg <https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg>
deep learning contrast-independent whole brain segmentation
(including cortical parcellation)
*
New: Segmentation-based (SB) cost function
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690540/pdf/nihms916015.pdf>
for multimodal registration in mri_robust_register
* New: better version control. You can create a file called
fs-allowed-versions.txt in $SUBJECTS_DIR with a list of allowable
versions for your analysis. If this file exists, then both the
current version of FS and the version listed in
$subject/scripts/build-stamp.txt must be in the list for recon-all
to proceed. This helps to prevent using different/incompatible
versions of FS within the same analysis while allowing the mixture
of compatible versions.
* New: interface for X11 virtual frame buffer (fsxvfb). When you run
freeview from fsxvfb, no X server is needed. This is good for taking
a bunch of pictures when you don't want freeview popping up all the
time. Eg, fsxvfb freeview orig.mgz -ss mypic.png --quit
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