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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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Dear AFNI expert,
I try to use make_random_timing.py to generate timing files for our experiment. In this experiment, we use a fast-scanning protocol with a short TR (199ms). We also want to synchronize the presentation of stimulus with TR, with jittered ITIs following some kind of distribution (e.g., decay, or uniform). There are three conditions (each with a stimulus duration), thus there ar
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qiuhai
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AFNI Message Board
Hi rick,
Since you mentioned multi-band scanning, I assume you refer to the MGH Simultaneous Multi-Slice sequence. In our case, each volume has 69 slices, with a SMS factor of 3 (e.g., 3 bands). TR=1500ms. I use Dicominfo in Matlab to read the slice timing information (see below) from the DICOM file, and assign such timing information to slices using to3d with a customized txt file given to tp
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qiuhai
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AFNI Message Board
Oh Peter, I just find your name on the poster of the Haskins pediatric template and atlas. Is there any paper that we can cite if we use these template and atlas? Actually, the anatomical data that I do the nonlinear warping comes from a child, so we also consider using a pediatric template. Thanks!
Qiuhai
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qiuhai
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AFNI Message Board
What I can update here is that, if I inverse-apply the anat.un_shft.1D (given by auto_warp.py) to the output (i.e., inverse-warped atlas), it gave a somewhat good match between the inverse-warped atlas and the individual's anatomical image in the native space. However, a few top slices of the inverse-warped atlas were missing (see the sagittal view of my previous post), probably due to the p
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qiuhai
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AFNI Message Board
Hi Peter,
I carefully checked the results, but the mask file is still far away from the anatomical image. Please see pictures attached for details. Underlay shows the anatomical image in native space, and Overlay shows the atlas file given by the script that I posted in my last message. The shape looks okay, but I am not sure why it is superior to the anatomical image. All terminal output of
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qiuhai
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AFNI Message Board
Hi Peter,
Thank you for your response. Actually, your answer reminded me a warning information about deoblique at the beginning when I ran auto_warp.py. Then I took anther version of T1 image (skull stripped) from Freesurfer and the result of inverse warping looks reasonable now, although it is still a little off, but I think that might be due to the alignment between T1 and template.
I wo
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qiuhai
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AFNI Message Board
Hi-
This question was originally asked on an existing thread, and is really a specific question of its own. As such, it has been split into its own new topic.
Because it contained two separate "starting" points, I have also merged those here.
Hope that isn't confusing, but this should be clearer to follow as a single thread now, I think.
Thanks,
pt
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qiuhai
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AFNI Message Board
Hi Daniel,
Thank you for your help! I would give it a try.
Best,
Qiuhai
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qiuhai
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AFNI Message Board
Hi Rick,
I have a relevant question here. Actually, what I want to do is to nonlinearly-warp back the data from the standard space to individual native space. For example, I would like to obtain a set of masks (i.e., atlas) in each individual's native space. Those masks have been registered to a template in standard space. I used auto_warp.py to warp a subject's structural image to
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qiuhai
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AFNI Message Board
Dear AFNI experts,
I notice that the most recent Freesurfer version also provides DKT parcellation results (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation). Is there any way that @SUMA_Make_Spec_FS can extract and create this parcellation volume as well (something like aparc.a2009s_aseg_rank.nii but for DKT atlas labelling)? Or any other AFNI scripts can do this? Thanks!
Bes
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qiuhai
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AFNI Message Board
Hey,
It looks like 3dECM still does not work. However, is there any way to just get the correlation matrix (for all pairs of voxels) in a given masked region, without the following eigenvector calculation? Or is there any other command in AFNI could do this? Thanks!
Qiuhai
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qiuhai
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AFNI Message Board
Hi rick,
I do still have a question regarding the censor file in regression. I notice that, by default, it censored the high motion volume (based on enorm) and one volume before. Is there any reference for doing this? I mean like why high motion volume plus one BEFORE, but not both BEFORE and AFTER? I know 1d_tool.py can add AFTER as well, but just want to check in if there is a reference that
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qiuhai
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AFNI Message Board
Thanks rick! Now I can see that using -derivative and -demean together means de-meaning of derivatives.
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qiuhai
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AFNI Message Board
Hi Rick,
I have a question regarding the values in motion_deriv.1D file (generated by afni_proc.py, or actually by 1d_tool.py with -derivative option). When I look at the enorm values (from motion_sub01_enorm.1D), it makes sense to me that the first value of each run is 0, since the derivatives of each run are specified to 0. However, in motion_deriv.1D, there are small numbers for the first v
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qiuhai
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AFNI Message Board
Hi Rick,
Yes. This problem came out when I upgraded OSX system to 10.11 (El Capitan). I noticed Peter's comments both here and from your Email when we discussed this issue. I haven't tried Peter's method, as I can use other MACs on old OSX system in my lab. But I'm still waiting a way to this issue from either AFNI group or Apple. So I appreciate if you have a method to tho
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qiuhai
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AFNI Message Board
Hi rick,
Thank you for your prompt response. But the question is: even if I set up for both shells well, when I run afni commands directly in terminal which contain 3dSkullStrip (e.g. @auto_tlrc, or align_epi_anat.py), it will gives this error "dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib".
Qiuhai
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qiuhai
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AFNI Message Board
Hi all,
I just met a problem when I run 3dSkullStrip on my mac. This problem might be not specific to 3dSkullStrip, but I was just trying to figure out the reason. For your reference: I recently updated OSX to EI Capitan (10.11).
1. When I ran @auto_tlrc and other preprocessing steps (e.g., 3dDespike) in a "bash" script (heading with #! /bin/bash), it has error as follow:
Skull
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qiuhai
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AFNI Message Board
Dear all,
I just want to know which AFNI script (and relevant option) I can use to transform a dataset in TLRC space back to the orig space? (e.g. I have a 0/1 mask file in TLRC space which has the same low resolution as EPI data, and I want to transform it back to the original space for one subject. The subject's high resolution anat+orig and anat+tlrc are available, as well as the low r
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qiuhai
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AFNI Message Board
Hi all,
Could anyone help to post me a sample of .sumarc file. The link on help-file page seems broken. Thank you!
Qiuhai
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qiuhai
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AFNI Message Board
I guess the author refer to the individual estimation for each trial here. Thus it results a beta-series for one condition in a run (vs. what we usually called time-series). Someone used this "beta-series" to do the correlation or connectivity analysis with ER design. I think "-stim_times_IM" option in 3dDeconvolve could do this.
But -Gang, Does it make sense, in statistic
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qiuhai
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AFNI Message Board
Hi rick,
Thank for your suggestion.
If we try in this way, there are both trial-level random (within individual blocks) and block-level random (across whole runs). And I think this would take much time to do the iteration evaluation procedure. In fact, what I want to make is similar to ordinary ER-design, with only one restriction that the same number of trials for one factor are grouped tog
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qiuhai
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AFNI Message Board
Hello,
I'm wondering if there is a good way to make an optimal timing files with a mixed design (e.g. using make_random_timing.py). For example, I have two types of stimuli, say A and B, and each type has three conditions (A1, A2, A3, and B1, B2, B3). In a run, A and B are separated with different blocks, while within the block, the three conditions are played randomly (with jitterred int
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qiuhai
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AFNI Message Board
Hi Rick,
That's really helpful. I'll try it out. Thank you so much!
Qiuhai
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qiuhai
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AFNI Message Board
Deal all,
I meet a problem when using make_random_timing.py to make up the stimuli timing files. In my delay recognition task, there is a long trial, including 2s sample stage, then (6s, 8s, or 10s) delay stage, and finally 3s probe stage. Within a trial (sample-interval-probe), the sample and probe duration is fixed, but interval has three types of duration (equally divided in each condition)
by
qiuhai
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AFNI Message Board