Dear Jeff,

On 31 May 2021, at 18:44, Jeff Browndyke wrote:

> Thank you, Christian!
>
> The addition of the BPM-like voxel-wise covariate analysis capacity is 
> most appreciated and sorely needed since BPM is quite outdated.
>
> Are there any limitations on the data map types that can be used for 
> voxel-wise covariance?
You can use voxel-wise volume data or vertex-wise surface data that 
should be in the same space. The only limitation so far is that for 
statistical analysis the TFCE toolbox is needed and the „on-the-fly“ 
contrast definition is probably not that intuitive. Furthermore, it’s 
quite slow.

Best,

Christian

>
> Warm regards,
> Jeff
>
>
>
>> On May 31, 2021, at 12:30 PM, Christian Gaser 
>> <[log in to unmask]> wrote:
>>
>> Dear CAT12 users,
>>
>> a new CAT12.8 beta version is available for download:
>>
>> http://www.neuro.uni-jena.de/cat12/cat12_latest.zip
>>
>> I have also prepared precompiled CAT12 versions that don't require a 
>> Matlab license. This will be especially helpful in cluster 
>> environments with the cat_standalone.sh script in the standalone 
>> folder:
>>
>> http://www.neuro.uni-jena.de/cat12/cat12_latest_R2017b_MCR_Mac.zip
>>
>> http://www.neuro.uni-jena.de/cat12/cat12_latest_R2017b_MCR_Linux.zip
>>
>> Best,
>>
>> Christian
>>
>> Changes in version CAT12.8 (1830)
>> Changes in preprocessing pipeline (which affects your results 
>> compared to CAT12.7)
>> Volumetric templates, atlases, and TPMs are now transformed to 
>> MNI152NLin2009cAsym space to better match existing standards. The 
>> templates_volume folder is now renamed to 
>> ''templates_MNI152NLin2009cAsym'' to indicate the template space 
>> used. The Dartel and Geodesic Shooting templates are renamed or 
>> relocated:
>> templates_volumes/Template_0_IXI555_MNI152_GS.nii -> 
>> templates_MNI152NLin2009cAsym/Template_0_GS.nii
>> templates_volumes/Template_1_IXI555_MNI152.nii -> 
>> templates_MNI152NLin2009cAsym/Template_1_Dartel.nii
>> templates_volumes/TPM_Age11.5.nii -> 
>> templates_MNI152NLin2009cAsym/TPM_Age11.5.nii
>> templates_volumes/Template_T1_IXI555_MNI152_GS.nii -> 
>> templates_MNI152NLin2009cAsym/Template_T1.nii
>> spm12/toolbox/FieldMap/T1.nii -> templates_MNI152NLin2009cAsym/T1.nii
>> spm12/toolbox/FieldMap/brainmask.nii -> 
>> templates_MNI152NLin2009cAsym/brainmask.nii
>> The volumetric atlases have been revised and are now defined with a 
>> spatial resolution of 1mm, except for the Cobra atlas, which is 
>> defined with 0.6mm resolution. The labels of the original atlases 
>> were either transformed from the original data or recreated using a 
>> maximum likelihood approach when manual labels were available for all 
>> subjects (Cobra, LPBA40, IBSR, Hammers, Neuromorphometrics). In 
>> addition, the original labels are now used for all atlases if 
>> possible. Some atlases were updated to include new regions 
>> (Julichbrain, Hammers) and a new atlas of thalamic nuclei was added. 
>> Please note that this will also result in slight differences in ROI 
>> estimates compared to previous versions.
>> The bounding box of the Dartel and Geodesic Shooting templates has 
>> been changed, resulting in a slightly different image size of the 
>> spatially registered images (i.e. modulated normalized 
>> segmentations). Therefore, older preprocessed data should not (and 
>> cannot) be mixed with the new processed data (which is intended).
>> Transformed T1 Dartel/GS surface templates to the new 
>> MNI152NLin2009cAsym space:
>> templates_surfaces/lh.central.Template_T1_IXI555_MNI152_GS.gii -> 
>> templates_surfaces/lh.central.Template_T1.gii
>> templates_surfaces/rh.central.Template_T1_IXI555_MNI152_GS.gii -> 
>> templates_surfaces/rh.central.Template_T1.gii
>> templates_surfaces_32k/lh.central.Template_T1_IXI555_MNI152_GS.gii -> 
>> templates_surfaces_32k/lh.central.Template_T1.gii
>> templates_surfaces_32k/rh.central.Template_T1_IXI555_MNI152_GS.gii -> 
>> templates_surfaces_32k/rh.central.Template_T1.gii
>> The surface pipeline has been optimized to better handle data at 
>> different spatial resolutions.
>> Older preprocessing pipelines (12.1, 12.3, 12.6) were removed because 
>> their support became too difficult.
>> Important new features
>> The Mahalanobis distance in the quality check is now replaced by the 
>> normalized ratio between overall weighted image quality (IQR) and 
>> mean correlation. A low ratio indicates good quality before and after 
>> preprocessing and means that IQR is highly rated (resulting in a low 
>> nominal number/grade) and/or mean correlation is high. This is 
>> hopefully a more intuitive measure to combine image quality 
>> measurement before and after preprocessing.
>> CAT12 now allows the use of the BIDS directory structure for storing 
>> data (not possible for the longitudinal pipeline). A BIDS path can be 
>> defined relative to the participant level directory. The segmentation 
>> module now supports the input of nii.gz files (not possible for the 
>> longitudinal pipeline).
>> The "Basic models" function has been completely restructured and 
>> simplified. There are now only two models available for: (1) 
>> cross-sectional data and (2) longitudinal data. Options that are not 
>> relevant for VBM or SBM have been removed. In addition, a new 
>> experimental option has been added that allows a voxel-wise covariate 
>> to be defined. This can be used (depending on the contrast defined) 
>> to (1) remove the confounding effect of structural data (e.g., GM) on 
>> functional data or (2) examine the relationship (regression) between 
>> functional and structural data. Additionally, an interaction can be 
>> modeled to investigate whether the regression between functional and 
>> structural data differs between two groups. Please note that the 
>> saved vSPM.mat file can only be evaluated with the TFCE toolbox.
>> Added a new function cat_io_data2mat.m to save spatially registered 
>> volume or resampled surface data as Matlab data matrix for further 
>> use with machine learning tools. Volume data can be resampled to 
>> lower spatial resolutions and can optionally be masked to remove 
>> non-brain areas.
>> Added a new function cat_vol_ROI_summarize.m to summarise 
>> co-registered volume data within a region of interest (ROI). This 
>> tool can be used in order to estimate ROI information for other 
>> (co-registered) modalities (i.e. DTI, (rs)fMRI) which can be also 
>> defined as 4D data. Several predefined summary functions are 
>> available, as well as the possibility to define your own function.
>> Added a new function cat_stat_quality_measures.m to estimate and save 
>> quality measures for very large samples.
>> Added standalone tools for de-facing, DICOM import, and estimating 
>> and saving quality measures for large samples.
>>