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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
History of AFNI updates
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Hi Daniel,
I should have been more clear with my questions. I am pasting the steps again and the results with the respective units. Basically, my goal was to extract mean beta weights/percent signal changes from the bilateral, left, and right area 6 to double check if those masks are working well, that is, if the means from left + right equal the mean for the bilateral mask. I am trying to fig
by
maria
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AFNI Message Board
Hi,
I am just posting again to bump up my previous question in the chain.
Thanks,
Maria
by
maria
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AFNI Message Board
Hi,
Here is one specific example, which I ran to double check myself. I wanted to see if the value from left + right equals the value for the bilateral mask. I am trying to understand why there is this discrepancy and how to fix it.
whereami -mask_atlas_region CA_MPM_18_MNIA::Area_6 -prefix mask_B_6_ms
whereami -mask_atlas_region CA_MPM_18_MNIA:left:Area_6 -prefix mask_L_6_ms
whereami -m
by
maria
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AFNI Message Board
Hi,
I have a related question. If I have a bilateral ROI mask and also separate masks for left and right for that same region then the beta weights from left plus right do not equal the value from the bilateral mask. In fact, adding left and right yields noticeably larger numbers. I understand that this probably has to do with the clip level and the choices made where left and right border and
by
maria
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AFNI Message Board
Hi Rick,
Yes, you raise good points and I will take them into account. I failed to mention earlier that I wanted to add @ seed = $seed +1 and 3dDeconvolve to my command. If I run the following shorter command (see first script below), then I see the LC[0] norm. std. dev number going through 100 iterations while the process is running in the terminal. However, I have trouble integrating the it
by
maria
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AFNI Message Board
Hi Rick,
Thanks for your quick response! Here are the outputs:
out.3dD.001
cmd.3dd.001: No such file or directory.
-- have 2 stim and 2 runs, prefix = stim_times.001
-- run_time : 240 240
-- num_reps : 15 15
-- stim_dur : 2 2
-- max_consec : 3 3
-- pre_stim_rest=0, post_stim_rest=0, seed=1234567.0
min_rest=2, max_rest=0, offset=0, t_gran=4, t_digits=1
labels are: first, sec
by
maria
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AFNI Message Board
Hi,
I need some help fixing my script for make_random_timing.py. Based on the help file for make_random_timing.py, the how to #03 example, as well as the the first example in this thread I am trying to come up with a script that includes 100 iterations and outputs the normalized standard deviation for each trial. I have made many efforts but my scripting skills are not good enough to set up th
by
maria
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AFNI Message Board
Hi,
I have another question related to the MNI atlases. Whereami distributes code numbers for each region in the overlap statistics (e.g., for CA_ML_18 MNI). I am trying to find a list that has the key to the code numbers and have been unsuccessful.
Thanks,
Maria
by
maria
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AFNI Message Board
I went through all steps again and now it's working! I think I had the MNI atlases in the wrong folder.
Thanks,
Maria
by
maria
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AFNI Message Board
Hi,
I ran into the same problem described above. When I use the Whereami button in Clusterize, the only atlas that is used to report overlap is MNI_VmPFC and that is of limited help. For uber_subject.py I used MNI_avg15T1. I followed your steps outlined above to add the MNI atlases and set the environment to include the MNI atlases, however, this did not change anything. I am trying to trouble
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maria
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AFNI Message Board
Hello,
I have read the above thread with interest because I am also working through steps to incorporate B0 distortion correction. I am using FSL for the correction and then include the corrected files in AFNI. I wanted to show you my steps to make sure they make sense. I also had a couple questions along the way.
1) Convert Siemens DICOM files to fsl NIFTI using MRIConvert
2) First, pre
by
maria
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AFNI Message Board