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 2
Pages: 12
Results 1 - 30 of 32
Hi all,
I'm using the Princeton MVPA toolbox in MATLAB, with AFNI.
I did a searchlight analysis and got four of the accuracy maps for each fold (see the 'MAE_L_srch_x' in the pattern in the attached image).
Then, I got an averaged accuracy map by averaging those four maps (i.e., 'MAE_L_srch_avg'), which is a format of .
My question is how to write an AFNI-readable
by
Mpark
-
AFNI Message Board
Thanks for your reply Gang!
My experiment is visual motion adaptation paradigm, so there are adaptation phase and test phase in a trial.
Specific design is that, in a trial, there are 36-sec adaptation phase, 12-sec blank phase, 4~6-sec test phase, and 2-sec blank phase, which of four phases are 8 times repeated in a run.
Here's my 3dDeconvolve script:
3dDeconvolve \
-input ${inp
by
Mpark
-
AFNI Message Board
Thanks for the great suggestions, Peter and Daniel!
I'm doing one by one you've suggested.
As for the suggestion by Peter, I've noticed I have subject's Freesurfer atlas after making retinotopic map. So I successfully did the whole procedure and created the conjunction of freesurfer atlas and my four chunks mask.
But I noticed that the T1.nii in SUMA generated after doin
by
Mpark
-
AFNI Message Board
Hi all,
I have a functional localizer data to define middle temporal area. I did 3dDeconvolve and set threshold at a p=.001 on AFNI GUI. Then I did 'clusterize' on GUI with default NN level and number of voxels.
As shown in an attached image, I can see the four big clusters, and two of them are the bilateral MT areas which I'm looking for, but results from 'clusterize
by
Mpark
-
AFNI Message Board
Hi experts,
Always thanks for your help!
I'm wondering if I can use the output of '-fitts' from 3dDeconvolve as the input data for MVPA.
And wondering if there are any concerns if using fitts output data for MVPA.
Thanks!
by
Mpark
-
AFNI Message Board
You're my lifesaver!!!
I clearly got what was the issue and solved the problem.
Thank you so much!
by
Mpark
-
AFNI Message Board
Hi,
To create training/testing dataset for MVPA, I'm doing 3dDeconvolve to extract beta values for each condition for each run.
My '-input' in 3dDeconvolve is a preprocessed file that concatenated 16 runs.
I have onset timing txt files for each condition that consists of 16 rows (i.e. for each run) and N columns (i.e. for each trial).
I put '-concat' to let 3dDe
by
Mpark
-
AFNI Message Board
Hi
I'm trying to see results of retinoproc called @ShowResult, but when I click the menu 'object controller' it's suddenly terminated.
Below is the output. What should I do?
tcsh @ShowResult
[1] 32209
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #1/9(Local Domain Parent), loading ...
1
SUMA_niml_call: Contacting on tcp:127.0.0.1:53219 (6), maximum wait 300.000 sec
(You
by
Mpark
-
AFNI Message Board
Hi,
I emailed freesurfer team with the issue and I fixed the problem of @SUMA_Make_Spec_FS.
I updated freesurfer as recommended in this link:
Hope this help to anyone who is in trouble with the same issue!
by
Mpark
-
AFNI Message Board
Hi Rick
Thanks for your kind response!
I set the PATH thing also in bash shell as you recommanded! Many thanks!
Probably I should ask this issue from @SUMA_Make_Spec_FS to Freesurfer, but if there are any suggestions you can give I'd also happy about that!
The output of 'mri_convert --help' is
############
bash-3.2$ mris_convert --help
Usage: mris_convert <input file
by
Mpark
-
AFNI Message Board
Oops, I changed bash to tcsh, then afni gui popped up!
But I have another question. When I was using @SUMA_Make_Spec_FS, it seemed something is processed but suddenly it aborted. This error is still not fixed after updating afni and xquartz.
@SUMA_Make_Spec_FS returns like below:
###############
writing to /Volumes/M.Park/fMRI_MAE_MVPA/Latest_MAE_fMRI/060717KHW/T1_MPRAGE_SAG_1_0ISO_0006/
by
Mpark
-
AFNI Message Board
Hi experts,
I've used afni on MAC (high sierra 10.13.6) without any problem except for a function "@SUMA_Make_Spec_FS".
So I searched a similar case that I've gone through and I updated afni with this command:
@update.afni.binaries -defaults -package macos_10.12_local
But it required the latest XQuartz, so I updated XQuartz as 2.7.11. Updating afni was done
by
Mpark
-
AFNI Message Board
Hi,
I'm doing MVPA using 3dsvm, and I'm having trouble making a training model.
Using functional localizer, I've made an MT mask where there are 75 voxels.
With this and beta dataset to be trained, I tried making a model. Below is the command lines:
3dsvm -trainvol trainBlock.nii \
-trainlabels trainLabel.1D \
-model trainSet.model.nii \
-mask ${baseDir}/roiMT.top75.nii
by
Mpark
-
AFNI Message Board
Hi all,
I'm running 'retinoproc' for mapping a retinotopy.
I've used this pipeline with my laptop, but the problem happened on the linux desktop (ubuntu 14.04LTS).
There was no error after finishing the retinoproc script, but there was no output of '@ShowResults' in the output folder (and in computer).
I appreciated if somebody who experienced this problem befo
by
Mpark
-
AFNI Message Board
Thank you so much! I've looked at some of your recommendation but I'll look into them more. Thank you.
by
Mpark
-
AFNI Message Board
Hi all,
I'm a new with afni and making MT Roi for mvpa. I got contrast map with functional localizer and afni's 3dclust (in GUI) clusterized MT and V1 together in each hemisphere.
1. I want to use just MT not V1 but I think it requires another way to separation over adjusting threshold. How can I do this? Appreciate if you instruct also how I can merge two MT in each hemisphere i
by
Mpark
-
AFNI Message Board
Thank you for your help.
I'll look at the paper first. Thank you
by
Mpark
-
AFNI Message Board
Hi,
This is a very naive question, I'm using afni for fMRI anlaysis and planning to use support vector machine for mvpa.
I downloaded LIBSVM in matlab.
How can I do mvpa with afni and matlab version of LIBSVM?
Also, if I download matlab library for afni, can I write a script for fMRI analysis as like shell script?
Thank you!
by
Mpark
-
AFNI Message Board
Oh my goodness. The sphere was behind the cortex.
Thank you so much!
by
Mpark
-
AFNI Message Board
Yes, I did. The command line was "3dUndump -srad 8 -master sbj1_MT_B5+tlrc. -orient RAI -prefix mask_rMT -xyz peakXYZ.txt".
In the peakXYZ.txt file, "49.5 70.5 8.5" were written.
Thank you
by
Mpark
-
AFNI Message Board
Hi, I'm trying to make ROI mask of MT area with functional localizer.
I've done preprocessing and 3dDeconvolve, and am looking at the result in afni.
I loaded the bucket file generated in 3dDeconvolve and put #0 Full-Fstat in both Olay and thr.
With this, I clusterized and made a table with xyz peak coordinate, and wanted to make sphere roi because one part of the cluster will be us
by
Mpark
-
AFNI Message Board
Thank you for your reply.
But when I use card2oblique (is this command to make dataset oblique?) to match T1 to oblique epi, @RetinoProc did not finished completely. So I thought that input datasets of @RetinoProc have to be not oblique. Is this right?
by
Mpark
-
AFNI Message Board
Hi experts!
I'm doing retinotopic mapping by using @RetinoProc with oblique epi images (axial to calcarine sulcus).
To match the oblique epi and sagittal image of T1, the oblique epi images were transformed deobliquely by using '3dWarp -deoblique' before running @RetinoProc, while T1 had no transformation.
But when running @RetinoProc, warning message that is
"If you
by
Mpark
-
AFNI Message Board
Here are the outputs:
# afni -ver
Precompiled binary macosx_10.7_local: Aug 9 2017 (Version AFNI_17.2.07)
# afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.3.0
version: Darwin Kernel Version 15.3.0: Thu Dec 10 18:40:58 PST 2015; root
by
Mpark
-
AFNI Message Board
Hi ptaylor
I think the version of afni might be the cause!
The output of 'afni -ver' is "Precompiled binary macosx_10.7_Intel_64: Aug 4 2017 (Version AFNI_17.2.06)", but my mac osx is 10.11.3 (El Capitan).
I'm not sure what is the 'local' mac version, but if that means 10.11+ mac osx, do I just download new afni following the step 2?
In command lines of
by
Mpark
-
AFNI Message Board
Dear Daniel,
I did mris_convert itself, as your advised, like 'mris_convert ./surf/lh.smoothwm lh.smoothwm.asc' (which was error line when running the script), then the lh.smoothwm.asc file was made.
Would you please check my script whether there is something to make this error?
Thank you!
SCRIPT:
--------------------------------------------------------------------------
by
Mpark
-
AFNI Message Board
Hi,
Yes, I saw the link and I updated the fs by 'sudo -E fs_update', but still the same error happened.
Thanks for your another tip that '-NIFTI' should be included, I added that option.
Then a little changed error messages poped up.
If there is anything that I missed, please let me know.
Thank you.
Error messages after includeing '-NIFTI'
---------------
by
Mpark
-
AFNI Message Board
Hi all,
I'm trying to run @SUMA_Make_Spec_FS after processing with Freesurfer.
But when I ran the command, error message poped up like 'failure: could not create surface lh.smoothwm.asc'.
I already made csrutil enabled but the problem happened.
Also, in the reply for latest post relevant to my issue, Daniel recommended fs_update (sudo -E fs_update) and then sourcing the frees
by
Mpark
-
AFNI Message Board
Page 1 of 2
Pages: 12