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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
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Hello,
I am still having the same problem as I indicated above. Any support with how to get afni to display the cluster corrected values to appear in afni in the cluster report would be appreciated.
Thank you
by
Stephanie
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AFNI Message Board
Hi,
Thank you for your response. I am still a new afni user, so I appreciate your support.
I have been able to run 3dClustSim with the following command:
3dClustSim -mask Collapsed_Sync_Async_TD_forclustTry1+tlrc -nxyz 61 73 61 -dxyz 3 3 3 -both -NN 3 -athr 0.05 0.01 -prefix Collapsed_Sync_Async_TD_forclustTry1_Clust
After it ran I got a message that said to append the data to:
3dr
by
Stephanie
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AFNI Message Board
Hello,
I have been able to use 3dClustSim to produce a 1d file. However, I am having trouble with getting it to work with the afni gui. Can you please provide assistance with how to get 3dClustSim to work interactively with the afni gui?
Thank you,
Stephanie
by
Stephanie
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AFNI Message Board
Hello,
I am trying to understand exactly how the lim command makes ROIs when using ROIgrow. The help function lists it as:
"Distance to cover from each node. The units of LIM are those of the surface's node coordinates. Distances are calculated along the surface's mesh."
If I wanted to make the ROI have a 6mm radius, would using of lim of 6 be similar? Is there some f
by
Stephanie
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AFNI Message Board
Hello Rick,
It worked with using column 1!
Although it worked, here is the output with3dinfo ROImask_lh_sup_post_Sync-Async.niml.dset
3dinfo: AFNI version=AFNI_2011_12_21_1014 (Mar 21 2014) [64-bit]
Dataset File: ROImask_lh_sup_post_Sync-Async.niml.dset
Identifier Code: XYZ_lq_WhVFYKskEZJxfbIwnEQ Creation Date: Thu Aug 6 10:15:46 2015
Template Space:
Dataset Type: Anat
by
Stephanie
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AFNI Message Board
Hello Nick,
I tried using 3dROIstats with the following command and go this error:
3dROIstats -nzmean -mask ROImask_lh_sup_post_Sync-Async.niml.dset 'stats.surf_individual_conditions.lh.niml.dset[8]' > ROIstats_IndividualValues01_lh.txt
Error 3dROIstats: Somehow I boned computing how many ROIs existed
Stephanie
by
Stephanie
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AFNI Message Board
Hello Nick,
That you for all of your assistance. I was able to make the ROI in the correct location by changing the spec and surface file. Now that I have a mask, I should be able to use 3dmaskave with this mask correct?
Thank you again,
Stephanie
by
Stephanie
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AFNI Message Board
Hi Nick,
Yes now it opened. However, I am assuming that I made the ROI with the wrong file now. I identified the ROIs with opening suma with this command:
suma -spec 118_both.spec -sv 118_SurfVol+orig
However, I made the ROI with
ROIgrow -overwrite -spec std.141.118_lh.spec -surf_A std.141.lh.smoothwm.asc -roi_nodes nodevalue_all_ROIs_lh.1D -lim 6 -full_list -roi_labels nodelabel_all_RO
by
Stephanie
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AFNI Message Board
Hello,
Thank you for your response.
The top of the text file has this information:
#Col. 0 Node index
#Col. 1 ROI val.
The file has two columns, one with the nodes and the other has what I assume should be 0s and 1s(however around the nodes that should make up the ROI it is actually 3s). There is a total of 198811 nodes in the file.
Is this helpful?
by
Stephanie
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AFNI Message Board
Hello,
I wanted to send quick follow up to see if anyone has any suggestions?
Thank you,
Stephanie
by
Stephanie
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AFNI Message Board
Hello,
I am relatively new to using suma and working in surface space, so please let me know if I am not including all necessary information. I am trying to create ROIs in surface space, which I can then use to extract values from those ROIs of interest in contrasts of interest.
I used the following command to create 1D files for all the ROIs I identified in the left hemisphere:
ROIgrow -
by
Stephanie
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AFNI Message Board
I figured out an alternate solution. Not sure how to delete the post.
by
Stephanie
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AFNI Message Board
Hello,
I am working with surface space data and trying to do some single subject level analyses. After I ran 3dDeconvolve and looked at my contrasts of interest, I wanted to run some analyses with any negative activation removed. I ran 3dmerge -1noneg on the conditions of interest and now want to run some contrasts at the single subject level. Neither 3dANOVA nor 3dttest++ will work on the si
by
Stephanie
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AFNI Message Board