Show all posts by user
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
Page 1 of 1 Pages: 1
Results 1 - 11 of 11
That time worked! I uploaded it as a .tgz file since that's how I've done other submissions, but let me know if you'd rather have me upload all the individual files instead
by
kyrieamara
-
AFNI Message Board
Ok so I have a bit of an update, although I'm not sure if it means much. I have changed my sublist text file to be a string so it looks like this:
001 002 003 ...
I've also added a few more printf commands (thanks for that tip) to get an idea of what it's doing. It looks like it now can read the sublist_string.txt correctly, but now I get new errors on the foreach line for th
by
kyrieamara
-
AFNI Message Board
Ha! You are correct I do not have a directory named "abunchofdirectories" I changed it for simplicity's sake. I have checked for those possible errors in the syntax but I don't have any, so I don't think that's the issue. I am including the unedited script and additional files in the submission for ptaylor (once I have access I will upload it). Thank you both for you
by
kyrieamara
-
AFNI Message Board
Hi again,
I can't seem to access the Box folder with either of my Microsoft accounts. I get this error:
Sorry, but we’re having trouble signing you in.
AADSTS50020: User account 'sellnowk@uwm.edu' from identity provider '; does not exist in tenant 'National Institutes of Health' and cannot access the application 'box.net'(NIH BOX) in that tenant. T
by
kyrieamara
-
AFNI Message Board
Thanks for the quick response! Unfortunately, neither of the suggestions you sent worked. There are zero bad characters in my script, and when I put the subject numbers in the set command as a string, it gives the error: set - variable name must begin with a letter. I can send my script and sublist text file, do you need the .nii files I'm trying to call too?
by
kyrieamara
-
AFNI Message Board
Hi everyone,
I'm hoping you can help me with what I thought would be a simple tcsh script to loop through my subjects and run 3dmasksave and 3dROIstats on each. Here's my script:
#!/bin/tcsh
module load pkgsrc/2018Q3
module load pkgsrc/gcc-base
module load /directoryofafniprogram/07.17.2019
set datapath = /abunchofdirectories/
set output = /abunchofdirectories/outputdir
by
kyrieamara
-
AFNI Message Board
Sorry for all the back and forth, let me know if there's anything I can send to make things clearer.
Age does not vary within subjects, so I tried "~1" but it failed. I also tried the "~PCLTotal" which also failed, although PCLTotal is the primary outcome measure I am interested in. Essentially, I have two sessions, one at 2 weeks and one at 6 months, and I want to asse
by
kyrieamara
-
AFNI Message Board
Ah, sorry I copied this from my excel spreadsheet. In the text file I had changed it to InputFile already, but it still fails the model.
by
kyrieamara
-
AFNI Message Board
it does, PCLTotal should be a different value for each time point. Here is a clip of my data table.
Note: I had changed the variable names in the original post for simplicity's sake, so that is not the issue. Also there are 121 subjects, but this is just a portion:
Subj Time Gender Racial_Category age2wk PCLTotal_Both Input.File \
2 1 1 4 24.8 35 REST/results/firstlevel/allsubs_ICC/BETA
by
kyrieamara
-
AFNI Message Board
You're right, PCLTotal should also be included in the qVars line. Time and Gender are both dichotomous variables, so they would not go in the qVars, correct? Here is my model now:
3dLME -prefix final_PCLTotal_LME -jobs 24 \
-model "Time*PCLTotal+age+Gender" \
-qVars "PCLTotal,age" \
-ranEff "~1+age" \
-SS_type 3 \
-dataTable @CONN_LME_DataTable.txt
by
kyrieamara
-
AFNI Message Board
Hi there,
I'm currently trying to run a simple 3dLME with the following:
3dLME -prefix final_PCLTotal_LME -jobs 24 \
-model "Time*PCLTotal+age+Gender" \
-qVars "age" \
-ranEff "~1+age" \
-SS_type 3 \
-dataTable @CONN_LME_DataTable.txt
The script successfully reads the input files, but then gets stuck on the model test before killing it after a
by
kyrieamara
-
AFNI Message Board