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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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I have a question i would like to add to this thread. When you add these asterisks to denote the absence of all conditions for a given run does that run get ignored entirely or is it incorporated into baseline BOLD signal for comparison against ones modelled conditions?
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Lordbyron001
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AFNI Message Board
Yep, thanks so much. I did happen to see the two asterisks in the relevant help file but just wanted to check and make sure real quick. Thanks again!
Austin
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Lordbyron001
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AFNI Message Board
Hello,
I just have a very quick question regarding stimulus timing files. If for instance an experiment has 4 separate runs but on one of those runs (lets say run 2 for this example) there was no presence of a given condition (such as an error trial), should the stimulus file just be left blank for that second row? I know this is a very noobie question but thanks very much for help.
Austin
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Lordbyron001
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AFNI Message Board
Hello,
Is it possible to conduct an analysis that calculates voxel-by-voxel correlations across ~100 subjects between a continuous variable and the magnitude of the brain activation associated with a task condition within AFNI?
If this type of analysis is possible what program/command would be recommended to implement this? Finally, what would I expect as far as the output AFNI provides is conc
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Lordbyron001
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AFNI Message Board
Well with the data we have collected we are primarily interested in group differences in grey matter based activations. So ultimately we are trying to eliminate unnecessary voxels, such as those from white matter, from our analyses to reduce the number of statistical tests (we have nearly 290,000 total voxels) AFNI performs during group analysis. Some preliminary group analyses that have been ra
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Lordbyron001
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AFNI Message Board
Hello,
Thank you for your quick response to my questions. Your answers make sense. I just have one follow up question for right now. I had read through help section regarding the SSW templates and saw that the 4th volume is a dilated GM mask. Is it possible/what is the easiest way to use only the 4th volume of the MNI template as a mask for volume wise analysis? Or am I again misinterpreting wha
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Lordbyron001
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AFNI Message Board
Hello,
I am looking to get a bit of guidance on how to generate a grey matter mask using SSwarper. I have never used this program before but one of my lab mates has used it for some issues she was having with her data. I am attaching the script used below for reference.
I have been reading as much documentation that I can find but as a novice am confused about a few things. First, when you run
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Lordbyron001
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AFNI Message Board
Yes I did, here is what I used.
afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-blocks align volreg surf blur scale regress \
-copy_anat $anat_dir/E001_anat_nudge+orig \
-dsets
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Lordbyron001
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AFNI Message Board
HI there, pretty simple question this time but just want to make sure. Should I be interpreting intensity values in SUMA as % signal change when scaling is applied to the preprocessing? I know this is the case with beta weight values in afni when scaled and I would figure it is the same with SUMA but just would like to confirm. Thanks very much 8)
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Lordbyron001
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AFNI Message Board
Thanks, I had no idea you could just append .niml.dset onto the end of your prefix name to have MEMA output a niml format file instead of a 1d. Label problem is all fixed up now.
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Lordbyron001
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AFNI Message Board
Awesome, so Im assuming that using ConvertDset to change my 1d files to niml format should do the trick?
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Lordbyron001
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AFNI Message Board
First I just want to say thanks for the help given with my previous SUMA problem. That said im back with another 8). I ran my analysis for all my individual subjects, creating standard 141 mesh surfaces for all of them for group analysis as I was instructed to do. The niml dsets all look good. I zero-padded them prior to group analysis as it seemed like a good idea ( I still have the non zero-pa
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Lordbyron001
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AFNI Message Board
Hi again, sorry to keep bugging about SUMA but I am having alot of trouble figuring out whats wrong with my datasets that are produced by my script. The script produced by afni_proc.py. runs its course with no fails. When i open afni and suma within the results folder I have volreg files in BRIK/HEAD formats. Past that my surf/blur/scale/ and stats files are all niml.dset. These files do not show
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Lordbyron001
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AFNI Message Board
Got the script to run... however when i use Cntl-S to load a .dset file, specfically stats.E001.l/rh.niml.dset i get an error that SUMA cant read the 1d file.
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Lordbyron001
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AFNI Message Board
Well that is wonderful to know, thanks for that info!
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Lordbyron001
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AFNI Message Board
Well I did remove the tlrc section from my script and when i did my results came out very good, much better than initially, but I will give it another go with the info you provided. Thanks very much.
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Lordbyron001
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AFNI Message Board
I am using the -sv option, my process for loading afni and SUMA is roughly this
afni -niml &
suma -spec SubId_lh/rh.spec -sv SubId_SurfVol_Alnd...+orig &
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Lordbyron001
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AFNI Message Board
Hi there, back again with another newbie question that I cant seem to find an answer to within the SUMA pdf. I have recently begun working with SUMA and was curious about the manner in which to map the volumetric data to the surface. To start I used FreeSurfer to create the surface models for my subjects and @SUMAMAKESPECFS worked perfectly to create my appropriate files. From there I also used @
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Lordbyron001
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AFNI Message Board
Hello, just want to preface this post by saying that I am very new to AFNI and fMRI data processing in general so if I omit any relevant information to my question then please let me know and ill do my best to provide the information.
That said, I am having issues with coregistration of my individual subjects that are propagating into group analyis. Specifically I am having voxels that are par
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Lordbyron001
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AFNI Message Board