PESTICA & SLOMOCO: physio and motion correction tools Releases

SLOMOCO SLOMOCO-20250102

wanyongshin@stage.nitrcce.org (Wanyong Shin) — Tue, 18 Feb 2025 17:57:00 GMT

SLOMOCO-20250102 is released. SLOMOCO-YYYYMMDD version runs seprately from PESTICA. SLOMOCO is developed and distributed in https://github.com/wanyongshinccf/SLOMOCO/releases
Please check the latest version of SLOMOCO in the linke above.
Wanyong Shin
shinw@ccf.org

pestica PESTICA-20250106

wanyongshin@stage.nitrcce.org (Wanyong Shin) — Tue, 18 Feb 2025 17:40:00 GMT

PESTICA is distributed seperately from SLOMOCO. Future PESTICA will be announed with "PESTICA-"YEAR/MM/DD" name. PESTICA is developed and distributed in  <a title="Github PESTICA project" href="https://github.com/wanyongshinccf/PESTICA">https://github.com/wanyongshinccf/PESTICA</a> Please check the latest version of PESTICA in a github link above.
Wanyong Shin
shinw@ccf.org

pestica PESTICA_AFNI_v5.5

wanyongshin@stage.nitrcce.org (Wanyong Shin) — Thu, 19 May 2022 16:02:00 GMT

PESTICA_v5.5

PESTICA is an open source software package, running on bash window. Please feel free to modify it.
If you use PESTICA in your work, please cite

Shin W, Koenig KA, Lowe MJ. A comprehensive investigation of physiologic noise modeling in resting state fMRI; time shifted cardiac noise in EPI and its removal without external physiologic signal measures. Neuroimage. 2022 Jul 1;254:119136. doi: 10.1016/j.neuroimage.2022.119136. Epub 2022 Mar 26. PMID: 35346840.
Beall, E. B., and Lowe, M. J. (2014). SimPACE: Generating simulated motion corrupted BOLD data with synthetic-navigated acquisition for the development and evaluation of SLOMOCO: a new, highly effective slicewise motion correction. NeuroImage 101, 21–34. doi: 10.1016/j.neuroimage.2014.06.038

PESTICA&SLOMOCO PESTICA/SLOMOCOv5.2

wanyongshin@stage.nitrcce.org (Wanyong Shin) — Wed, 04 Dec 2019 20:01:00 GMT

PESTICA/SLOMOCO v5.2 is released.

PESTICA&SLOMOCO PESTICA4(SLOMOCO)

wanyongshin@stage.nitrcce.org (Wanyong Shin) — Thu, 30 Jun 2016 15:15:00 GMT

Updated;
new PESTICA templates from 240 subjects
SMS (MB) acquisition comparable in PESTICA and SLOMOCO

SLOMOCO SpinHistory simulation using SLOMOCO

ebeall@stage.nitrcce.org (Erik Beall) — Mon, 05 Jan 2015 16:44:00 GMT

This set of scripts is a work in progress package for simulating T1 spin history effects in 2D EPI timeseries (e.g. functional MRI or connectivity) data due to fast head motion. It is meant to replace the slomoco sub-package released recently, by incorporating additional T1 preparation scripts and a simulator that is reasonably fast (<1hr for 128x128x31 dataset) and simulates at 1% of the slice thickness. T1 effects are all about out-of-plane motion, and that is all that is simulated here, by combining this with SLOMOCO, the goal is to perform a complete correction of motion effects in BOLD rs-fMRI and fMRI data.

Also included is a new PESTICA filter script and a new physio estimator script for SLOMOCO output. SLOMOCO estimates nearly always contain sufficient respiratory noise to isolate respiratory trace, and sometimes contain sufficient cardiac signature (works most of the time at 7T but not often at 3T). This script can be used with SLOMOCO output to produce respiratory traces and sometimes cardiac traces that could be used similar to PESTICA estimators and monitored pulse and respiration. Also still a work in progress.

SLOMOCO SLOMOCO_July2014

ebeall@stage.nitrcce.org (Erik Beall) — Wed, 16 Jul 2014 15:44:00 GMT

pestica pestica v2.0 (recommended)

ebeall@stage.nitrcce.org (Erik Beall) — Thu, 21 Feb 2013 19:34:00 GMT

Version 2.0 of PESTICA is released. Major changes include bug-fixes, algorithmic improvements, fMRI specific instructions and pulse ox/respiratory bellows (PMU) signal handling.

pestica script fix for pestica v1.3 for AFNI users

ebeall@stage.nitrcce.org (Erik Beall) — Fri, 30 Nov 2012 21:44:00 GMT

This script is intended to be used as a replacement for the run_pestica.sh master shell script in the pestica_afni_v1_3 release. This fix is due to a major bug in stage 5; the original script deleted the physiologic noise-removed 3D+time datafile immediately after it was written and this fix does not have that bug. The structure of the script has also been altered in an attempt to prevent the script from halting after completing arbitrary stages. Some installations were observing that the script would simply stop after a stage, despite all stages or further stages being selected. It is not known if this will fix the stages problem, please let me know if you see unexpected behavior.

pestica pestica v1.3 for AFNI users (recommended)

ebeall@stage.nitrcce.org (Erik Beall) — Wed, 08 Aug 2012 17:34:00 GMT

New release of PESTICA for AFNI. Major change is the use of a single master script to control all functions of PESTICA and IRF-RETROICOR data correction and quality assurance plot creation. Additional changes:
-use of a datafile-specific pestica/ working file subdirectory (in case you wish to run estimation on different processing stages of the same data)
-options for running PESTICA with dropped initial volumes, different processing level of raw data, individual stages of PESTICA, and run the original RETROICOR correction algorithm.
-auto-creation of masked brain volume using 3dSkullStrip and 3dcalc to dilate mask by 1 voxel
-QA process that creates jpegs of coupling maps overlain on raw data, coregistered spatial priors overlain on raw data and plots of the cardiac and respiratory impulse response functions (IRFs)
This is the new recommended version of PESTICA.