Last modified by puchades on 2022/02/18 13:55
From version 18.4
edited by puchades
on 2020/04/07 16:03
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To version 21.2
edited by puchades
on 2020/04/07 16:12
Change comment: There is no comment for this version

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11 11  
12 12  == (% style="color:#c0392b" %)Preparation of the image series(%%) ==
13 13  
14 -Before you get started with image registration, make sure your images are the right size, and files are named according to the QUINT naming convention. See [[2. Image pre-processing with Nutil Transform>>2. Image pre-processing with Nutil Transform]] for details.
14 +Before you get started with image registration, make sure your images are the right size, and files are named according to the QUINT naming convention. See [[2. Image pre-processing with Nutil Transform>>doc:Collabs.quint.1\. Preparing the images.WebHome]] for details.
15 15  
16 16  === (% style="color:#c0392b" %)Generate your image descriptor file with FileBuilder(%%) ===
17 17  
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23 23  
24 24  A detailed //QuickNII// user manual as well as a demo dataset can be found on [[https:~~/~~/www.nitrc.org/projects/quicknii/>>https://www.nitrc.org/projects/quicknii/]]
25 25  
26 ->(% style="color:#27ae60" %)The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole series as these should be consistent throughout. Once found in a few sections, apply the same angles to the rest of the series.
27 -
28 28  == (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
29 29  
30 -**The basic steps are:**
28 +(% class="box infomessage" %)
29 +(((
30 +The alignment procedure consists of two main tasks:
31 31  
32 +1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
33 +1. Adjust the atlas slices generated along these angles to match individual sections.
34 +)))
35 +
36 +=== (% style="color:#c0392b" %)A) To determine the cutting angles:(%%) ===
37 +
32 32  (% style="color:#000000" %)-(%%)Open one image in the beginning of the series and use anatomical landmarks to find the approximate anteroposterior position of the section. Select the atlas modality to be overlayed on the image (MRI, Atlas, etc..)
33 33  
34 34  -Use the** transparency slider** continuously to determine how well the atlas fits the section. Determine the sectioning angles (dorso-ventral and medio-lateral) by tilting the atlas and adjust the atlas borders.