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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
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Dear all,
We are looking for a highly motivated postdoctoral associate in the Neuromodulation for Addiction Laboratory at the Menninger Clinic and Baylor College of Medicine (BCM). The Menninger Clinic, BCM affiliated private inpatient psychiatry clinic, is a world leader in psychiatric treatment, research, and education. The lab focuses on identifying a biomarker for psychiatric disorders, pa
by
Hyuntaek
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AFNI Message Board
The Research Department at The Menninger Clinic and the Menninger Department of Psychiatry and Behavioral Sciences at Baylor College of Medicine seek a full-time Computational Psychiatry Postdoctoral Fellow to join our team. In a nationwide survey, psychiatrists selected The Menninger Clinic as a top psychiatric hospital, ranking it #8 on U.S. News & World Report's annual Best Hospitals
by
Hyuntaek
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AFNI Message Board
The Research Department at The Menninger Clinic and the Department of Psychiatry and Behavioral Sciences at Baylor College of Medicine seek a full-time Research Assistant to join our team. In a nationwide survey, psychiatrists selected The Menninger Clinic as a top psychiatric hospital, ranking it #8 on U.S. News & World Report's annual Best Hospitals list, and The Menninger Clinic has b
by
Hyuntaek
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AFNI Message Board
Great! Thank you for your followup Taylor!
So...if i put the number of time points (nfft), DFT will be performed without zero-padding. I will try to test it!
Thank you so much,
Taek
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Hyuntaek
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AFNI Message Board
Sorry for the confusion!
I don't know what is meant by frequency "8". At what Hertz is your frequency?
>> The stimulus in the experiment has a periodicity at every 42 secs (~.023Hz). Like I said earlier, the data includes 112 time points - (4: stimuli + 10: resting) * 8 times and TR = 3s.
So, firstly, you are processing on a surface?
>> Yes Correct.
And y
by
Hyuntaek
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AFNI Message Board
Hey Taylor,
Thank you for your answer.
Could you explain more specifically about "powers of 2 combined with powers of 3 and 5 (no more than 3^3 and 5^5, though)"..? Does this mean that 3dDFT adds 8 zero-paddings consisting of 3 and 5? Does zero-padding affect the magnitudes and phases of the DFT?
After performing DFT, I calculated the phases and amplitudes at specific frequenci
by
Hyuntaek
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AFNI Message Board
Hello,
I'm trying to run 3dDFT on a surface and wondering why 3dDFT is changing DFT length. The data includes 112 time points - (4: stimuli + 10: resting) * 8 cycles.
Here is my script file and output:
3dDFT -prefix sample.DFT pb06.TMSfMRI.subj1_lh.lh.r01.detrend.niml.dset
++ Authored by: Kevin Murphy & Zhark the Transformer
++ Data length = 112 ; FFT length = 120
++ Output co
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Hyuntaek
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AFNI Message Board
It works! Thank you Peter and Rick!
I have one more question. well...this is something that i would like to get confirmation from you whether or not i am doing right thing.
I have a TLRC coordinate to create a ROI as a 1D file. (e.g. Intersection_tlrc.1D). The file contains x y z coordinates 40.931076 2.956589 55.040066 (placed on left hemisphere).
1. Find the closest node to ROI's
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Hyuntaek
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AFNI Message Board
Hello AFNI team,
I would like to do resting state analysis on surface. I've created afni_proc.py script file for each hemisphere and I've got an error saying...** FATAL ERROR: Mask creation fails for unknown reasons!
My afni_proc.py command is below.
afni_proc.py -subj_id ${subj}_${hemisphere} \
-script proc.${subject}_${hemisphere} -scr_overwrite
by
Hyuntaek
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AFNI Message Board
Hello AFNI team,
I have a question to create full flat maps from subject surface. I've created the subject surface using FreeSurfer (recon-all -all -subjid xxx) and then created the spec files (@SUMA_Make_Spec_FS -NIFTI -sid xxx). Under the SUMA folder, I've got SmoothWm, Inflated, Pial, Spherical spec files. At this point, I would like to create the full flat maps (e.g. full.flat.pa
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Hyuntaek
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AFNI Message Board
Hello AFNI team,
I have a high resolution mprage and low resolution mprage. I obtained each mprage from same subject but different session. In each mprage, there are 4 fiducial markers outside the subject head (markers are attached in the TMS coil), and I want to do transforms the coordinates of 4 fiducial markers in low resolution mprage to high resolution mprage (if this works, i do not need
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Hyuntaek
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AFNI Message Board
Thank you Peter and Rick!
I will try to use the timing file with '* *' and see how it looks like.
Taek
by
Hyuntaek
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AFNI Message Board
Thanks Taylor!
Here is my afni_proc.py command.
afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat $anat_dir/t1_mprage+orig \
-anat_has_skull no
by
Hyuntaek
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AFNI Message Board
Hello afni team,
I have a question about the best way to analyze my fMRI data.
Now I have 3 runs and each run includes different condition separately (e.g. 1st run: high intensity stimulation/ 2nd run: low intensity stimulation/ 3rd run: finger movement). A simple block design was used for each run ((3TRs: stimulus + 7TRs: rest) * 10).
Before processing the data, I concatenated 3 runs i
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Hyuntaek
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AFNI Message Board
Hello all,
Can anyone help with these issues?
Thanks,
Taek
by
Hyuntaek
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AFNI Message Board
Hello,
I have two questions related to the output from @RetinoProc. I am using the script to create the somatotopy map and two sets of data (ccw/clw) to get the phase information.
1. I am wondering how the @RetinoProc script calculate the power from the time series. I think we can calculate the power by taking abs after applying Fast Fourier Transform. However, when I calculate the power ma
by
Hyuntaek
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AFNI Message Board
Hello afni,
I have a question about the output file from the RetinoProc script file.
I am using the RetinoProc script file to create the somatotopic map and wondering whether or not there is a way to open the output file in the Matlab. In other words, can I open the xxx.sm.lh.pol.field.niml.dset file in the Matlab?
I've tried to use ConvertDset to convert the .niml.dset file to ASCI
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Hyuntaek
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AFNI Message Board
Thank you Taylor,
So...when I am using @RetinoProc script to generate the phase map with our experimental design (48 seconds of stimulus and 12 seconds of rest. 48 seconds stimulus include 6 seconds x 8 locations), can I setup as following in the script..?
...
-period_pol: 60
-on_pol: 8 6
...
In this way, can @RetinoProc (or 3dRetinoPhase) calculate the highest amplitude and phase val
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Hyuntaek
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AFNI Message Board
Hello afni team,
I'd like to use @RetinoProc script to process somatotopic mapping. The idea is very similar to the retinotopic paradigm. Our experiment design includes 8 cycles of consecutive stimulus of 8 body parts from L fact to R face and each stimulus of each body part lasts 6 seconds. The whole stimulus of 8 body parts last 48 seconds (6 seconds * 8 body parts = 48 seconds) followe
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Hyuntaek
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AFNI Message Board
Hello afni team,
I have a quick question related to this. So in this example, ON_POL is 8 and N_BLOCKS is 4, correct?
I am using afniRetinoDemo files and @Proc.All_D.
@RetinoProc \
-sid Hildebrand \
-surf_vol SUMA/Hildebrand_SurfVol+orig.HEAD \
-spec_left SUMA/Hildebrand_lh.spec \
-spec_right SUMA/Hildebrand_rh.spec \
-anat_vol afni/Hildebrand_3_1.nii \
by
Hyuntaek
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AFNI Message Board
Hello Rick,
Thank you for your explanation. One of my concerns is how afni generates the regressors if a stimulus happens within TR.
Our TR is 3.17s and actual stimulus onset is 3085ms (I have attached our stimulus design). The first TR grid point following the first actual stimulus is at t=19.02s (6TR), 85ms after the stimulus. We have 3 blocks of this, so are the basis functions evaluate
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Hyuntaek
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AFNI Message Board
Thank you, Gang! I have one more question related to match the timing resolution.
With a situation where the stimulus onset times are not synchronized with the TR grids, a regressor is generated using a finer grid that roughly matches the timing resolution, and then a new regressor at the TR grids is created through up-sampling.
> When a regressor is generated using a finer grid that ma
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Hyuntaek
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AFNI Message Board
Hello afni team,
I have a question about the stim_times file. We are working on the concurrent TMS/fMRI study and here is our current setup (please see the attached figure).
TR = 3.17s
First stimulus block initiates @ 5TR (= 15.85s) and the first TMS pulse is delivered 3085ms after the first stimulus block. We deliver 3 TMS pulses during 3 blocks (volumes), followed by 7 blocks of rest.
by
Hyuntaek
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AFNI Message Board
Hello AFNI team,
I have a question about the output parameters from SurfToSurf.
I have an anatomical T1 images data from a TMS study and would like to position the TMS with fiducial marker. The marker includes 3 points which are located outside the cortex (S1) and I am trying to project from each point of S1 to the cortex (S2, skull-stripped anatomical). I am using SurfToSurf with 3 points
by
Hyuntaek
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AFNI Message Board