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June 14, 2022 09:38PM
Spent some time with this data. This data was pretty "challenging" because it's only about 5 slices of data, low resolution, spatially and temporally noisy, non-uniform enhancements, and shapes are changing throughout. That's plenty of trouble. Mostly, your recipe seemed pretty close to what I thought I was best.

# restrict data to range
3dcalc -a 'RA_B017_ZDS3_GEPI2D_Rep1_SampleNOMASK+orig.<30000..100000>' -expr a -prefix temprange
# cluster (interactive or command line)
3dClusterize -nosum -1Dformat -inset /Users/dglen/edwinb/EdwinB/temprange+orig.HEAD \
-idat 4 -ithr 0 -NN 2 -clust_nvox 4000 -pref_map Clust_mask
# make dataset fit only around a smaller box around the cluster (I used only 1st 100 volumes for testing)
3dAutobox -prefix tempab2 Clust_mask+orig
3dZeropad -master tempab2+orig. -prefix temp100ab RA_B017_ZDS3_GEPI2D_Rep1_SampleNOMASK+orig.'[0..99]'
# alignment with correlation cost
3dAllineate -base temp100ab+orig'[0]' -prefix temp100ab_al2ls -cost ls -linear -input temp100ab+orig.
Subject Author Posted

Help with Registration of Abdominal images

ebaldelo June 10, 2022 01:44PM

Re: Help with Registration of Abdominal images

ebaldelo June 10, 2022 02:56PM

Re: Help with Registration of Abdominal images

Daniel Glen June 10, 2022 05:28PM

Re: Help with Registration of Abdominal images

ebaldelo June 10, 2022 06:05PM

Re: Help with Registration of Abdominal images

Daniel Glen June 10, 2022 07:36PM

Re: Help with Registration of Abdominal images

ebaldelo June 13, 2022 12:17PM

Re: Help with Registration of Abdominal images

Daniel Glen June 13, 2022 02:35PM

Re: Help with Registration of Abdominal images

ebaldelo June 13, 2022 05:33PM

Re: Help with Registration of Abdominal images

Daniel Glen June 13, 2022 06:24PM

Re: Help with Registration of Abdominal images

ebaldelo June 13, 2022 06:27PM

Re: Help with Registration of Abdominal images

Daniel Glen June 13, 2022 08:00PM

Re: Help with Registration of Abdominal images

Daniel Glen June 14, 2022 09:38PM

Re: Help with Registration of Abdominal images

ebaldelo June 15, 2022 09:38AM

Re: Help with Registration of Abdominal images

Daniel Glen June 15, 2022 12:46PM



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