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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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Thank you both for your extensive replies; I will be studying what you wrote!
Ilaria
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Ilaria
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AFNI Message Board
Dear AFNI experts,
I have been convinced to use fMRIprep for the initial steps of the preprocessing.
First question: motion parameter file
fMRIprep returns a very large file with all the regressors that one might want to remove (e.g., the motion parameters, among others). However, I'm unsure how to correctly create the motion regressor file to possibly continue using AFNIproc.py.
1-
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Ilaria
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AFNI Message Board
Hi
thank you for clarifying my doubts about volume dimensions. Do I understand correctly that what you are referring to is a full brain mask. I want an anatomical localizer of only a specific sub region of the brain, in this case the bilateral parietal lobes. My understanding is that only the atlas has the information regarding the regions, or did I miss something else? Therefore the only solut
by
Ilaria
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AFNI Message Board
Oh, I have used 3dresample to change it's dimension and now the mask is in the same dimensions as my data.
I was able to run the 3dttest++... But is this correct?
by
Ilaria
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AFNI Message Board
Hello,
we obviously already miss the AFNI bootcamp!
What am I trying to do: run 3dttest++ with an anatomical mask on bilateral parietal lobes.
What error I get:
++ 3dttest++: AFNI version=AFNI_19.0.17 (Feb 22 2019) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as LONG form (label label dset label dset ...)
++ have 20 volumes corresponding to option '-setA'
by
Ilaria
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AFNI Message Board
Hello,
sorry for not replying earlier but the computer was still running analyses.
What I think you want from the output is this. If you want more, please let me know.
I suppose I need to install something like Netbpm?
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program mpeg_encode for Save to MPEG-1
++ Can't find program cjpeg for Save to JPEG
++ Can't
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Ilaria
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AFNI Message Board
Here it is!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 4
apparent login shell: bash
shell
by
Ilaria
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AFNI Message Board
Hello,
yes I do have the @ss_review_html in the folder. This is a different computer and I am using a more recent version of AFNI compared to my practice proc.py with Daniel. Attaching a picture of the current output if it can help. It is still very useful except for the alignment of anat and EPI.
Thanks!
Edited to add that this proc.py is within a batch file and the training was an indivi
by
Ilaria
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AFNI Message Board
Thank you, I will try the -giant_move.
Also regarding the QC output, when I checked the output of the processing that you helped me with, I could see the movement graphs as well as the brain alignment. With my current preprocessing, I only get numerical output (TR removed, # TRs...). I don't understand what I have changed for it to not show the same output. It is much less informative now.
by
Ilaria
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AFNI Message Board
Hello,
I am checking the alignment between the final anatomical and the full mask for each participant to ensure that coverage is appropriate. I have a couple of instances where the coverage is really off and others where some voxels appear around the actual brain.
What may I do to improve the coregistration? Finally, how much off is acceptable? For example, would sub-020 in the picture be c
by
Ilaria
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AFNI Message Board
Thank you so much for taking the time to clarify these basic coding questions. It is running and has done 4 participants... finger crossed!
Ilaria
by
Ilaria
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AFNI Message Board
Hello,
I feel I am abusing of this message board but I tried to create my batch file to loop through all my participants without success.
My script does create the new output directories and creates in the subject output directory the run.afni_proc.py for the first participant and then stops.
I am copying here the first part and the last part omitting part of the preprocessing to make the
by
Ilaria
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AFNI Message Board
Hello,
I was wondering if there is a quick way to run the first level/single subject general linear tests without having to preprocess anew the subject. Let say that I realize after preprocessing that I forgot a specific contrast, is it possible to make the adjustment without repreprocessing everything. I have a pretty slow computer and would like to be a bit more efficient. If there is a page
by
Ilaria
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AFNI Message Board
Dear Rick,
my .afnirc already contains the AFNI_NIFTI_VIEW = orig
I have added: setenv AFNI_NIFTI_VIEW orig to the proc. file at the very top... but the same error was returned.
Should I use 3dcopy to convert my nii file into BRIK & HEAD and make sure they are +orig?
thank you
Ilaria
UPDATE:
I have also converted my anat and func files with 3dcopy for the subject and the same
by
Ilaria
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AFNI Message Board
Hello,
new user here and struggling with what probably is a basic error.
Running the preprocessing I get this error and have searched online and on the message board to figure out what it could be to no avail.
The error is:
#Script is running (command trimmed):
3dNotes -h "auto_warp.py -base HaskinsPeds_NL_template1.0+tlrc -input \
sub-006_ses-T1_T1w_ns+orig -skull_strip_inp
by
Ilaria
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AFNI Message Board