AFNI version info (
Precompiled binary linux_ubuntu_16_64: Nov 7 2023 (Version AFNI_23.3.07 'Septimius Severus')
I like to save clusters as a mask following Rpt GUI.
I can save all SaveMsk (it combine all to a single mask), but I need each one separately.
This is the error I get for *Plot* and *Save*( (*Jump* and *Flash* works fine.):
**can't get data!!!**
**Need Aux Dataset!**
My data is save on storwis (remote disk mounted as a CIFS(Samba) file system) I run and save results_dir on my local computer.
The overlay is the output from (many subjects, I added here only one for an example)
> #!/bin/tcsh -xef
> # ---------------------- set process variables ----------------------
> set mask_dset = /storwis/mask.epi_anat.union.nii.gz
> set dirA = /storwis/
> # specify and possibly create results directory
> set results_dir = test.results
> if ( ! -d $results_dir ) mkdir $results_dir
> # ------------------------- process the data -------------------------
> 3dMEMA -prefix $results_dir/ER \
> -mask $mask_dset \
> -missing_data 0 \
> -set cong.N45 \
> sub01 \
> "$dirA/sub01.stats.REML+tlrc[XXX#0_Coef]" \
> "$dirA/sub01.stats.REML+tlrc[XXX#0_Tstat]" \
If I understand the question, in the Clusterize plugin, "SaveMsk" saves all the clusters in order of size, with the largest cluster getting the number "1" value in the mask, the next largest "2", and so on. To save any individual mask as a separate dataset, you could specify the value of the mask in a range selector like this - Clust+tlrc'<1>' for the largest cluster for example or pick the "Write" button next to the cluster you do want. That writes out just that one cluster as in this screen capture. The terminal shows the record that it has been written out to disk.
Thank you, Write indeed work
I just wonder why for Plot I get this error
can't get data!!!
Need Aux Dataset!
Clusterizing defines ROIs: maps of regions in a 3D volume (DSET_A).
"Plotting" is for showing the average value of a separate dataset (DSET_B) within each ROI (which were created from DSET_A), and typically that separate dataset is a 4D one, so that plotting shows a time series of average values (of DSET_B) across time. There is nothing to plot without a separate/auxiliary dataset provided.
Thank you, how can I provide the 4D (time series): all_runs.* afni_proc output.
When you have the Clusterizing menu open, click the white arrow at the start of the row of buttons with "3dclust", "SaveTabl", and "SaveMsk", like shown in this AFNI Academy video:
AFNI GUI: Clusterizing
A new menu segment opens, and you can click "Aux" in the first line to load in a dataset (and, as shown there, you could open multiple aux dsets at once, if you like).