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start [2019/08/19 14:59] – [Other Useful IT information] Pat Butlerstart [2026/01/19 11:03] (current) – Robyn Dillon
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 This wiki is intended to help researchers share knowledge and information about the imaging techniques and projects that are running at CISC. To contribute to this wiki you should click on the Login button at the top or bottom of this page. This wiki is intended to help researchers share knowledge and information about the imaging techniques and projects that are running at CISC. To contribute to this wiki you should click on the Login button at the top or bottom of this page.
  
-A quick-start guide to help you contribute to this wiki is found [[:contributing|here]].+A quick-start guide to help you contribute to this wiki is found **[[:contributing|here]]** . Some suggested sections to create include:
  
-If you are a new user you need to **Register** by the clicking the link in the top right of this page+  * CISC contact list (including radiographers, technical support, medical covers, admin etc.) 
 +  * Virtual tour of the control room with different PCs and equipment labelled 
 +  * Table of senior staff researchers, their contacts and areas of imaging expertise 
 +  * Accessing the sn_analysis servers and mapping the cisc1 and 2 drives
  
-**Join the cisc forum email list ** to ask questions, get involved with discussions, and keep up-to-date with the latest developments at CISC. Subscribe to the mailing list at [[https://lists.sussex.ac.uk/mailman/listinfo/ciscforum|https://lists.sussex.ac.uk/mailman/listinfo/ciscforum]]+If you are a new user you need to **Register**  by the clicking the link in the top right of this page
  
-===== MRI Forms and Documentation =====+===== CISC Inductions =====
  
-This section contains forms and documentation relevant to MRI Scanning at CISC (**NOTE: you must login before downloading these files**)+Before working in CISC you will need to have the following:
  
-   * {{:safety_questionnaire_v7_oct2018.pdf|MRI Safety Questionaire}}+  * Building induction 
 +  * MRI safety session with our MR Safety Expert
  
-  * {{:consent_for_mri_scanning_of_research_volunteer_with_a_tattoo.docx|Consent for MRI scanning of research volunteer with a tattoo}}+Both of these can be arranged by contacting Jan Bush [[j.bush@bsms.ac.uk|]]
  
-  * {{:adviceforresearchersregardingtattoos.doc|Advice for Researchers regarding tattoos }}+===== Get Connected =====
  
-  * {{:cisc_policy_for_radiological_review_of_diagnostic_images.doc|CISC Policy for Radiological Review of Diagnostic Images}}+Join the cisc forum slack workgroup and email list to ask questions, get involved with discussions, and keep up-to-date with the latest developments at CISC.
  
-  * {{:how_to_wear_ear_plugs.pdf|:how_to_wear_ear_plugs.pdf}}+**Slack Workgroup:**  [[https://bit.do/ciscslack|https://join.slack.com/t/ciscforum/shared_invite/zt-1qkpxz3xy-HEtCU0kbwQnkMYPSM2o4PA]]
  
-===== CISC Project Documentation =====+**CISC Forum Mailing List:**  You can request access to the CISC Forum mailing group by sending a message to Chris Racey (c.racey@sussex.ac.uk). This group is used to disseminate information relevant to CISC users, and advertise for the Cognitive Neuroscience and Imaging (CNI) meetings. For more information, **[[:ciscforum|click here]]**.
  
-This section explains the administrative process necessary before scanning and contains examples of successful applications to CISC for MRI projects+**CNI Seminar Series: **The Cognitive Neuroscience and Imaging (CNI) meetings are for discussing planned, ongoing and completed projects andto seek CISC approval for project applications. For more information, **[[:imagingresearchmeeting|click here]].**
  
-  * [[:projectapplications?media=projectapplications|The application process]] - introduction to what is required before you can scan +===== Applying for a Project at CISC =====
-  * [[:projexampleholle|Examples of completed Ethics and CISC Applications forms]]+
  
-**Quick Downloads**+This section explains the administrative process necessary before scanning and contains examples of successful applications to CISC for MRI projects.
  
-  * {{:cisc_project_proposal_form_-_master_2019.docx|:CISC Project Application Form 2019.docx}} +  * [[:projectapplications?media=projectapplications|The Application Process]] - introduction to what is required before you can scan and links to the various forms you'll need 
-  * {{:research_scan_costing_pro_forma_v20_-_july_2019.doc|:CISC Scan Costing Proforma 2019.doc}}  - you will need to fill this out as part of a grant application and send to Stuart Welling (sjw@cooden.plus.com ) +  * [[:projexampleholle|Examples of Completed Ethics and CISC Applications Forms]]
-  * {{:cisc_scanning_protocol_w._guidelines_1.doc|CISC Scanning Protocol w. guidelines.doc}}+
  
 +Quick Downloads:
  
-===== Bookings (Calpendo) =====+  * {{:cisc-project-proposal-form-master-2025.docx|:cisc-project-proposal-form-master-2025.docx}} 
 +  * {{:research_scan_costing_pro_forma_v27_-_july_2025.doc|Research Scan Costing Pro Forma }} 
 +  * {{:cisc_scanning_protocol_w._guidelines_1.doc|CISC Scanning Protocol}}
  
-This section contains details about booking the CISC resources including the MRI Scanner and Seminar Room.+Complete these three documents and send to the CISC inbox [cisc@bsms.ac.uk] copying in Jan Bush [j.bush@bsms.ac.uk].
  
-  * [[https://cisc.calpendo.com|Link to Calpendo Bookings System]] +===== MRI Forms and Documentation =====
-  * {{:calpendo.pptx|Calpendo User Guide}}  (Powerpoint Presentation) **you need to login to the wiki to download this file**+
  
-===== Scanner Information ===== +This section contains forms and documentation relevant to MRI Scanning at CISC (**NOTE: you must login before downloading these files**)tattoos }}
- +
-This section contains details about the scanner hardware we have available at the CISC. +
- +
-  * [[:mri_info|MRI Scanner]] - general information about the scanner hardware +
- +
-  * [[:siemensdocs|Siemens Documentation]] - information about the scanner and pulse sequences +
- +
-  * [[:interactiveqa|Interactive Scanner QA]] - Browse the scanner QA archive (2007-present) +
- +
-  * [[:physics:physicsupdate|QA Reports]] - archive for scanner performance reports +
- +
-  * [[:petct_info|PET/CT Scanner]] - PET scanner hardware information +
- +
-  * [[:peripheralequipment|Peripheral Equipment]] - details of some of the peripheral equipment used with th MRI scanner +
- +
-  * [[:pulse_sequences|Pulse Sequence Acquisition Parameters]] - Standard acquisition sequences frequently used in MR studies at CISC +
- +
-  * Projector information: Visual stimuli are projected via a Sony Bright Era 3LCD projector +
- +
-===== Your Data and Analysis Facilities ===== +
- +
-This section includes information about how imaging data is stored and accessed at CISC and what hardware is available to researchers to analyze their data. +
- +
-  * [[:data_pathway|Getting your data]] - Where is your imaging data stored? How can you access it? +
- +
-  * [[:cisc_network_disk|Network Diskspace for cisc]] - useful for users of the apollo cluster +
- +
-  * [[:sussexhpc|The Sussex High-Performance Computing (HPC) Cluster]] +
- +
-  * [[:matlab|Matlab Specific Information]] +
- +
-  * [[:stimpcs|Stimulus PCs]]+
  
-  * Leonardo Multimodality workstation+  * {{:a14_-_cisc_radiological_review_of_diagnostic_images_v7_1_.doc|Notes on Incidental Findings}} 
 +  * {{:adviceforresearchersregardingtattoos.doc|:advice for researchers regarding tattoos}} 
 +  * {{:mri_safety_questionnaire_pt_2025.docx|mri safety questionnaire pt 2025}} 
 +  * {{:how_to_wear_ear_plugs.pdf|How to Wear Ear Plugs}} 
 +  * {{:cisc_pilot_policy_aka_policy_for_enabling_effective_scanning_at_cisc.pdf|CISC Pilot Policy}}
  
-===== Bookings (Calpendo) =====+===== Booking Scan Slots with Calpendo =====
  
 This section contains details about booking the CISC resources including the MRI Scanner and Seminar Room. This section contains details about booking the CISC resources including the MRI Scanner and Seminar Room.
  
   * [[https://cisc.calpendo.com|Link to Calpendo Bookings System]]   * [[https://cisc.calpendo.com|Link to Calpendo Bookings System]]
-  * {{:calpendo.pptx|Calpendo User Guide}}  (Powerpoint Presentation) **you need to login to the wiki to download this file**+  * {{:calpendo.pptx|Calpendo User Guide}}  - **you need to login to the wiki to download this file** 
 + 
 +As soon as you have booked your scan slot, email cisc@bsms.ac.uk with details of your participant/s including name, date of birth and if they indicate that they have been scanned here before. This needs to be done at least 24 hours in advance of the scan time.
  
 ===== Scanner Information ===== ===== Scanner Information =====
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   * [[:mri_info|MRI Scanner]] - general information about the scanner hardware   * [[:mri_info|MRI Scanner]] - general information about the scanner hardware
- 
   * [[:siemensdocs|Siemens Documentation]] - information about the scanner and pulse sequences   * [[:siemensdocs|Siemens Documentation]] - information about the scanner and pulse sequences
- 
   * [[:interactiveqa|Interactive Scanner QA]] - Browse the scanner QA archive (2007-present)   * [[:interactiveqa|Interactive Scanner QA]] - Browse the scanner QA archive (2007-present)
- 
   * [[:physics:physicsupdate|QA Reports]] - archive for scanner performance reports   * [[:physics:physicsupdate|QA Reports]] - archive for scanner performance reports
- 
   * [[:petct_info|PET/CT Scanner]] - PET scanner hardware information   * [[:petct_info|PET/CT Scanner]] - PET scanner hardware information
- 
   * [[:peripheralequipment|Peripheral Equipment]] - details of some of the peripheral equipment used with th MRI scanner   * [[:peripheralequipment|Peripheral Equipment]] - details of some of the peripheral equipment used with th MRI scanner
- 
   * [[:pulse_sequences|Pulse Sequence Acquisition Parameters]] - Standard acquisition sequences frequently used in MR studies at CISC   * [[:pulse_sequences|Pulse Sequence Acquisition Parameters]] - Standard acquisition sequences frequently used in MR studies at CISC
- 
   * Projector information: Visual stimuli are projected via a Sony Bright Era 3LCD projector   * Projector information: Visual stimuli are projected via a Sony Bright Era 3LCD projector
  
-===== Your Data and Analysis Facilities =====+===== Data and Analysis =====
  
-This section includes information about how imaging data is stored and accessed at CISC and what hardware is available to researchers to analyze their data. +This section includes information about how imaging data is stored and accessed at CISC and what hardware is available to researchers to analyse their data.
- +
-  * [[:data_pathway|Getting your data]] - Where is your imaging data stored? How can you access it? +
- +
-  * [[:cisc_network_disk|Network Diskspace for cisc]] - useful for users of the apollo cluster+
  
 +  * [[:data_pathway|Getting your Data]] - Where is your imaging data stored? How can you access it?
 +  * [[:cisc_network_disk|Network Diskspace for CISC]] - useful for users of the apollo cluster
   * [[:sussexhpc|The Sussex High-Performance Computing (HPC) Cluster]]   * [[:sussexhpc|The Sussex High-Performance Computing (HPC) Cluster]]
- 
   * [[:matlab|Matlab Specific Information]]   * [[:matlab|Matlab Specific Information]]
- 
   * [[:stimpcs|Stimulus PCs]]   * [[:stimpcs|Stimulus PCs]]
  
-  * Leonardo Multimodality workstation+===== Participant Recruitment =====
  
-===== Other Useful IT information =====+We aim to support your volunteer recruitment efforts as much as possible by maintaining a database of individuals interested in participating in research projects at CISC. We can share details about your upcoming projects with these individuals via a mailing list. If they meet your screening criteria and express interest, they can reach out to you directly. Additionally, if you currently have participants who may be interested in taking part in future projects led by other researchers, please encourage them to complete the consent form and send it to cisc@bsms.ac.uk or follow the link below.
  
-  * [[:computerproblems|IT Problems]] - add any IT problems you may have to this page+[[https://forms.cloud.microsoft/Pages/ResponsePage.aspx?id=kLsAqf6UWEaLNN1yCExQZFKuZs-ksHFOtvlZ0_aY1pxUMUZDMVdYTjE1RzBPU0k1RExGVzc1S1A5SS4u|https://forms.cloud.microsoft/Pages/ResponsePage.aspx?id=kLsAqf6UWEaLNN1yCExQZFKuZs-ksHFOtvlZ0_aY1pxUMUZDMVdYTjE1RzBPU0k1RExGVzc1S1A5SS4u]]
  
-  * [[:contributing|Contributing to the CISC wiki]] - a quick-start guide to creating/editing your own wiki pages+  * {{:consent_form_participant_database.docx|:consent_form_participant_database.docx}}
  
 +===== IT Issues =====
  
-===== Meetings and Communications ===== +  * For any IT issues encountered regarding servers or VPN connections, for example, please log a ticket below, or alternatively post the issue in the CISC slack workgroup. **[[:computerproblems|Click here to log a ticket]].**
- +
-  * [[:quinab:quinab|QuINAB]] - quantitative imaging of the normal-appearing brain +
- +
-  * [[:computergroup|CISC Computer Group]] +
- +
-  * [[:imagingresearchmeeting|Imaging Research Meetings]] - Wednesday lunchtime meetings to discuss planned, ongoing and completed projects AND to seek CISC approval for project applications +
- +
-  * [[:susx_nimaging_methods|Sussex Neuroimaging Methods meetings]] 2018 - 2019 schedule +
- +
-  * [[:ciscforum|CISCforum Mailing List]] +
- +
-  * [[:mri_technique_users|MRI technique users]] - if you are looking for advice on a particular analysis technique, this page lists the neuroimaging skills and expertise of CISC members +
- +
-  * {{:cisc_feb_19th_2016_dl_and_np.pptx|Clinical Trials Unit presentation}}  (19/02/2016) - the slides from Nicky Perry and Debbie Lambert's presentation are available here+
  
 ===== Guides and Tutorials ===== ===== Guides and Tutorials =====
  
-  * [[:fmri_guides|fMRI Acquisition and Analysis]] +  * [[:fmri_guides|Technical Guides]] 
 +  * [[:chrisb|fMRI Crash Course]]
   * [[:qmr_guides|Quantitative MR Acquisition Guides]]   * [[:qmr_guides|Quantitative MR Acquisition Guides]]
- 
   * [[:mr_processing|MR data processing guide]] - a work-in-progress page to unify data analysis at CISC   * [[:mr_processing|MR data processing guide]] - a work-in-progress page to unify data analysis at CISC
- 
   * [[:online_guides|Useful Online tutorials]] - a collection of links to tutorials for MRI or related analysis   * [[:online_guides|Useful Online tutorials]] - a collection of links to tutorials for MRI or related analysis
 +  * [[https://youtu.be/N2hGMtfbr_8|Video Guide to prepreprocessing with fmriprep for Sussex/CISC acquired data]] - walks through step by step fmriprep processing using the Sussex Neuroscience analysis infrastructure, the cisc volumes, and the Apollo2 HPC cluster. All necessary script files are available [[https://canvas.sussex.ac.uk/courses/20867/files/4771674/download?download_frd=1|here]].
 +  * [[https://youtu.be/MvNXgoFdV2M|Topup Fieldmap Video Guide]] - for generating topup field maps to apply for subsequent processing in MATLAB/SPM/FSL/HCP pipeline. All of the example scripts and dependencies can be found [[https://canvas.sussex.ac.uk/courses/20867/files/5305765?wrap=1|here]]
 +  * [[https://youtu.be/ucWoxb5KMIE|Working with parcellated data in wbview (HCP Pipeline)]] - for loading in and working on parcellated cifti files in wbview. Example scripts and functions are available [[https://canvas.sussex.ac.uk/courses/20867/files/4797877/download|here]].
 +  * [[https://youtu.be/sIHa90Hk68g|Video Guide to freesurfer processing for Sussex/CISC acquired data]] - walks through step by step freesurfer processing using the Sussex Neuroscience analysis infrastructure, the cisc volumes, and the Apollo2 HPC cluster.
  
-===== Chris's FMRI Course ===== +===== Archive =====
- +
-  * [[:chrisb|Link to some info]] +
- +
-=====   ===== +
- +
- +
-===== Meetings and Communications ===== +
- +
-  * [[:quinab:quinab|QuINAB]] - quantitative imaging of the normal-appearing brain +
- +
-  * [[:computergroup|CISC Computer Group]] +
- +
-  * [[:imagingresearchmeeting|Imaging Research Meetings]] - Wednesday lunchtime meetings to discuss planned, ongoing and completed projects AND to seek CISC approval for project applications +
- +
-  * [[:susx_nimaging_methods|Sussex Neuroimaging Methods meetings]] 2018 - 2019 schedule +
- +
-  * [[:ciscforum|CISCforum Mailing List]]+
  
 +  * [[:susx_nimaging_methods|Sussex Neuroimaging Methods meetings]] 2018 - 2019 schedule. Incorporated into CNI - See above
   * [[:mri_technique_users|MRI technique users]] - if you are looking for advice on a particular analysis technique, this page lists the neuroimaging skills and expertise of CISC members   * [[:mri_technique_users|MRI technique users]] - if you are looking for advice on a particular analysis technique, this page lists the neuroimaging skills and expertise of CISC members
- 
   * {{:cisc_feb_19th_2016_dl_and_np.pptx|Clinical Trials Unit presentation}}  (19/02/2016) - the slides from Nicky Perry and Debbie Lambert's presentation are available here   * {{:cisc_feb_19th_2016_dl_and_np.pptx|Clinical Trials Unit presentation}}  (19/02/2016) - the slides from Nicky Perry and Debbie Lambert's presentation are available here
- +  * Covid Safety Induction - We are happy to announce that general research activity will be resuming in the CISC building. If you are planning to restart your project at CISC you will first need to complete the induction procedure. [[:covidadvice|Click here to visit the CISC COVID-safety Induction page]].
-===== Guides and Tutorials ===== +
- +
-  * [[:fmri_guides|fMRI Acquisition and Analysis]] +
- +
-  * [[:qmr_guides|Quantitative MR Acquisition Guides]] +
- +
-  * [[:mr_processing|MR data processing guide]] - a work-in-progress page to unify data analysis at CISC +
- +
-  * [[:online_guides|Useful Online tutorials]] - a collection of links to tutorials for MRI or related analysis +
- +
-===== Chris's FMRI Course ===== +
- +
-  * [[:chrisb|Link to some info]] +
- +
-=====   =====+
  
  
start.1566223191.txt.gz · Last modified: 2019/08/19 14:59 by Pat Butler

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