Submitted by YAN Chao-Gan on Wed, 12/26/2012 - 15:36
Dear all,
Merry Christmas and Happy New Year!
It’s said that December 21, 2012 is the end of the world, thus it marks the beginning of a new era. Here, we celebrate the Christmas and New Year in the new era, and are pleased to release the stable version of REST V1.8 and DPARSF V2.2. :)
To facilitate parallel computing and lots of new features, many functions were re-structured, especially for DPARSF advanced version. Thus, we released the pre-release of REST V1.8 and DPARSF V2.2 on September 5, 2012 and invited users to help us to refine them. Many thanks to our users, for testing, using and reporting bugs or problems encountered, we kept updating the pre-release and now believe REST V1.8 (REST_V1.8_121225) and DPARSF V2.2 (DPARSF_V2.2_121225) have reached a more stable stage (probably there still will be bugs, we will fix them soon and make a next stable release upon receiving reports).
We encourage the users to re-perform the analyses with the stable version if you used the earlier pre-releases of REST V1.8 and DPARSF V2.2. We expect most of the results will keep the same, but there are several changes in the stable version.
Of note, the default parameter in the pre-release is set to “Calculate in Original Space” which calculates the R-fMRI measures on the data before spatial normalization and resampling. This way was suggested to maintain the intrinsic fidelity of spontaneous fluctuations, and thus be beneficial in revealing changes in subtle small brain areas (Wu et al., 2011. Empirical Evaluations of Slice-Timing, Smoothing, and Normalization Effects in Seed-Based, Resting-State Functional Magnetic Resonance Imaging Analyses. Brain Connect 1, 401-410). We set the default parameter in the pre-release to promote the capability of calculating in original space with DPARSF. However, the same study (Wu et al., 2011) found no significance between strategies of calculating in original space or MNI space, and they suggested using the latter way when targeting large and robust functional networks by providing consistent spatial extent. In the stable release of DAPRSF (DPARSF_V2.2_121225), the default parameter is conservatively set back to “Calculate in MNI Space” for a better comparison with most of the previous studies. Another consideration is that if data of multiple sites were involved (e.g., the FCP 1000 data), ReHo and degree centrality need to be performed in MNI space to address the issue with difference in voxel size. Nonetheless, users could choose either way by selecting from “Template Parameters” based upon their objectives.
In addition, before VMHC calculation, DPARSF_V2.2_121225 now can create a symmetric mean T1 template from all the participants, and will normalize the T1 image for each subject to the symmetric T1 template (created in Step 2), and apply the transformations to the functional data. In addition, REST-GCA could handle multiple ROIs (other than 2) in ROI-wise GCA in REST V1.8 pre-release, but the outputs were flipped. We fixed this bug in the REST_V1.8_121225, now the outputs were put in according to the description in REST-GCA readme.
We hope REST_V1.8_121225 and DPARSF_V2.2_121225 can continually help our users in your research and applications and thus promote the resting-state fMRI studies.
On behalf of the REST Team, I wish you a happy, healthy and prosperous 2013!
Best,
Chao-Gan