Neuroimaging Laboratory - Unicamp

Neuroimaging Laboratory

Departament of Neurology - School of Medical Sciences - Unicamp - Brasil



UF²C - User Friendly Functional Connectivity

UF²C - User Friendly Functional Connectivity



UF²C Introduction

    UF²C is an open source software developed at the Neuroimaging Laboratory at Unicamp that aims to simplify and organize functional connectivity studies in neuroimaging through a clean and validated methodology, without sacrificing quality.
    UF²C has a full processing pipeline: The user only needs to select the raw functional and structural NIfTI files from the subjects. The graphical user interface makes the processing and analysis options accessible for neuroscientists, with reasonable choices of default settings. UF²C allows the user to study functional connectivity both through a quantitative view that provides detailed values of average connectivity and through a spatial view that provides statistical maps that can be directly used for further analyses. All results are carefully organized in distinct folder for each subject, and a common folder is generated with a log file reporting the quantitative results of all the analyzed subjects.
    Several UF²C modalities and tools runs combined with Statistical Parametric Mapping functions.

    UF²C is open source software, distributed under a BSD-style License.

UF²C Requirement

  • Windows, Linux or Mac OS X operating system
  • SPM (Statistical Parametric Mapping, version 8 or 12)
  • MATLAB (version R2010a or later, required by SPM)
  • MATLAB Statistics toolbox
  • MATLAB Signal Processing toolbox.
  • MATLAB Image Processing toolbox.
  • It is a great effort to make UF²C compatible with all possible combinations of operational systems, Matlab and SPM versions.
    Some problems can occur in Matlab older than 2010 versions, for example. Please contact me if you find any compatibility problems.
    Thank you!

UF²C Team

Contact: brunno


UF²C has currently the folowing modalities:

Modalities for Functional Connectivity:

  • Seed based functional connectivity (Statistical maps and quantitative outputs)
  • Functional Interactivity - Automated multi-seed positioning (Statistical maps outputs)
  • ROIs Cross-Correlation - Connectivity between coordinates or ROIs (corr-matrix, graphos and quantitative outputs)
  • Cross-Correlation Second level - Comparison between groups (corr-matrix and graphos outputs)
  • Sliding window connectivity - (Statistical maps, graphics and quantitative outputs)

Modalities for Functional MRI analysis:

  • fMRI Preprocessing
  • First Level Blok Design Analysis (code by Raphael Fernandes Casseb)


UF²C has currently the folowing tools:

Tools:

  • Movement Viewer (graphical visualization)
  • Movement Analysis (quantifies sample head motion)
  • Image Editor (remove volumes, temporal parts and etc...)
  • Filename Changer (in mass file name changer)
  • Tissue Segmentation (SPM tool)
  • Volumetry - calculates the volume (mm³, mL and L) of image (ROI) added or the intracranial volume
  • Interpolation tool - convert image bonding box and voxel sizes to SPM8 default
  • R-score to z-score tranformation (Fisher's) - works on .mat files (vector, matrices..) and NIfTI files


UF²C Interface and output examples:





Who are using UF²C


  • de Campos, B. M., Coan, A. C., Lin Yasuda, C., Casseb, R. F. and Cendes, F. (2016), Large-scale brain networks are distinctly
    affected in right and left mesial temporal lobe epilepsy. Hum. Brain Mapp.. doi: 10.1002/hbm.23231
  • Almeida, S. R. M., Vicentini, J., Bonilha, L., De Campos, B. M., Casseb, R. F. and Min, L. L. (2016),
    Brain Connectivity and Functional Recovery in Patients With Ischemic Stroke. Journal of Neuroimaging. doi: 10.1111/jon.12362
  • Vicentini, J.E., Weiler, M., Almeida, S.R.M. et al. Depression and anxiety symptoms are associated to
    disruption of default mode network in subacute ischemic stroke. Brain Imaging and Behavior (2016). doi:10.1007/s11682-016-9605-7
  • Weiler M, de Campos BM, Teixeira CV, Casseb RF, Carletti-Cassani AF, Vicentini JE, Magalhaes TN, Talib LL, Forlenza OV, Balthazar ML. Intranetwork and internetwork connectivity in patients with Alzheimer disease and the association with cerebrospinal fluid biomarker levels. J Psychiatry Neurosci. 2017 Apr 4;42(3):160190. doi: 10.1503/jpn.160190
  • TNC Magalhes, MS; M Weiler, PhD; CVL Teixeira, MS; T Hayataa; AS Moraes, MS; VO Boldrini, MS; LM dos Santos,PhD; BM de Campos, PhD; TJR de Rezende, MS; HPG Joaquim, MS; LL Talib, PhD; OV Forlenza, MD,PhD; F. Cendes, MD, PhD; MLF Balthazar, MD, PhD. Systemic inflammation and multimodal biomarkers in amnestic Mild Cognitive Impairment and Alzheimers disease. Molecular Neurobiology, 2017 (in press)
  • Awards using UF²C


  • PhilliP M. Rennick AWARD: Best research by graduate student. International Neuropsychological Society Congress. Cape Town, South Africa, 2017
    Functional reorganization of the Default Mode Network in ischemic stroke: a prospective study
    Jessica Vicentini, Marina Weiler, Brunno Machado de Campos, Lenise Valler, Sara Regina Meira de Almeida, Li Min Li


  • How to Cite?

    If UF²C was useful for your work and you want to cite, please use the fallowing paper:

  • de Campos, B. M., Coan, A. C., Lin Yasuda, C., Casseb, R. F. and Cendes, F. (2016), Large-scale brain networks are distinctly
    affected in right and left mesial temporal lobe epilepsy. Hum. Brain Mapp.. doi: 10.1002/hbm.23231

  • For example:
    "...UF²C toolbox (User Friendly Functional Connectivity) ...(de Campos et al., 2016)..."
    or:
    "...UF²C toolbox (http://www.lni.hc.unicamp.br/app/uf2c/)...(de Campos et al., 2016)..."

    Thank you for using and citing the UF²C!!




    Downloads:

      - The updates are cumulative

      - Please, report bugs!

      - UF²C is always updating due the continuous feedbacks, corrections, ideas or necessities. Thank you!


    Version 7.1 (Jul, 2017)

    • uf2c-7_1 - UF²C Software(29 Mb).
    • UF2C__Tutorial.pdf - UF²C Tutorial (3.49 Mb).
    • Compatibility: SPM12

      News:
      - First, a new User Manual, still under improvements, but with lots of new topics is available!
      - We added a new pre-processing modality, presenting the NoVolEx correction that improves the head motion
      correction through a brand new methodology.
      - Now, all modalities can estimate the Framewise Displacement and/or the signal Derivative Variance (DVAR).
      These parameters can be used as regressors or even as censors, excluding noisy volumes from the analysis.
      - The code was improved a lot in several ways. However, no conceptual errors were found in the last version.

      In TOOLS:
      - A new tool that enables to find Outliers on files, images, vectors, matrices, input numbers and etc.
      In the case of the images, the tool can also create a mask with and without the Outliers. We recommend to add
      this mask on "SPM --> Explicit mask input", to improve second level analysis.
      - The tool for r-score to z-score conversion was improved!
      - A new tool, "Maps ROIs Quantification" that enables to extract quantitative values from several images adding
      several ROIs.
      - And much more!

    Version 7.0 (Dec, 2016)

    • uf2c-7_0 - UF²C Software(29 MB).
    • UF2C__Tutorial.pdf - UF²C Tutorial (944 kB).
    • Compatibility: SPM12

      - The "Seed-Based" modality now performs an anatomical descriptive analysis of the resultant individual parametric
      map using the Neuromorphometrics, Inc, atlas and labels.
      - The "ROI-to-ROI first level" modality now performs an anatomical descriptive analysis of each ROI included in the
      model using the Neuromorphometrics, Inc, atlas and labels.
      - Now, we can pre-process and analyze images with distinct number of dynamics in the same run.
      - 2016 codes review.
      - Minor bugs corrections.
      - And more....

    Version 6.8 (Nov, 2016)

    Version 6.7 (Sept, 2016)

    • uf2c-6_7 - UF²C Software(25 MB).
    • UF2C__Tutorial.pdf - UF²C Tutorial (944 kB).
    • Compatibility: SPM12

      - BUGs fixed: Error on 3d resultant figure of Roi-to-ROI modality fixed
      - New tutorial
      - New outputs for connectivity analysis
      - various smalls improvements

    Version 6.6 (Jul, 2016)

    • uf2c-6_6 - UF²C Software(25 MB).
    • UF2C__Tutorial.pdf - UF²C Tutorial (944 kB).
    • Compatibility: SPM12

      - BUGs fixed
      - New outputs for connectivity analysis

    Version 6.5 (Apr, 2016)

    • uf2c-6_5 - UF²C Software(25 MB).
    • UF2C__Tutorial.pdf - UF²C Tutorial (944 kB).
    • Compatibility: SPM12

      - Now, UF²C have a modality for fMRI analysis as block design expirements.
      - A new function was added. A straightforward GUI you easy perform Block Design experiments.
      - This new functionality it is a fantastic collaboration of Rafael Fernandes Casseb (modality developer)

    Version 6.4 (Mar, 2016)

    • uf2c-6_4 - UF²C Software(25 MB).
    • UF2C__Tutorial.pdf - UF²C Tutorial (944 kB).
    • Compatibility: SPM12

      - New tool to check the UF²C compatibility (with you OS, Matlab, SPM, Toolboxes....).
      - New preprocessing tool added. Now you can preprocess you fMRI or strutural data to use or run your general expirements, not just for connectivity.
      - Some improvements and funcionalities in all modalities.
      - BUGs corrections.

    Page updated on 2017-10-02 16:12