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Title

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1		-2. Image preparation with Nutil Transform
	1	+2. Image preparation with Nutil

Content

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13	13
14	14	=== Naming convention: ===
15	15
16		-For running the QUINT analysis the segmentation files and the customized atlas maps need to match and therefore the segmentation files should follow the same naming format.The file name that correspond to a particular section must contain a unique ID in the format: sXXX.., with XXX.. representing the section number. The section number should reflect the serial order and spacing of the sections (e.g. s002, s006, s010 for every 4^^th^^ section starting with section 2).
	16	+The file names of the segmentation and atlas maps that correspond to a particular section must contain a unique ID in the format: sXXX.., with XXX.. representing the section number. The section number should reflect the serial order and spacing of the sections (e.g. s002, s006, s010 for every 4^^th^^ section starting with section 2).
17	17
18	18	Example: tg2345_MMSH_s001_segmentation.png
19	19
20	20	(It is fine to include a string of letters and numbers followed by the unique ID).
21	21
	22	+For running the QUINT analysis the segmentation files and the customized atlas maps need to match and therefore the segmentation files should follow the same naming format.
22	22
23		-=== Running the transformation ===
	24	+=== ===
24	24
25		-Consult the Nutil user manual for detailed procedure (link to Manual on Nitrc.org)
	26	+==== ====
26	26
27		-[[image:Figure_2_v3.jpg]]
	28	+[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
	29	+
	30	+Photo by David Clode
	31	+
	32	+==== Or code ====
	33	+
	34	+Code blocks can be added by using the code macro:
	35	+
	36	+{{code language="python"}}
	37	+x = 1
	38	+if x == 1:
	39	+ # indented four spaces
	40	+ print("x is 1.")
	41	+{{/code}}
	42	+
	43	+(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
	44	+