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Public Software Tools

  • ReStNeuMap: a tool for automatic extraction of resting state fMRI networks
    • Outline:  Resting State functional Magnetic Resonance Imaging (rs-fMRI) represents a promising and cost-effective alternative to task-based fMRI for pre-surgical mapping in patients undergoing awake resection of brain tumor, epilepsy and vascular malformations. However, the lack of clinically streamlined and reliable rs-fMRI analysis tools has prevented wide adoption of this technique. In this work, we introduce a rs-fMRI data analysis pipeline (ReStNeuMap) for automatic single-subject rs-fMRI network analysis. We also investigate the agreement between the localization of rs-fMRI networks determined with our pipeline and neural activation of intraoperatively recordings using Direct Electrical Stimulation (DES).
    • Paper: Zacà D, Jovicich J, Corsini F, Rozzanigo U, Chioffi F, Sarubbo S. ReStNeuMap: a tool for automatic extraction of resting state fMRI networks in neurosurgical practice J Neurosurg 2018 (pubmed)
    • Download ReStNeuMap tool
  • Method for estimating head motion during structural T1 image acquisition
    • Outline: Head motion during structural T1 MRI acquisition can be subtle and introduce brain morphometry biases without giving strong visible artifacts. This tool estimates the average edge strength (AES) in structural images, which as an index of image blurring, has been seen to correlate with head motion. The AES metric may be used in cross sectional or longitudinal studies to characterize head motion differences in the studied groups, and potentially also used as a nuisanse covariate in statistical models.
    • Paper: Zacà D, Hasson U, Minati L, Jovicich J. Method for retrospective estimation of natural head movement during structural MRI. J Magn Reson Imaging. 2018  (pubmed)
    • Download AES tool
  • Method for correcting geometric distortions from gradient non-linearities: gradient unwarp
    • Outline: The Brain Morphometry testbed of the BIRN provides a tool to correct gradient non-linearity distortions in MR structural images. This correction improves test-retest reproducibility crucial for multi-site studies.
    • Paper: Jovicich J, Czanner S, Greve D, Haley E, van der Kouwe A, Gollub R, Kennedy D, Schmitt F, Brown G, Macfall J, Fischl B, Dale A. Reliability in multi-site structural MRI studies: effects of gradient non-linearity correction on phantom and human data. Neuroimage. 2006 Apr 1;30(2):436-43. (pdf)
    • Download gradient unwarp tool​
  • Method for static magnetic field mapping (B0) with multichanel RF coils in MRI 
    • Outline: This tool computes a map of the static magnetic field when using a multichannel receiver coil. The tool allows for the use of different methods to combine the phase information from the different channels, using as default our recommended separate channel method. The tool offers options for field map denoising and local thresholding for the maximal achievable geometric distortion correction if used to distortion correct EPI data. on-correct EPI.
    • Paper: Robinson S, Jovicich J. B0 mapping with multi-channel RF coils at high field. Magn Reson Med. 2011 Oct;66(4):976-88. (pdf)
    • Download multichannel B0 mapping tool
  • Method for eye movement artifact identification and removal in EEG: ADJUST
    • Outline: ADJUST is a completely automatic algorithm for artifact identification and removal in EEG data. ADJUST is based on Independent Component Analysis (ICA), a successful but unsupervised method for isolating artifacts from EEG recordings. ADJUST identifies artifacted ICA components by combining stereotyped artifact-specific spatial and temporal features. Features are optimised to capture blinks, eye movements and generic discontinuities. Once artifacted IC are identified, they can be simply removed from the data while leaving the activity due to neural sources almost unaffected. ​ADJUST runs in Matlab as a plugin of the EEGLAB software, the most popular software for analysis of electrophysiological data. No Matlab toolboxes are required.
    • Paper: Mognon A, Jovicich J, Bruzzone L, Buiatti M. ADJUST: An automatic EEG artifact detector based on the joint use of spatial and temporal features. Psychophysiology, 2011, 48(2):229-240. (pdf)
    • Download ADJUST tool

 

Public Datasets

  • Resting State fMRI Speech Arrest Network
    • Outline: The Speech Arrest Network was constructed from 7 low-grade tumor patients who underwent a presurgical clinical resting state scan (1.5T GE,  full-brain axial acquisition with ascending interleaved slice order, TR/TE = 2600/45 ms, flip angle = 87 degrees, square FOV = 256 mm, isotropic voxel size = 43 mm3, slice gap = 0.8 mm, fat saturation, ASSET acceleration factor = 2, number of volumes = 275) and direct electrode stimulation during awake surgery. The functional connectivity network was constructed as a group average from the seed-based networks constructed in each patient using the speech arrest locations defined during surgery.
    • Paper:  Zacà D., Corsini F., Rozzanigo U., Dallabona M., Avesani P., Annicchiarico L., Zigiotto L., Faraca G., Chioffi F., Jovicich J., Sarubbo S. Frontiers Human Neuroscience. 2018 (in press, doi: 10.3389/fnhum.2018.00405).
    • Speech Arrest Network Atlas
  • Multi-site test-retest T1 anatomy
    • Outline: The Pharmacog project makes available structural T1 MRI data from 40 healthy Caucasian subjects (50-80 years). Participants were scanned in two sessions at least a week apart in 8 clinical 3T scanners distributed in Europe (5 subjects per site). Each acquisition session has two 3D T1-weighted images (1x1x1 mm3). Scanner vendors were Siemens (Allegra, TrioTim, Verio, Skyra), Philips (Achieva) and GE (Signa HDxt). Two volumes were not acquired giving a total of 158 brain volumes available. Images are anonymous.
    • Paper: Jovicich J, Marizzoni M, Sala-Llonch R, Bosch B, Bartrés-Faz D, Arnold J, Benninghoff J, Wiltfang J, Roccatagliata L, Nobili F, Hensch T, Tränkner A, Schönknecht P, Leroy M, Lopes R, Bordet R, Chanoine V, Ranjeva JP, Didic M, Gros-Dagnac H, Payoux P, Zoccatelli G, Alessandrini F, Beltramello A, Bargalló N, Blin O, Frisoni GB; PharmaCog Consortium. Brain morphometry reproducibility in multi-center 3T MRI studies: a comparison of cross-sectional and longitudinal segmentations. Neuroimage. 2013 Dec;83:472-84. (pdf)
    • Download Pharmacog T1 MRI data
  • Multi-site test-retest DTI 
    • Outline: The Pharmacog project makes available DTI data from 50 healthy Caucasian subjects (50-80 years). Participants were scanned in two sessions at least a week apart in 10 clinical 3T scanners distributed in Europe (5 subjects per site). Each acquisition session has one diffusion acquisition 2x2x2 mm3, b=700 s/mm2, 5 b0 and 30 diffusion weighted volumes. Scanner vendors were Siemens (Allegra, TrioTim, Verio, Skyra, MRBiograph), Philips (Achieva) and GE (Signa HDxt). The 100 raw diffusion datasets are available. Images are anonymous.
    • Paper: Jovicich J, Marizzoni M, Bosch B, Bartrés-Faz D, Arnold J, Benninghoff J,Wiltfang J, Roccatagliata L, Picco A, Nobili F, Blin O, Bombois S, Lopes R, Bordet R, Chanoine V, Ranjeva JP, Didic M, Gros-Dagnac H, Payoux P, Zoccatelli G, Alessandrini F, Beltramello A, Bargalló N, Ferretti A, Caulo M, Aiello M, Ragucci M, Soricelli A, Salvadori N, Tarducci R, Floridi P, Tsolaki M, Constantinidis M, Drevelegas A, Rossini PM, Marra C, Otto J, Reiss-Zimmermann M, Hoffmann KT, Galluzzi S, Frisoni GB; PharmaCog Consortium. Multisite longitudinal reliability of tract-based spatial statistics in diffusion tensor imaging of healthy elderly subjects. Neuroimage. 2014 Nov 1;101:390-403. (pdf)
    • Download Pharmacog DTI data
  • Multi-site test-retest resting state fMRI
    • Outline: The Pharmacog project makes available resting state fMRI data from 65 healthy Caucasian subjects (50-80 years). Participants were scanned in two sessions at least a week apart in 13 clinical 3T scanners distributed in Europe (5 subjects per site). Each acquisition session included a full brain resting state fMRI acquisition: 3 mm isotropic, TR=2.7s, TE=30ms, flip angle=85 deg, fat suppression. Scanner vendors were Siemens (Allegra, TrioTim, Verio, Skyra, MRBiograph), Philips (Achieva) and GE (Signa HDxt, Discovery)
    • Paper: Jovicich J, Minati L, Marizzoni M, Marchitelli R, Sala-Llonch R, Bartrés-Faz D, Arnold J, Benninghoff J, Fiedler U, Roccatagliata L, Picco A, Nobili F, Blin O, Bombois S, Lopes R, Bordet R, Sein J, Ranjeva JP, Didic M, Gros-Dagnac H, Payoux P, Zoccatelli G, Alessandrini F, Beltramello A, Bargalló N, Ferretti A, Caulo M, Aiello M, Cavaliere C, Soricelli A, Parnetti L, Tarducci R, Floridi P, Tsolaki M, Constantinidis M, Drevelegas A, Rossini PM, Marra C, Schönknecht P, Hensch T, Hoffmann KT, Kuijer JP, Visser PJ, Barkhof F, Frisoni GB; PharmaCog Consortium. Longitudinal reproducibility of default-mode network connectivity in healthy elderly participants: A multicentric resting-state fMRI study. Neuroimage. 2016 Jan 1;124:442-54.(pdf)
    • Download Pharmacog fMRI data