AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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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