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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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Hi Paul,
>>>>>I am confused-- what does "as anatomy files" mean? I am afraid I don't understand what this means. And how is this "verified" with 3dinfo?
Sorry that was confusing. This is what 3dinfo says:
Dataset File: ./reward_pos_vs_neg_feedback_subcortical_vox_tstat_uncparap_c1.nii
Identifier Code: NII_FyQ-kpj_FPGUqCi_ZKDy5g Creation Da
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shanaadise
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AFNI Message Board
Hi All,
1. First, I hope you are staying safe and sane.
2. Second, I have a question that is hopefully simple to answer.
CONTEXT: I have vertex and voxel level data that were analyzed with a complicated pipeline and saved as .mgz files. The group analysis was conducted using FSL's PALM. PALM's output provides several files: t maps, p maps, beta weights etc. I wanted to view th
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shanaadise
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AFNI Message Board
Thanks for this information. I went ahead and did that but I am still having difficulty getting the group analysis to recognize the GIFTI files - any thoughts?
1. Run conversion from .mgz to .gii
mris_convert -f taskBOLD_nBack_scan_8_lh.mgz $FREESURFER_HOME/subjects/fsaverage/surf/lh.white S1.l.func.gii
2. Use HCP pipeline to align to a standard mesh and merge hemispherse --> dscalar.n
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shanaadise
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AFNI Message Board
Hi Gang,
Yes, we do have other explanatory variables (e.g., behavioral measurements, BMI, traits etc). It is a large dataset. Solving the issue of nested random effects will be useful for multiple projects.
I would really appreciate your help.
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shanaadise
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AFNI Message Board
We are working with two large datasets (separate research projects) with thousands of subjects (n1= 2000 and n2=6000). N2 has twins and triplets (MZ and DZ) while the other only has siblings. Eventually, we will code for MZ and DZ but for now, we just want to control for site and family. There are about 500ish subjects per site and not every family has multiple children enrolled. Every family has
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shanaadise
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AFNI Message Board
> Could you describe a little bit more about these 3 variables and explain why you consider them as random-effects variables? If you treat them as random-effects variables, they should not be included in the model specification because that is for fixed-effects variables:
1. Gotcha. So just to be clear, ranEff "~1" will estimate random intercepts for any variables specified in the
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shanaadise
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AFNI Message Board
Hi Paul,
Thanks for your reply.
1. We don't have a directory called "DDD" with subdirectories such as "label/", "mri/", "scripts/", etc. All we have are surface data files that have already been aligned to a standard mesh and linked to the volume data (separately for left and right hemispheres), which allows us to do group analyses. The end resu
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shanaadise
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AFNI Message Board
Hi,
This is a pretty basic question. I have freesurfer data for the left and right hemisphere in .mgz format. The volumetric data has already been linked etc. I would like to use SUMA to create .niml datasets so that we can use 3dMVM or 3dLME for our group analysis. Running the following errors:
@SUMA_Make_Spec_FS -sid taskBOLD_SST_S10 -use_mgz -NIFTI
failure: cannot find directory &
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shanaadise
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AFNI Message Board
Hi Gang,
This thread has been useful but I have a few additional questions:
We are using 3dLME over 3dMVM because:
1. missing data
2. multiple random effects (e.g., site, family, sibling)
3. w/s repeated continuous measures (e.g., age at time 1 and time 2)
My questions are as follows:
1. How do you specify the random effect for multiple variables? Ignoring age (see question 2), wou
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shanaadise
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AFNI Message Board
Hello all,
Please see the below postdoctoral advertisement sent on behalf of Hugh Garavan.
We are seeking a postdoctoral fellow who will join a consortium of leading addiction researchers to work on an exceptionally large neuroimaging-genetics project. ENIGMA-Addiction (http://www.enigmaaddiction.com) performs secondary analyses on datasets contributed by labs from over the world. T
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shanaadise
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AFNI Message Board
Thanks, Rick.
Yes, you are right step 6 is not necessary.
The overall goal is to do some task-based functional connectivity analysis that correlates brain data to a continuous behavioral variable. . The next steps would be to extract the timeseries using an atlas with whole brain coverage. However, since I had multiple runs for my task, I had to subtract out scanner drift rate and motion.
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shanaadise
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AFNI Message Board
Hi Rick,
Thanks for your reply. It may be my misunderstanding but when I followed your suggestion above after step 3, it did work. However, I was able to zero out the censored motion after step 4 and it worked:
1. Run 3dDeconvole with the -cbucket option
- This produces the file called: c.stats.$subj+tlrc
2. Use the command grep ColumnLabels X.xmat.1D to find which columns to put
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shanaadise
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AFNI Message Board
Hi Rick,
Thank you for your reply. I followed your steps along with the information here: . However, I had massive spikes in my "cleaned" dataset. Another user had the same problem (https://afni.nimh.nih.gov/afni/community/board/read.php?1,148918,148923#msg-148923) in which Gang suggested that this might be due to censoring out time points and thus, 3dSynethesize would not be a good
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shanaadise
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AFNI Message Board
Subject: Post-doctoral Fellowship Positions (2) starting January 2019
Dear Colleagues,
I am currently accepting applications for 2 post-doctoral fellowships (NIH-NRSA), starting as early as January 2019, within an exciting new training program on the application of Big Data methods to large-scale, multi-modal (neuroimaging, genetic, psychometric) datasets, in the context of addiction resea
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shanaadise
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AFNI Message Board
Hi All,
My understanding is that during 3ddeconvolve the GLM automatically creates a baseline regression that models baseline shifts between and within runs (via the polort function). This is all incorporated to the output file: stats.subj+tlrc. After 3ddeconvolve has run my script concatenates all of the runs in my task (named: all_runs+subj+tlrc). I have four runs that were all collected du
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shanaadise
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AFNI Message Board
Hi Gang,
Thanks for replying and that is a good question. I guess across runs and from beginning to end (with all runs combined). My data has already been preprocessed and run through 3dMVM, however, we would just like to test for habituation effects over time.
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shanaadise
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AFNI Message Board
Hi All,
This is a very basic question.
1. The AFNI22_Indiana PDF states that you can use AFNI to look across runs to look for habituation effects.
2. How is this done? Is there an example of how to do use? I am assuming this is a simple command in 3dDeconvolve?
2b. Would this then require creating separate stimulus timing files for each run and condition. For example:
Subj1_run1_fac
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shanaadise
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AFNI Message Board
Hello,
I am trying to use the Haskins template for my sample of kids (7-11). I have a silly question. Does using this template slow down preprocessing? I am able to preprocess and align (nonlinearlly) to the MNI template in about ~35-40 min per subject. Using the Haskins pediatric template increased my preprocessing time to about 1.5 hours.
Perhaps this is a simple fix of my code? I just r
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shanaadise
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AFNI Message Board
Hello,
I was wondering if there was a way to create a mask of spheres that are labeled 1 though 20? I have taken the following approach:
1) Created a text file with a list of coordinate files (separate lines for each xyz) --> 3dundump to draw spheres
2) Used 3dROIstats to extract beta weights
*Problem: since 3dundump labels all the spheres as 1, it is impossible to extract specific b
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shanaadise
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AFNI Message Board
This post doctoral announcement is on behalf of Dr. Kathleen Keller, Penn State:
The Metabolic Kitchen and Children’s Eating Behavior Laboratory in the Department of Nutritional Sciences (http://nutrition.hhd.psu.edu) at The Pennsylvania State University seeks a Post-Doctoral Fellow in the area of neuroimaging and childhood obesity. We are examining the brain mechanisms of food portion size a
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shanaadise
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AFNI Message Board
Hello,
I am having a problem running @SUMA_AlignToExperiment - this worked for me yesterday. When I run @SUMA_AlignToExperiment, I get the following error:
set: Variable name must contain alphanumeric characters.
I have @SUMA_AlignToExperiment written into the script generated by afni_proc.py. Even when I try @SUMA_AlignToExperiment by itself outside of the script, I get the same erro
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shanaadise
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AFNI Message Board
Hi Peter,
Just a follow up to the above.
#1 I wrote my own command to generate a script, so I didn't need to use uber_subject.py but I guess the answer would be helpful for others.
#2 I still have the question about preprocessing... which I am assuming the answer is yes, that the surf anatomy and spec needs to be incorporated into my preprocessing script. And therefore, it would h
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shanaadise
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AFNI Message Board
Hi Peter,
Thank you so much for your quick reply and pointing me in the right direction.
A have a few follow-up questions. I would like to use uber_subject.py to do this since I have limited scripting abilities. So, my questions are based on that.
1) Is there an option to specify surf_anat and -surf_spec
- I changed the processing blocks to remove mask and incorporate surf but
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shanaadise
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AFNI Message Board
Hi Rick,
I am also having issues with my data not aligning correctly. I think I am missing a step but I cannot find anything on the message about it. I have taken the following steps:
APPROACH #1
1) Use FreeSurfer recon-all on my T1 image that has not been skull stripped or warped to MNI <-- is this problem?
2) Run @SUMA_Make_Spec_FS -sid Subject#
3) Run @SUMA_AlignToExperiment -exp_
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shanaadise
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AFNI Message Board
Hi Gang,
Thank you for your quick reply. I fixed my code:
3dMVM -prefix WholeBrain_MVM_Contrasts5 -jobs 12 \
—bsVars Weight \
-wsVars Reward \
-num_glt 3 \
-gltLabel 1 ‘weight_F_N’ -gltCode 1 ’Weight : 1*HW -1*OW Reward : 1*FA -1*NA’ \
-gltLabel 2 ‘weight_F_M’ -gltCode 2 ‘Weight : 1*HW -1*OW Reward : 1*FA -1*MA’ \
-gltLabel 3 ‘weight_M_N’ -gltCode 3 ‘Weight : 1*HW -1*OW Reward : 1
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shanaadise
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AFNI Message Board
Hello,
Thank you in advance for any help you can provide. I am running into several issues with 3dMVM. Below is my code.
3dMVM -prefix WholeBrain_MVM_Contrasts5 -jobs 12 \
-bsVars Weight \
-wsVars Reward \
-num_glt 3 \
-gltlabel 1 -gltCode 1 ’Weight : 1*HW -1*OW Reward : 1*FA -1*NA’ \
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shanaadise
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AFNI Message Board
Hello,
I am having a problem with using @auto_tlrc. The individual subject's Talairach anatomical image is appearing larger than the TT27 template. Therefore, the alignment of the CC and other structures are off. I am trying to warp children's anatomical images to the standard adult talairach template. I am unsure how to fix this issue. I've tried to upload a jpg but the image
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shanaadise
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AFNI Message Board
Hello,
I am using uber_subject.py to create my preprocessing steps. I have not changed much from the default settings. However, I am having an issue with skull stripping, which is performed via align_epi_anat.py. My MPRage images are collected in the sagittal orientation, which may be creating the problem?? When I look at my skull_stripped image, there are errors with it -see the attachment sp
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shanaadise
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AFNI Message Board
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