freesurfer 7.3.2 (August 2022)

dnkennedy@stage.nitrcce.org (David Kennedy) — Mon, 01 Aug 2022 4:00:00 GMT

Stable v4.5.0

11 Aug 2009

Stable release version 4.5.0 is a minor release containing bug fixes and new features affecting both the default (cross-sectional) and longitudinal analysis streams.

What's New

* Bug fixes:
o fixed mri_glmfit-sim, mri_glmfit, and mri_surfcluster: when sign was set to abs, gave the same significance for all clusters.
o fixed mris_volmask (the -cortribbon stage of recon-all): segfaulted if not enough memory was available. a memory leak was plugged.
* New features:
o

improvements to the longitudinal stream further reducing bias found between cross-sectional and longitudinal runs. See LongitudinalChangeLog.
o

updated C.Destrieux atlas (aparc.a2009s). See DestrieuxAtlasChanges.
o -norandomness is the the default. The binaries in the recon-all stream which are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with the same number, with the result being that repeated runs of the recon-all stream on a subject on the same platform will always give identical results. The -randomness flag can be used to allow usage of a random seed.
o updated versions of aparcstats2table and asegstats2table have:
+ ability to choose common segmentations or all segmentations in asegstats2table
+ different invocations of these scripts produce outputs which have segs/parcs in the same order
+

better debug information ( with the -v or --debug switch )
o support for reading .vtk surface format, and writing patch files in gifti (.gii) format
o built against static libtiff, negating the problem of some systems having shared lib libtiff.so.3 and others libtiff.so.4

Known Issues

*

mri_ca_label: this message might appear: "GCA sequential renormalization: label 28 not consistently computed." prior to exiting. This error is invalid (an exit should not occur). There is no work-around. A fix will appear in the next release. Or users can download a new mri_ca_label for their platform here.
* mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. There is no work-around.
* make_average_volume: can exit with 'Cannot alloc memory' error if there are a lot of subjects. The work-around is to include the flag '-no-aseg', which will prevent creating the aseg.mgz.
* mris_make_face_parcellations: creates labels with spaces in the name, which causes table parsing in aparcstats2table to fail. a fix (using underscores) will appear in the next release.
*

aparcstats2table, asegstats2table: output the parcellations/segmentations in a random order compared to the input aseg.stats/?h.aparc.stats files. A fix will appear in the next release. For 4.5.0 users, they can be downloaded from here. Copy the files asegstats2table, aparcstats2table and datastruct_utils.py to your $FREESURFER_HOME/bin.
* mris_volmask: the VTK library dependency can be problematic on some systems, particularly clusters. The next release will include a new mris_volmask with the VTK library dependency removed.

Upcoming features (next release)

* QDEC:
o added Nuisance Factor menu in Design tab, allowing selection of any number of continuous variables of which will be treated as 'nuisance variables' in the glm (contrast matrix will have value '0' for these)
o

added FindClustersAndGotoMax button to run mri_surfcluster on a selected result, which will find clusters based on currently selected display threshold, output a table of results to the terminal, and move the cursor to the max vertex in the #1 cluster. 'Next' and 'Prev' buttons allow cycling movement of the cursor through the found clusters.
o added QuickSnapsTIFF option to automatically take snapshots of medial/lateral pial/inflated and save these four pics to an automatically generated filename
o added optional parsing of an 'ignore.factors' file to allow specifying columns in the qdec.table.dat to ignore (as would be case for columns containing alternate subject IDs)
o added optional parsing of an 'ordinal.factors' file to allow specifying which continuous factors are ordinals (integers, not floating point). only affects 'Save Data Table' menu option where the qdec.table.dat is written to disk (ordinals are not written as floats).
o added usage of NaN (or nan) to indicate missing data point, allowing automatic exclusion of that subject from an analysis
* mri_nu_correct.mni will use float internally instead of uchar. It will also rescale the output so that the global mean is the same as that of the input. These two changes are linked and can be turned off with --no-float.
* GPU support:
o

mri_em_register will make use of a GPU card, reducing runtime from 30-40 minutes down to 3 minutes. Adding the flag -use-gpu to recon-all will enable GPU support on CUDA-compatible Nvidia cards for this and future freesurfer executables.

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dnkennedy@stage.nitrcce.org (David Kennedy) — Tue, 14 Oct 2008 20:13:00 GMT

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