Hi All, as some of you have figured out, we have a beta version of FS
8.0.0. Please give it a spin and let us know if you have any problems or
concerns.
The release notes are here
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes which I have
copied below.
One bug that we have already found is that you must set environment
variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or
setenv FS_ALLOW_DEEP 1 (for csh/tcsh)
thanks
doug
*
Now uses SynthSeg
<https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg>, SynthStrip
<https://synthstrip.io>, and SynthMorph <https://synthmorph.io>
(deep learning algorithms). These make recon-all more robust and
much faster. Technically, SynthMorph <https://synthmorph.io> is not
needed for recon-all to run, but the nonlinear registration can be
used in multimodal analysis to map to the MNI152.
* There is now DL automatic segmentation of regions that often cause
errors in pial surface placement. These include the major sinuses
(sagittal and transverse) as well as a spot between frontal and
temporal lobes where the middle cerebral artery (MCA) and dura cause
bright areas.
* Several fixes in entorhinal cortex. First, the WM in EC is segmented
using DL. The WM is often only 0.5mm thick and very hard to see;
this often resulted in severe white surface areas in this location
requiring manual editing to fix. The new surface now represents
gyrus ambiens much better. Second, The white surface is extended to
the front of amygdala. Third, the binary cortex of label now covers
entorhinal cortex and parts of the temporal pole better allowing the
pial surface to extend out to its true edge.
* Some bugs where found in and around inferior frontal cortex causes
the white surface to extend too far into basal ganglia. This has
been fixed. This is above and beyond the issue reported in 7.3.2 below.
* All the bug fixes described below are now turned on by default.
* These changes will work with longitudinal with the caveat that the
volumetric segmentation will not be fully longitudinal. The
segmentation will be applied to the time point in the base space,
but it will not (and cannot) be initialized with the base
segmentation. Initial tests indicated that the change in power was
minimal and mixed.
* recon-all will now run in about 2h vs 8h on a single CPU. It will,
however, required about 24GB of memory to run.
*
The use of SynthStrip <https://synthstrip.io> should make recon-all
much more robust as the old skull stripping method often included
extra cerebral tissue.
* With synthseg, we are now supplying a segmentation-based total
intracrainial volume (sTIV) along with the registration-based
estimated TIV (eTIV)
* We have applied v8 to several studies (aging, AD crossectional, AD
longitudinnal, schizophrenia). There were no major changes in the
ability to detect effects, and there was no interaction between
effect and version. But let us know how it performs on your studies.
External Email - Use Caution
Hello Chemda,
Maybe you could let us know what version of freesurfer you are running, what version of Linux or Mac OS your machine is running, and how much memory the machine has. The recon-all.log could also be useful to send along. A machine lacking resources like memory, disk space, etc., could hang.
- R.
On Dec 1, 2024, at 05:41, chemda wiener <chemda10(a)gmail.com> wrote: External Email - Use Caution
Hi,
My name is Chemda Wiener. I am a PhD student in a Neuro-Engineering lab. We are working with MRI scans of patients with epilepsy and I am attempting to use freesurfer to create the mesh .pial files. When I run the freesurfer recon-all command, the command gets stuck at "correcting defects" with the last file it creates being the "lh.defect_chull". It has been stuck for a few days on this part until I finally killed the process. I tried running autorecon2 afterwards on this patient to see if it can pick up from where it stopped but it gets stuck again at the same place.
I would appreciate any help in the matter.
Thank you in advance for your time and your software!Chemda_______________________________________________
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