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Name
Jim
Byline
Xinapse Systems
Description
Jim is a commercial general medical image analysis tool geared towards the display and quantitative analysis of multi-dimensional image sets. It contains a large set of tools designed to encompass the whole range of sub-tasks needed to address many image analysis problems.

Jim takes the user from data retrieval (using the DICOM Query/Retrieve tool), data conversion, image management and display through to a large set of quantitative analysis tools. Jim has powerful 3-D image display facilities, and the ability to analyze diffusion-tensor datasets from warp correction through tensor calculation to fiber tracking and tract display.

It also has a free Java programming A.P.I for handling medical images, so that you can write your own image analysis applications.

NIfTI-1 support
Jim supports Analyze format images, NIFTI-1 format (one-file .nii and two-file .hdr/.img). Uncompressed and compressed datsets are supported. All data types are handled with the exception of Double Double, Double Double Complex and Unsigned Long. Images with any dimensionality allowed by the NIFTI-1 format are handled.

Creator
Xinapse Systems
Contact
support@xinapse.com
WWW
http://www.xinapse.com/Manual
Availability
Commercial offering
How to get
Go to http://www.xinapse.com/Manual for installation instructions.
Current version
7.0
Current version release date
October 2014
Open source
No
License
Commercial.
Available free of charge
No
Requirements
Microsoft Windows Linux Solaris Mac OS X 10.5 or later
Technical publications
Please the Xinapse Systems web site for a complete up-to-date list of publications.
Applications publications
Please the Xinapse Systems web site for a complete up-to-date list of publications.

"Effect of Laquinimod on MRI-monitored Disease Activity in Patients with Relapsing-Remitting Multiple Sclerosis: a Multicentre, Randomised, Double-Blind, Placebo-Controlled Phase IIb Study". Comi G, Pulizzi A, Rovaris M, Abramsky O, Arbizu T, Boiko A, Gold R, Havrdova E, Komoly S, Selmaj K, Sharrack B, Filippi M; LAQ/5062 Study Group. Lancet, 371:2085-2092 (2008).

"Phase III Dose-Comparison Study of Glatiramer Acetate for Multiple Sclerosis." Comi G, Cohen JA, Arnold DL, Wynn D, Filippi M, for the FORTE Study Group. Annals of Neurology, 69:75-82 (2011).

"Correlation between Angiogenesis and Islet Graft Function in Diabetic Mice: Magnetic Resonance Imaging Assessment." Sakata N, Obenaus A, Chan NK, Hayes P, Chrisler J, Hathout E. Journal of Hepato-Biliary-Pancreatic Sciences, 17: 692-700(2010).

"Clinically Isolated Syndrome Suggestive of Multiple Sclerosis: Voxelwise Regional Investigation of White and Gray Matter." Raz E, Cercignani M, Sbardella E, Totaro P, Pozzilli C, Bozzali M, Pantano P. Radiology, 254:227-234 (2010).

"Multiparametric MR investigation of the Motor Pyramidal System in Patients with 'Truly Benign' Multiple Sclerosis." Spano B, Cercignani M, Basile B, Romano S, Mannu R, Centonze D, Caltagirone C, Bramanti P, Nocentini U, Bozzali M. Mult Scler. 16178-88 (2010),

"Preserved Brain Adaptive Properties in Patients with Benign Multiple Sclerosis". Rocca MA, Ceccarelli A, Rodegher M, Misci P, Riccitelli G, Falini A, Comi G, Filippi M. Neurology, 74:142-149 (2010).

"High-b-Value Diffusion MR Imaging and Basal Nuclei Apparent Diffusion Coefficient Measurements in Variant and Sporadic Creutzfeldt-Jakob Disease." Hyare H, Thornton J, Stevens J, Mead S, Rudge P, Collinge J, Yousry TA, J���¤ger HR. AJNR Am J Neuroradiol., (2010).

"Spinal Cord Lesions and Clinical Status in Multiple Sclerosis: A 1.5 T and 3 T MRI Study". Stankiewicz JM, Neema M, Alsop DC, Healy BC, Arora A, Buckle GJ, Chitnis T, Guttmann CR, Hackney D, Bakshi R. J Neurol Sci, 279:99-105 (2009).

"Neuropsychological and MRI Measures Predict Short-Term Evolution in Benign Multiple Sclerosis". Portaccio E, Stromillo ML, Goretti B, Zipoli V, Siracusa G, Battaglini M, Giorgio A, Bartolozzi ML, Guidi L, Sorbi S, Federico A, Amato MP, De Stefano N. Neurology, 73:498-503 (2009).

"Investigation of Quantitative Magnetisation Transfer Parameters of Lesions and Normal Appearing White Matter in Multiple Sclerosis" Cercignani M, Basile B, Spano B, Comanducci G, Fasano F, Caltagirone C, Nocentini U, Bozzali M. NMR Biomed 22:646-653 (2009).

"Influence of task complexity during coordinated hand and foot movements in MS patients with and without fatigue. A kinematic and functional MRI study". Rocca MA, Gatti R, Agosta F, Broglia P, Rossi P, Riboldi E, Corti M, Comi G, Filippi M. Journal of Neurology, 256: 470-482 (2009).

"Is a Preserved Functional Reserve a Mechanism Limiting Clinical Impairment in Pediatric MS Patients?". Rocca MA, Absinta M, Ghezzi M, Moiola L, Comi G, Filippi M. Human Brain Mapping, 30: 2844-2851 (2009).

"White Matter Hemodynamic Abnormalities Precede Sub-Cortical Gray Matter Shanges in Multiple Sclerosis". Varga A, Johnson G, Babb J, Herbert J, Grossman R, Inglese M. J Neurol Neurosurg Psychiatry., 282: 28-33 (2009).

"State of the Cervical Section of the Spinal Cord in Patients with Remitting Multiple Sclerosis During Immunomodulatory Treatment". Shipova EG, Spirin NN, Kasatkin DS, Shumakov EI, Stepanov IO. Neuroscience and Behavioral Physiology, 39:47-51 (2009).

"High-Resolution Longitudinal Assessment of Flow and Permeability in Mouse Glioma Vasculature: Sequential Small Molecule and SPIO Dynamic Contrast Agent MRI". Pike MM, Stoops CN, Langford CP, Akella NS, Nabors LB, Gillespie GY. Magn Reson Med 61:615-625 (2009).

"Disconnection as a Mechanism for Cognitive Dysfunction in Multiple Sclerosis". Dineen RA, Vilisaar J, Hlinka J, Bradshaw CM, Morgan PS, Constantinescu CS, Auer DP. Brain 132:239-249 (2008).

"Structural and Metabolic Brain Abnormalities in Preclinical Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leucoencephalopathy". Stromillo ML, Dotti MT, Battaglini M, Mortilla M, Bianchi S, Plewnia K, Pantoni L, Inzitari D, Federico A, De Stefano N. J Neurol Neurosurg Psychiatry, 80:41-47 (2009).

"Plasma Levels of Asymmetric Dimethylarginine in Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarct and Leukoencephalopathy". Rufa A, Blardi P, De Lalla A, Cevenini G, De Stefano N, Zicari E, Auteri A, Federico A, Dotti MT. Cerebrovasc Dis, 26:636-640 (2008).

"Genomic Effects of Once-Weekly, Intramuscular Interferon-������²1a Treatment After the First Dose and on Chronic Dosing: Relationships to 5-year Clinical Outcomes in Multiple Sclerosis Patients". Weinstock-Guttman B, Bhasi K, Badgett D, Tamano-Blanco M, Minhas M, Feichter J, Patrick K, Munschauer F, Bakshi R, Ramanathan M. Journal of Neuroimmunology, 205:113-125 (2008).

"Cognitive Assessment and Quantitative Magnetic Resonance Metrics Can Help to Identify Benign Multiple Sclerosis". Amato MP, Portaccio E, Stromillo ML, Goretti B, Zipoli V, Siracusa G, Battaglini M, Giorgio A, Bartolozzi ML, Guidi L, Sorbi S, Federico A, De Stefano N. Neurology, 71:632-638 (2008).

"Carotid Intraplaque Hemorrhage Detected by Magnetic Resonance Imaging Predicts Embolization During Carotid Endarterectomy". Altaf N, Beech A, Goode SD, Gladman JR, Moody AR, Auer DP, MacSweeney ST. J Vasc Surg, 47:337-342 (2008).

"Effect of Laquinimod on MRI-monitored Disease Activity in Patients with Relapsing-Remitting Multiple Sclerosis: a Multicentre, Randomised, Double-Blind, Placebo-Controlled Phase IIb Study". Comi G, Pulizzi A, Rovaris M, Abramsky O, Arbizu T, Boiko A, Gold R, Havrdova E, Komoly S, Selmaj K, Sharrack B, Filippi M; LAQ/5062 Study Group. Lancet, 371:2085-2092 (2008).

"BIBF 1120: Triple Angiokinase Inhibitor with Sustained Receptor Blockade and Good Antitumor Efficacy". Hilberg F, Roth GJ, Krssak M, Kautschitsch S, Sommergruber W, Tontsch-Grunt U, Garin-Chesa P, Bader G, Zoephel A, Quant J, Heckel A, Rettig WJ. Cancer Res, 15:4774-4782 (2008).

"Thalamic Atrophy and Cognition in Multiple Sclerosis". Houtchens MK, Benedict RHB, Killiany R, Sharma J, Jaisani A, Singh B, Weinstock-Guttman B, Guttmann CRG, Bakshi R. Neurology, 69:1213-1223 (2007).

"The Effect of White Matter Lesions on Cognition in the Elderly - Small but Detectable". Frisoni GB, Galluzzi S, Pantoni L, Filippi M. Nature Clinical Practice Neurology, 3:620-627 (2007).

"Carotid Intraplaque Hemorrhage Detected by Magnetic Resonance Imaging Predicts Embolization During Carotid Endarterectomy". Altaf N, Beech A, Goode SD, Gladman JR, Moody AR, Auer DB, MacSweeney ST. J. Vacular Surgery, 46:31-36 (2007).

"Differentiation of Parkinson's Disease and Progressive Supranuclear Palsy with Magnetic Resonance Imaging: the First Brazilian Experience". Barsottini OG, Ferraz HB, Maia AC Jr, Silva CJ, Rocha AJ. Parkinsonism Relat Disord., 13:389-393 (2007).

"Perfusion Magnetic Resonance Imaging Correlates of Neuropsychological Impairment in Multiple Sclerosis". Inglese M, Adhya S, Johnson G, Babb JS, Miles L, Jaggi H, Herbert J, Grossman RI. J Cereb Blood Flow Metab., Published Online (2007).

"Quantitative Diffusion Weighted Imaging Measures in Patients with Multiple Sclerosis". Tavazzi E, Dwyer MG, Weinstock-Guttman B, Lema J, Bastianello S, Bergamaschi R, Cosi V, Benedict RH, Munschauer FE 3rd, Zivadinov R. NeuroImage, 36:746-754 (2007).

"Cardiac Autonomic Nervous System and Risk of Arrhythmias in Cerebral Autosomal Dominant Arteriopathy With Subcortical Infarcts and Leukoencephalopathy (CADASIL)". Rufa A, Guideri F, Acampa M, Cevenini G, Bianchi S, De Stefano N, Stromillo ML, Federico A and Dotti MT. Stroke, 38:276-280 (2007).

"Diffuse Structural and Metabolic Brain Changes in Fabry Disease". Marino S, Borsini W, Buchner S, Mortilla M, Stromillo ML, Battaglini M, Giorgio A, Bramanti P, Federico A, De Stefano N. J Neurol, 253:434-440 (2006).

"Patterns of Hemodynamic Impairment in Multiple Sclerosis: Dynamic Susceptibility Contrast Perfusion MR Imaging at 3.0 T". Adhya S, Johnson G, Herbert J, Jaggi H, Babb JS, Grossman RI and Inglese M. NeuroImage, 33:1029-1035 (2006).

"Brain Damage as Detected by Magnetization Transfer Imaging is Less Pronounced in Benign than in Early Relapsing Multiple Sclerosis". De Stefano N, Battaglini M, Stromillo ML, Zipoli V, Bartolozzi ML, Guidi L, Siracusa G, Portaccio E, Giorgio A, Sorbi S, Federico A, and Pia Amato MP. Brain, 129:2008-2016 (2006).

"A Magnetization Transfer MRI Study of Deep Gray Matter Involvement in Multiple Sclerosis". Sharma J, Zivadinov R, Jaisani Z, Fabiano AJ, Singh B, Horsfield MA, and Bakshi R. J Neuroimaging, 16:302-310 (2006).

"Gray and White Matter Brain Atrophy and Neuropsychological Impairment in Multiple Sclerosis". Sanfilipo MP, Benedict RHB, Weinstock-Guttman B and Rohit Bakshi. Neurology, 66:685-692 (2006).

"Cognitive Impairment is Associated with Subcortical Magnetic Resonance Imaging Grey Matter T2 Hypointensity in Multiple Sclerosis". Brass SD, Benedict RHB, Weinstock-Guttman B, Munschauer F and Bakshi R. Multiple Sclerosis; 12:437-444 (2006).

"Assessment of Mouse Glioma Vasculature Using SPIO and Small Molecule Contrast Agents: Sequential Implementation of Alternate Perfusion MRI Methodologies". Pike MM, Langford CP, Neumann CD, Nabors LB and Gillespie GY. Proc. ISMRM 14th Annual Meeting, Abstract 465 (oral presentation) (2006).

"Reduced Brain Functional Reserve and Altered Functional Connectivity in Patients with Multiple Sclerosis". Cader S, Cifelli A, Abu-Omar Y, Palace J and Matthews PM. Brain; 129:527-537 (2006).

"Cerebral White Matter Hyperintense Lesions are Associated with Unstable Carotid Plaque". Altaf N, Daniel L, Morgan PS, Lowe J, Gladman J, MacSweeney ST, Moody A and Auer DP. Eur J Vasc Endovasc Surg; 31:8-13 (2006).

"Systemic Blood Pressure Profile in Cerebral Autosomal Dominant Arteriopathy With Subcortical Infarcts and Leukoencephalopathy". Rufa A, Dotti MT, Franchi M, Stromillo ML, Cevenini G, Bianchi S, De Stefano N and Federico A. Stroke; 36:2554 (2005).

"Prediction of Longitudinal Brain Atrophy in Multiple Sclerosis by Gray Matter Magnetic Resonance Imaging T2 Hypointensity". Bermel RA, Puli SR, Rudick RA, Weinstock-Guttman B, Fisher E, Munschauer FE and Bakshi R. Arch Neurol; 62:1371-1376 (2005).

"Interhemispheric Asymmetry of Brain Diffusivity in Normal Individuals: a Diffusion-Weighted MR Imaging Study". Fabiano AJ, Horsfield MA and Bakshi R. AJNR Am J Neuroradiol AJNR; 26:1089-94 (2005).

"The Relationship Between Whole Brain Volume and Disability in Multiple Sclerosis: a Comparison of Normalized Gray vs. White Matter with Misclassification Correction". Sanfilipo MP, Benedict RHB, Sharma J, Weinstock-Guttman B and Bakshi R. NeuroImage; 26:1068-1077 (2005).

"Whole-Brain Atrophy in Multiple Sclerosis Measured by Automated Versus Semiautomated MR imaging Segmentation". Sharma J, Sanfilipo MP, Benedict, RHB, Weinstock-Guttman B, Munschauer FE and Bakshi R. AJNR Am J Neuroradiol; 25:985-996 (2004).

"Functional Imaging During Covert Auditory Attention in Multiple Sclerosis". Santa Maria MP, Benedict RHB, Bakshi R, Coad ML, Wack D, Burkard R, Weinstock-Guttman B, Roberts S and Lockwood AH. Journal of the Neurological Sciences; 218:9-15 (2004).

"Prediction of Neuropsychological Impairment in Multiple Sclerosis - Comparison of Conventional Magnetic Resonance Imaging Measures of Atrophy and Lesion Burden". Benedict RHB, Weinstock-Guttman B, Fishman I, Sharma J, Tjoa CW and Bakshi R. Archives of Neurology; 61: 226-230 (2004).

"Thalamic Involvement in Multiple Sclerosis: a Diffusion-Weighted Magnetic Resonance Imaging Study". Fabiano AJ, Sharma J, Weinstock-Guttman B, Munschauer FE , Benedict RH, Zivadinov R and Bakshi R. J Neuroimaging; 13:307-14 (2003).

"Whole-brain Atrophy in Multiple Sclerosis Measured by Two Segmentation Processes from Various MRI Sequences". Horsfield MA, Rovaris M, Rocca MA, Rossi P, Benedict RHB, Filippi M and Bakshi R. Journal of the Neurological Sciences; 216:169-177 (2003).

"A Semiautomated Measure of Whole-Brain Atrophy in Multiple Sclerosis". Bermel RA, Sharma J, Tjoa CW, Puli SR and Bakshi R. Journal of the Neurological Sciences; 208:57-65 (2003).

"Selective Caudate Atrophy in Multiple Sclerosis: a 3D MRI Parcellation Study". Bermel RA, Innus MD, Tjoa CW and Bakshi R. Neuroreport ; 14:335-339 (2003).

"Bicaudate Ratio as a Magnetic Resonance Imaging Marker of Brain Atrophy in Multiple Sclerosis". Bermel RA, Bakshi R, Tjoa C, Puli SR and Jacobs L. Archives of Neurology; 59:275-280 (2002).

"Hypointensity in the Deep Gray Matter of Patients with Multiple Sclerosis - A Quantitative Magnetic Resonance Imaging Study". Bakshi R, Benedict RHB, Bermel RA, Caruthers SD, Puli SR, Tjoa CW, Fabiano AJ and Jacobs L. Archives of Neurology; 59:62-68 (2002).

Other information
Jim is available with a free 30-day trial license. Please see the installation instructions in Chapter 2 of the on-line manual for how to install and send for your trial license.
Keywords
3-D display, algebra, bias correction, brain atrophy, brain extraction, brain lesion follow-up, cardiac segmental analysis, DCE-MRI, diffusion, functional, fuzzy connector, import, java A.P.I., least-squares fitting, movie display, MPR, multiple sclerosis, NIfTI-1 support, particle analysis, perfusion, region of interest, registration, ROI, segmentation, spinal cord atrophy, statistical, tensor, tractography, visualization, volume, warp correction, warping
Platforms
Java, Linux, MacOS, SunOS, UNIX, Windows
IATR listing last updated
11 Mar 2015