M. Mesdames, conclusion d'un travail de presque deux années et demi. L'internat étant plein de surprises, à l'image de la vie, je ne m'attendais pas en débutant mes études de médecine en septembre 2006 à écrire douze années et demi plus tard une thèse d'exercice portant sur les neurosciences en psychiatrie. Les rencontres et les soutiens, présents ou absents, m'ont permis de raffiner mes connaissances et ainsi, après moult errements et choix d'orientations, plusieurs échecs, est venue la conclusion de ce parcours d'études

J. , Cette thèse a pour ambition d'être une première pierre posée pour la construction d'une collaboration entre les services de radiodiagnostic, de médecine nucléaire, et de psychiatrie, dans le contexte souhaité de ma part d'une construction d'un laboratoire d'imagerie cérébrale en psychiatrie au sein du CHRU de Brest, ainsi que

, Pour reprendre deux citations d'Elon Musk, pionnier de la « rocket science » américain : « Optimism, pessimism, fuck that; we're going to make it happen ! » « Patience is a virtue, and I'm learning patience

E. Jules, . Psychiatrie, and . De-brest, , vol.115, p.146

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, Annexe 3 : Fonctionnement des algorithmes de traitement d, image Statistical Parametric Mapping, vol.12

. L'algorithme-fonctionne-en-Étapes, avec en entrée une image au format adapté (.nii) , en pondération T1 et orientée en Ca-Cp*

S. B. ?-première-Étape-;-À-la, L. Au, and . Au-crâne, aux autres tissus extraencéphaliques et à l'air (outil « New Segment » 17 ). SPM 12, contrairement aux versions antérieures, utilise comme « à priori » de la segmentation une « Tissue Probabilty Map » (illustration 18) qui est incluse dans le package logiciel, par défaut celle de l'atlas MNI. Le logiciel de segmentation va ensuite classer les pixels en classe avec une intensité suivant une gaussienne. Nous avons utilisé une régularisation de biais légère (0,001), un filtre « FWHM » à 60 mm, segmentation en 6 classes des voxels, les classes correspondant respectivement à la SG

. Seconde-Étape, Création du « template », le logiciel va à cette étape sélectionner les cartes de SG et/ou de SB issues de la segmentation de l'étape précédente, et ensuite recaler les cartes de SG des patients au moyen d'une déformation élastique (DARTEL), aligner en même temps les cartes de SB , moyenner, sommer et lisser itérativement ces cartes pour construire une image correspondant à la sommation de toutes les images 14 . Il s'agit du template de l'étude qui va servir à identifier les différences aux images individuelles

, ? Troisième étape : le « template » est normalisé sur un espace commun, par défaut l'espace MNI via des recalages par transformation affines rigides

, ? Quatrième étape : calcul des volumes intracrâniens totaux, cérébraux totaux via la segmentation

. ?-cinquième-Étape, Lissage, ici, avec un filtre gaussien de « FWHM » 8*8*8 mm

. Sixième-Étape, Cette étape normalise selon le volume cérébrale total (ou le volume intracrânien total) les valeurs obtenues. Nous avons utilisé un masque absolu explicite à 0,7 d'intensité. Les covariables ont été le volume intracrânien

, Cet algorithme fonctionne en plusieurs étapes qui ont toutes lieu au cours de l'exécution de la commande « recon-all », s'enchaînant les unes les autres. Les grandes étapes sont appelés « autorecon1 », « autorecon2 » et « autorecon3

». «-autorecon1 and . Successivement,

, ? Étape 1 de correction de mouvements si il existe plusieurs volumes sources, par moyennage entre ceux-ci

, Étape 2 de correction d'intensités. L'algorithme va alors utiliser une méthode dîte « non parametric, non uniform, intensity normalisation (N3) » pour normaliser les intensités avec un nombre d'itération de 4. Il s'agit de l'outil dit « nu_correct

, Illustration 31: Imagerie T1 d'entrée à Freesurfer ? Étape 3 de transformation en ré-échantillonant le volume original selon l'atlas MNI 305

, ? Étape 4 de Normalisation d'intensités, en adaptant l'intensité des voxels pour que la moyenne des intensités de la SB soit à un niveau de gris de 110

, Il s'agit des étapes préparatoires à la suite de l'analyse d'image qui est ensuite conduite dans les étapes « autorecon2 » et « autorecon3 ». Pour « autorecon1 » le choix a été fait d'utiliser la commande sans modifier les requêtes de fonctionnement de celle-ci, vol.142, p.146

, comporte ensuite successivement : ? Étape 6-11 de segmentation sous corticale automatique, ? Étape 6 de recalage par algèbre géométrique conforme, utilisant une fonction de type « Expectation/Maximization » pour recaler le volume issu de l'étape 2 à l'atlas GCA et avoir une transformation à utiliser. recalage qui trouve la transformation non linéaire permettant l, Imagerie T1 après correction d'intensité « Autorecon2, vol.32

?. Étape, , vol.9

, Étape 10 de recalage par fonction EM des images comprenant le crane

, Étape 11 d'identification des structures sous-corticales en utilisant l'atlas GCA recalé, avec en plus une section appelée « aseg stats » qui reporte les statistiques des volumes des structures sous-corticales sur un fichier texte

, Étape 12 de normalisation d'intensités utilisant les volumes sans le crane

, Étape 13 de segmentation de la substance blanche. L'algorithme va tenter de séparer la SB de tout le reste utilisant l'intensité

, Illustration 33: Image composite, aseg surimprimée sur l'image T1

, Étapes 14 et 15 d'édition de la substance blanche avec correction selon « aseg »,qui va identifier la masse sous-corticale, et permettre la création de la surface « orig », il s'agit de la dernière étape de traitement volumique

, Étape 16 de pavage, la surface « orig » est crée en recouvrant les hémisphères isolés de triangles, chaque angle de chaque triangle étant appelé sommet (« vertices »). A partir de cette étape

, Du fait de la méthode de constitution de la surface « orig » celle ci est très déchiquetée, le lissage permet de faciliter le processus d'inflation de la surface, ? Étape 17 de lissage de «orig surface

, Étape 18 d'inflation de la surface « orig », qui cherche à minimiser les distorsions pour conserver les surfaces et les distances ( l'analogie faite par les développeurs est celle de gonfler un sac en papier comparé à gonfler un ballon

, Étape 19 du « Qsphere », une transformation quasi-homéomorphe sphérique de la surface « orig » réalisée pour détecter les défauts de la suface « orig

, Étape 20 appelée « automatic topology fixer », qui va éditer la surface « orig » pour éliminer les défauts de celle ci

, Étape 21 dites « final surfaces » qui va créer la surface d'interface SB/SG et la surface d'interface SG/pie-mère. La surface dite « white surface » est créée en altérant la surface « orig » pour qu'elle soit superposée aux gradient d'intensité entre SB et SG en pondération T1. La surface dite « pial surface » est créée en réalisant une expansion de la « white surface

, Étapes 22 et 23 qui correspondent à un lissage et une inflation de la surface « orig

, Il s'agit là des étapes préparatoires à la cartographie corticale constituant « Autorecon3 » qui comporte ? Étapes 24-25 dites de recalage de surface (« spherical morph » ), qui correspond à un recalage entre la surface « orig

, ? Étape 26 dite de courbure moyenne

, Étape 27 de parcellarisation corticale selon l'atlas sphérique utilisé qui correspond à l'identification de chaque zone du cortex selon les atlas utilisés, selon des informations géométriques du modèle cortical et les conventions neuroanatomiques

, Étape 28 qui correspond à l'extraction des valeurs d'épaisseur, de surface et de courbures pour chaque zone corticales, vol.145, p.146

, Illustration 34: Image composite, atlas Desikan-Killiany surimprimée sur l'image T1

, Pour la plupart de ces étapes, il existe des possibilités d'entrer des préférences avant le lancement de l'algorithme qui modifient celles ci, par exemple, lors de l'étape 2, il est possible de changer le nombre d'itérations de la correction

, Illustration 35: Image composite, atlas Destrieux surimprimée sur l'image T1