Event name: scan session name, as will be entered on the console (eg, if your scan is acdc_spine_7t_033p, call the even the same)
Event description: Write a description into rthe logbook (see below) and link that entry, then add location (MNI, UNF, etc)
Event description: Write a description into the logbook (see below) and link that entry, then add location (MNI, UNF, etc)
Invities: if other people are joining you in the scan session, invite them as a courtesy/reminder
Details to book an MRI scanner is given in the specific MRI sub-section.
+Details to book an MRI scanner are given in the specific MRI sub-section.
-During scanning, please keep a log of your experiment:
Warning
-If you scan at UNF, you also need to fill up the UNF log book, which you can access from the UNF’s reservation booking form under the link “Link to logbook” if you are an operator. If you are not an operator, ask the person who operated the scan to fill the log book or to send you the link to the log book to fill it. It is important to fill the log book the day of the scan.
+If you scan at UNF, you also need to fill up the UNF log book, which you can access from the UNF’s reservation booking form under the link “Link to logbook” if you are an operator. If you are not an operator, ask the person who operated the scan to fill the logbook or to send you the link to the logbook to fill it. It is important to fill the log book the day of the scan.
Event name: scan session name, as will be entered on the console (eg, if your scan is acdc_spine_7t_033p, call the even the same)
Event description: Write a description into rthe logbook (see below) and link that entry, then add location (MNI, UNF, etc)
Event description: Write a description into the logbook (see below) and link that entry, then add location (MNI, UNF, etc)
Invities: if other people are joining you in the scan session, invite them as a courtesy/reminder
Details to book an MRI scanner is given in the specific MRI sub-section.
+Details to book an MRI scanner are given in the specific MRI sub-section.
During scanning, please keep a log of your experiment:
Warning
-If you scan at UNF, you also need to fill up the UNF log book, which you can access from the UNF’s reservation booking form under the link “Link to logbook” if you are an operator. If you are not an operator, ask the person who operated the scan to fill the log book or to send you the link to the log book to fill it. It is important to fill the log book the day of the scan.
+If you scan at UNF, you also need to fill up the UNF log book, which you can access from the UNF’s reservation booking form under the link “Link to logbook” if you are an operator. If you are not an operator, ask the person who operated the scan to fill the logbook or to send you the link to the logbook to fill it. It is important to fill the log book the day of the scan.
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15], "faster": [12, 13], "disk": [12, 13, 17, 30, 38, 39, 62], "than": [12, 13, 17, 20, 24, 30, 41, 50, 55, 62, 66, 92, 96, 97], "where": [12, 13, 17, 20, 22, 24, 26, 31, 34, 35, 38, 39, 40, 41, 54, 61, 62, 66, 69, 70, 77, 92], "home": [12, 13, 15, 17, 26, 27, 30, 43, 55, 62, 66, 76, 82, 85, 97, 98], "directori": [12, 15, 26, 30, 34, 38, 39, 53, 54, 66, 69], "temp": [12, 17, 24, 26], "file": [12, 14, 15, 17, 19, 20, 24, 25, 26, 27, 34, 37, 42, 43, 50, 55, 59, 61, 63, 65, 69, 71, 72, 78, 82, 85, 92, 98, 99, 105, 106, 107], "e": [12, 13, 15, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 34, 38, 39, 41, 50, 52, 53, 55, 57, 62, 66, 69, 74, 80, 83, 85, 88, 92, 95, 104], "clean": [12, 15, 24, 25, 26, 27, 53, 56, 66, 92, 98, 107], "locat": [12, 15, 18, 24, 26, 27, 30, 61, 66, 69, 75, 78, 96], "compress": [12, 24, 66, 74], "scan": [12, 74, 77, 78, 90, 96, 107], "myelin_06_rescan": 12, "command": [12, 13, 17, 27, 30, 38, 39, 40, 41, 43, 52, 53, 54, 57, 58, 62, 66, 69, 70, 72, 85, 92], "tar": [12, 37, 39, 69], "zcvhf": 12, "gz": [12, 13, 24, 27, 30, 31, 37, 39, 40, 41, 69], "unf": [12, 20, 26, 75], "dicom": [12, 50, 66, 73, 77, 78], "by_group": [12, 78], "myelin_map": 12, "download": [12, 13, 14, 15, 17, 19, 20, 34, 37, 39, 42, 49, 54, 61, 62, 63, 66, 69, 71, 74, 83, 99], "scp": [12, 13, 17, 77], "filezilla": [12, 77], "setup": [12, 72, 79, 80, 85], "connect": [12, 14, 16, 26, 30, 53, 63, 71, 72, 74, 80, 83, 95, 99, 107], "sftp": [12, 27, 66], "server": [12, 17, 23, 24, 25, 26, 27, 30, 38, 39, 53, 65, 71, 77, 80, 84, 105], "sun": 12, "grid": [12, 71], "termin": [12, 13, 17, 27, 30, 31, 34, 38, 49, 52, 53, 61, 62, 69, 70, 73, 85, 92], "ssh": [12, 26, 27, 46, 52, 77, 85, 99], "usernam": [12, 13, 15, 17, 26, 27, 30, 38, 46, 55, 62, 65, 70, 77, 83, 98, 99], "bin": [12, 13, 15, 17, 27, 30, 31, 34, 37, 41, 42, 49, 53, 58, 65, 66, 69, 72, 76, 82, 85, 104], "bash": [12, 13, 15, 27, 29, 31, 34, 53, 62, 65], "load": [12, 13, 17, 27, 30, 34, 39, 47, 50, 74, 98], "cd": [12, 13, 27, 30, 37, 38, 39, 53, 62, 72, 99], "start": [12, 15, 19, 24, 25, 31, 34, 38, 54, 62, 69, 78, 79, 88, 92, 97, 98, 99, 107], "launch": [12, 15, 17, 30, 53, 70], "sct_test": [12, 15, 26], "submit": [12, 13, 20, 89, 90, 96], "qsub": [12, 13], "my_job": [12, 13], "pb": [12, 13, 30, 96], "type": [12, 15, 17, 20, 24, 25, 30, 34, 38, 39, 49, 52, 55, 57, 65, 66, 69, 70, 74, 77, 84, 92], "qstat": [12, 13], "tip": [12, 20, 38, 66, 81, 95], "trick": [12, 66], "r": [12, 13, 15, 17, 25, 26, 27, 30, 31, 39, 41, 55, 58, 66, 71, 77, 85, 95], "src": 12, "grames_usernam": [12, 15, 26], "cp": [12, 30, 37, 53], "modul": [12, 17, 36, 39, 66, 92], "path": [12, 13, 17, 24, 27, 30, 34, 37, 38, 42, 49, 53, 54, 61, 62, 65, 66, 69, 70, 77, 82, 85, 96], "subfold": [12, 14, 88], "addpath": 12, "genpath": 12, "your_path": 12, "regist": [13, 20, 27, 66, 74, 95, 97], "ccdb": 13, "computecanada": [13, 27, 39, 85], "account_appl": 13, "sponsor": 13, "number": [13, 15, 17, 26, 27, 31, 38, 39, 41, 71, 85, 92, 107], "institut": [13, 20, 22, 24, 71, 83, 95, 106, 107], "montreal": [13, 20, 22, 24, 78, 83, 93, 95, 97, 106, 107], "electr": [13, 21, 22], "niagara": [13, 85], "graham": [13, 85], "hpc": [13, 85], "alloc": [13, 17], "identifi": [13, 15, 19, 27, 38, 74, 92], "rapi": 13, "guillimin": [13, 85], "clumeq": 13, "TO": [13, 58, 66, 82], "bash_profil": [13, 38, 42, 65, 69, 70, 82, 85], "bashrc": [13, 37, 49, 65], "bahsrc": 13, "ant": [13, 15, 85], "export": [13, 15, 17, 20, 27, 34, 37, 47, 49, 50, 65, 69, 70, 82, 85, 105, 107], "antspath": 13, "pre": 13, "instal": [13, 17, 27, 30, 54, 56, 65, 66, 70, 71, 74, 83, 85, 92, 99, 102, 107], "ll": [13, 27, 54, 62, 65, 66, 70, 85, 99], "cmake": [13, 69, 85], "put": [13, 14, 22, 26, 31, 38, 42, 61, 66, 69, 77, 80, 97], "module_nam": 13, "git": [13, 15, 17, 24, 26, 27, 29, 30, 31, 37, 52, 53, 58, 61, 66, 72, 85, 90, 92], "13": [13, 17, 20, 24, 26, 34], "0": [13, 17, 24, 27, 30, 31, 34, 35, 37, 39, 41, 43, 50, 53, 54, 62, 65, 69, 70, 71, 85, 92, 96, 99, 104, 107], "everyth": 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42, 55, 69, 85, 92, 99], "error": [13, 15, 17, 30, 34, 38, 39, 41, 46, 69, 74, 85, 92], "build_templ": 13, "final_data_t2": 13, "buildtemplateparallel": 13, "sh": [13, 15, 17, 30, 31, 37, 41, 58, 61, 65, 66, 82, 85], "avt": 13, "nii": [13, 24, 27, 30, 31, 39, 40, 41, 82, 85], "defin": [13, 15, 38, 41, 85, 92], "prioriti": [13, 74, 92, 99], "argument": [13, 30, 31, 41, 62, 66, 70], "integ": [13, 24], "1024": 13, "1023": 13, "inclus": [13, 28, 69, 92], "default": [13, 15, 17, 20, 27, 34, 39, 41, 56, 69, 92, 99], "equival": [13, 66], "begin": [13, 72], "direct": [13, 38, 40, 77, 89], "assign": [13, 22, 62, 89], "u": [13, 15, 27, 28, 30, 34, 38, 62, 66, 74, 77, 96, 102], "queue": 13, "checkjob": 13, "jobid": 13, "showq": 13, "qdel": 13, "6": [13, 15, 17, 22, 24, 27, 30, 34, 39, 41, 43, 54, 61, 66, 70, 72, 74, 76, 96, 106, 107], "virtual": [13, 17, 20, 30, 46, 61, 66], "virtualenv": [13, 17, 72, 82], "venv_nam": 13, "deactiv": [13, 72, 85, 99], "announc": 13, "westgrid": 13, "256": [13, 17], "1gb": [13, 17], "memori": [13, 17, 50, 62], "def": [13, 27], "jcohen": [13, 27, 38, 85, 98], "slurm": 13, "system": [13, 14, 15, 17, 39, 53, 54, 55, 62, 65, 66, 69, 76, 78, 84, 89, 90, 99, 102, 107], "sbatch": 13, "ntask": 13, "mpi": 13, "255": 13, "worker": 13, "mem": [13, 17], "1024m": 13, "unit": [13, 20, 24, 92, 107], "megabyt": 13, "03": [13, 17, 20], "dd": [13, 30, 62, 88], "hh": [13, 30], "mm": [13, 30, 76, 88], "save": [13, 19, 20, 24, 27, 30, 39, 41, 50, 70, 83, 96, 107], "workdir": 13, "data_path": 13, "subject": [13, 27, 30, 31, 38, 39, 58, 71, 74, 92], "sct_pipelin": 13, "nb": [13, 15], "cup": 13, "f": [13, 17, 24, 30, 31, 38, 39, 41, 53, 77, 82, 85], "sct_propseg": 13, "big_dataset": 13, "t2": [13, 40, 71, 74, 104], "propseg": 13, "chmod": [13, 15, 26, 30, 34, 39, 55, 66], "750": 13, "my_sct_script": 13, "execut": [13, 26, 30, 35, 41, 53, 54, 69, 70], "squeue": 13, "uid": [13, 39, 62], "One": [13, 20, 66], "smaller": [13, 20, 41, 50], "scale": [13, 22, 41, 74], "salloc": 13, "wait": [13, 38, 95], "give": [13, 15, 20, 30, 38, 39, 62, 70, 74, 77, 95, 97], "longer": [13, 24, 27, 38, 69, 77], "Then": [13, 15, 17, 20, 24, 27, 30, 34, 38, 41, 62, 65, 66, 70, 84, 107], "interfac": [13, 66, 98], "poq": 13, "coloss": 13, "cq": 13, "laval": 13, "mcgill": [13, 20, 85], "briare": 13, "same": [13, 15, 17, 18, 24, 27, 39, 41, 42, 50, 69, 75, 78, 83, 92], "mammoth": 13, "sherbrook": 13, "mp2": 13, "usherbrook": [13, 20], "helio": 13, "quebec": [13, 20, 22, 27, 80, 94, 97, 106, 107], "version": [13, 17, 20, 24, 26, 27, 30, 34, 38, 49, 54, 66, 69, 70, 72, 73, 77, 94, 106, 107], "compil": [13, 17, 37, 41, 69, 70], "wheelhous": 13, "tensorflow": [13, 17, 54], "gcc": [13, 17, 53], "5": [13, 15, 17, 20, 24, 30, 31, 37, 38, 39, 40, 41, 54, 61, 74, 76, 96, 104, 107], "cuda": [13, 17, 54], "7": [13, 15, 17, 20, 26, 37, 39, 54, 58, 69, 72, 76, 107], "lib": [13, 17, 34, 37, 41, 69, 70], "cudnn": [13, 17, 37, 54], "correct": [13, 38, 69, 74], "env_nam": 13, "specifi": [13, 15, 20, 24, 27, 38, 66, 72], "pip": [13, 37, 58, 72, 85], "version_numb": 13, "isn": [13, 27, 70], "moab": 13, "name": [13, 15, 17, 20, 26, 27, 30, 31, 39, 42, 46, 50, 62, 66, 69, 70, 71, 75, 77, 78, 80, 84, 88, 92], "msub": 13, "option": [13, 15, 17, 20, 24, 27, 31, 34, 38, 39, 41, 43, 46, 54, 62, 69, 70, 83, 95], "host": [13, 15, 17, 25, 27, 30, 46, 53, 54, 62, 107], "pi": [13, 19, 96, 98, 99], "specif": [13, 15, 17, 24, 27, 30, 39, 75, 80, 97, 105, 107], "spinalcordmri": [13, 74], "offic": [14, 15], "gb": [14, 38, 74, 85], "storag": [14, 37, 62], "fr": [14, 17, 22, 42, 95], "product": [14, 70, 96, 102], "address": [14, 15, 17, 18, 21, 25, 26, 38, 52, 66, 72, 78, 83, 84, 92], "spam": 14, "screen": [14, 15, 17, 34, 50, 71, 73, 92], "password": [14, 26, 27, 52, 62, 65, 70, 73, 83, 84, 98, 99], "polymtlca0": 14, "sharepoint": 14, "microsoft365": 14, "spreadsheet": 14, "upload": [14, 19, 20, 24, 30, 39, 49, 92], "drive": [14, 15, 16, 20, 25, 26, 41, 65, 74, 79, 90, 99, 106, 107], "sender": 14, "button": [14, 20, 38, 66], "drag": [14, 25, 66, 70], "drop": [14, 15, 25, 30, 66, 70], "view": [14, 15, 27, 50, 66, 74, 96], "secret": [14, 72], "messag": [14, 15, 17, 24, 26, 27, 30, 66, 69, 80, 85], "si": [14, 74, 99], "account": [15, 17, 19, 20, 38, 39, 52, 54, 55, 66, 74, 77, 78, 80, 83, 84, 89, 107], "log": [15, 19, 24, 27, 30, 38, 39, 77, 80, 83, 85, 90, 107], "onto": [15, 17], "anoth": [15, 24, 27, 30, 39, 53, 69, 77, 78, 80, 107], "passwd": 15, "duke": [15, 17, 23, 24, 71, 77], "desktop": [15, 25, 69, 80, 98], "creer51": [15, 105], "creer52": [15, 105], "creer53": 15, "your_polygrames_usernam": 15, "your_polygrames_password": 15, "desk": 15, "pick": [15, 17, 26, 27, 39, 80], "particular": [15, 92], "someon": [15, 27, 30, 38], "els": [15, 17, 31, 38, 39, 69, 83, 85], "laptop": [15, 27, 30, 80, 83], "ticket": [15, 21, 27, 89], "off": [15, 17, 24, 27, 57, 66, 69, 72, 92], "campu": [15, 26, 27, 79, 83], "\u00e9cole": 15, "consult": [15, 28, 79, 80, 95, 96, 106], "happen": [15, 17, 38, 40], "gestion": 15, "vpn_": 15, "actif": [15, 22], "cisco": 15, "anyconnect": 15, "maco": [15, 20, 26, 38, 39, 50, 58, 62, 63, 73, 83, 85, 99], "reach": [15, 27, 38, 89], "first": [15, 17, 19, 20, 22, 24, 27, 31, 39, 41, 58, 61, 66, 77, 78, 88, 92, 106, 107], "client": [15, 20, 30, 39, 53, 74, 83, 84], "openconnect": 15, "secur": [15, 17, 18, 66, 83], "mobil": 15, "distro": [15, 39], "brew": [15, 39, 58], "keychain": [15, 66], "item": [15, 53, 66], "your_cas_usernam": 15, "enter": [15, 26, 27, 38, 52, 62, 66, 70, 75, 78, 83, 102], "icloud": 15, "script": [15, 17, 24, 25, 26, 27, 30, 35, 37, 41, 42, 53, 65, 66, 72, 82, 83], "eo": 15, "pipefail": 15, "polyssl": 15, "polyinvit": 15, "statu": [15, 17, 38, 53, 66, 85, 92], "sudo": [15, 26, 27, 30, 34, 37, 38, 49, 55, 61, 62, 65, 66, 69, 70, 99], "authgroup": 15, "stdin": [15, 27], "reconnect": 15, "timeout": [15, 17], "ssl": 15, "apt": [15, 17, 34, 37, 38, 39, 53, 58, 61, 62], "your_cas_password": 15, "step": [15, 17, 24, 27, 30, 34, 37, 38, 43, 62, 65, 66, 70, 78, 80, 89, 92, 98], "english": [15, 22, 85, 94], "abov": [15, 17, 20, 24, 27, 38, 39, 54, 62, 66, 80, 92, 98, 107], "ever": [15, 89], "break": [15, 38, 92, 99], "licens": [15, 17, 69, 71, 107], "sort": [15, 30, 66], "authent": [15, 27, 71, 83], "utilis": [15, 84], "du": [15, 17, 22, 30, 39, 84, 95, 97, 107], "servic": [15, 20, 34, 53, 77, 83, 84, 89, 92, 95, 107], "requri": 15, "sign": [15, 20, 38, 58, 77, 84], "newli": [15, 27, 93], "configur": [15, 17, 27, 30, 34, 37, 39, 42, 61, 65, 69, 76, 81, 98, 99], "down": [15, 30, 61, 66, 77, 92], "choos": [15, 20, 24, 27, 28, 40, 43, 70, 92], "profil": [15, 17, 58, 81, 82, 83], "p123123": 15, "ge_usernam": 15, "packag": [15, 17, 37, 44, 46, 47, 61, 66, 92], "wsl": [15, 39], "putti": 15, "cmder": 15, "allow": [15, 17, 20, 22, 24, 27, 28, 38, 40, 47, 49, 53, 54, 61, 63, 66, 69, 70, 76, 83, 92, 94, 97], "cat": [15, 17, 27, 30, 34, 39], "config_neuropoli": 15, "eof": [15, 39], "betti": 15, "coltran": 15, "davi": [15, 85, 95], "django": [15, 23, 43, 66, 85], "ella": 15, "jarrett": 15, "kirk": 15, "marsali": 15, "mingu": 15, "parker": 15, "tatum": 15, "hostnam": [15, 16, 30, 38, 98], "remov": [15, 27, 31, 34, 41, 55, 61, 66, 69, 85, 92], "comment": [15, 20, 38, 57, 85, 88, 92], "mnt": [15, 17, 26, 62, 65], "issu": [15, 21, 24, 27, 28, 38, 39, 55, 66, 89], "90": [15, 17], "preferredauthent": 15, "config": [15, 27, 37, 38, 42, 52, 61, 92], "retyp": 15, "controlmast": 15, "auto": [15, 39, 71, 85, 98], "controlpath": 15, "controlpersist": 15, "wai": [15, 20, 24, 27, 38, 39, 69, 70, 74, 86], "sshf": 15, "appear": [15, 27, 38, 39, 69, 71], "were": [15, 22, 27, 37, 38, 92], "yet": [15, 27, 38, 52, 71, 92], "mac": [15, 26, 30, 55, 62, 71], "monterei": 15, "cask": 15, "osxfus": 15, "mkdir": [15, 17, 26, 27, 38, 39, 65, 99], "cluster_fold": 15, "noth": [15, 34, 39, 42], "shown": [15, 66], "rel": [15, 41, 42, 61], "project1": 15, "attach": [15, 27, 30, 96], "exact": 15, "tmp": [15, 17, 37, 41, 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