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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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Results 31 - 60 of 149
Hi Rick,
Thank you for the very helpful reply. So I am attempting to do resting state example #11 in afni proc py. I am not as well versed in Freesurfer so bare with me. I am having some trouble finding the freesurfer file names listed in the afni example. I am using the latest Freesurfer and it did say it ran without error at the terminal.
So, for the FT_Surf_Vol.nii, is the anat that is
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Emily
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AFNI Message Board
Hi AFNI experts,
I wanted your opinion on resting state analysis. I am looking for the most updated/accepted practice of analyzing resting state data. I have looked at both 11 and 5c on afni proc py. Is 11 perhaps a better way to analyze resting state data now than 5c?
Thanks,
Emily
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Emily
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AFNI Message Board
Hi Gang,
Yes I used the TENT function as the basis function to estimate BOLD response at single subject level and have already averaged those betas for each stimulus condition.
Yes, each voxel was assigned to a specific subregion based on probability information. Each voxel belongs to only one subregion, so that there is no overlap. I guess what I am asking is that I would like the voxels
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Emily
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AFNI Message Board
Hello AFNI Experts,
I would like to examine activation within the amygdala subregions (centromedial amygdala, basolateral amygdala) to different stimuli (CS+, CS- in a fear conditioning paradigm). I have probability information, so that I know which voxels are least likely to compose of each of the subregions and which voxels have the lowest probability. I would like to incorporate this proba
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Emily
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AFNI Message Board
Hello AFNI experts,
I was wondering if you forsee any problems with running afni proc preprocessing on a single linux machine as well as a cluster of other linux machines. I would like to do this to speed up processing ( we are using non-linear warp).
I know with Freesurfer there are known differences across different computers, but wasn't sure if this may also apply to afin proc py?
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Emily
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AFNI Message Board
Hi AFNI Experts,
I was wondering if any one could guide me on how to combine 2 resting state data sets, each collected on a different scanner? I would like to combine these data sets so that I have a bigger N to work with.
I am assuming I would need to normalize them in some way?
Thanks so much,
Emily
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Emily
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AFNI Message Board
Hi Rick,
I use the following regress options:
-regress_censor_motion 0.3
-regess_censor_outliers 0.2
-regress_bandpass 0.01 0.1
-regress_apply_motion_types demean deriv
regress_est_blur_errts
* I am starting to use -volreg_align_to MIN OUTLIER
I am guessing that would throw things off if I put all 3 runs into afni proc py.
If I can do it this way, i would get errts_r01, errts_r
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Emily
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AFNI Message Board
Hello afni experts,
I have collected 3 rest scans in between a fear conditioning paradigm. Is it possible to preprocess all 3 scans in one afni proc py script? I will want to analyze them separately for group analysis so will need 3 errts files
Wasn't sure if they would get concatenated into one eerts file if I processed them all in one afni proc script.
Thanks
Emily
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Emily
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AFNI Message Board
Hello AFNI experts,
I know that we are now being encouraged to use 3dttest++ instead of 3dRegAna to run regressions. So, lets same I am interested in looking at anxiety ratings and it's association with whole brain activity to a stimulus. I know I would set up a covariates file with my anxiety scores.
*My question is, when I look at the 3dttest, is there a bucket that will show me anxi
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Emily
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AFNI Message Board
Hi Daniel,
Thank you! So I actually was able to warp my FA to T1 space okay. Now, for my ROI which is in MNI space. Do I warp this to the T1 and then apply the matrix I generated from the T1 to FA warp?
Thanks again,
emily
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Emily
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AFNI Message Board
Hi Daniel,
Sorry I think I am being incredibly obtuse.
So we have my MNI template, my FA image which is in diffusion space, and my ROI which is already in MNI space (I don't have transform matrices from this, this was made from an afni atlas already in MNI space).
I guess I am getting confused on where to put what. Does my FA image serve as the input to auto_warp.py. So this will ge
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Emily
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AFNI Message Board
Hi Daniel,
Just for clarification, first I would use @auto_tlrc and auto_warp py to do an initial affine registration and then non-linear registration of my DTI data to standard space. Then I would use these matrices for 3dNwarp to go back to diffusion space.
*At what point do I put in my ROI to warp to diffusion space? Does this occur at 3dNWarp apply?
@auto_tlrc -base TT_N27+tlrc -i
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Emily
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AFNI Message Board
Hello AFNI experts,
I have used 3dAllineate to transform an MNI template to a participant's diffusion space (their FA image). I then use this transformation to warp an ROI (originally in MNI space) to the participant's diffusion space. Unfortunately, the corpus collusum is slightly misaligned on my first transformation, so this affects my ACC ROI registration. I used nearest neighbor
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Emily
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AFNI Message Board
Hello afni experts,
I am working on changing the label of my mask which is currently a "1" to a "-1".
I am using the following command: 3dcalc -a /media/larson_buffalo/MRI7/KAward/Conditioning_From_Cluster/K_dti/${subject}/${subject}_DTI_Prep/L_CMA_Superficial_Exclusion_Mask_diff_final.nii -expr "-1*step(a)" -prefix /media/larson_buffalo/MRI7/KAward/Conditioni
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Emily
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AFNI Message Board
Hello afni experts,
I did a resting state connectivity with amygdala subregions as seeds (basolateral amygdala, centromedial).
I would like to look at differences in BOLD activation in these regions during the task as well. However, I would like to use the same procedure as the resting state sample. For the resting state sample, the time course was probability weighted, so that the voxels
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Emily
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AFNI Message Board
Hello afni experts,
I have a question regarding setting up my 3dDeconvolve model after I have done all the initial preprocessing steps for a generalized PPI analysis.
I conducted a typical differential delay fear conditioning task with a fear acquisition phase and a fear extinction phase. In my initial 3dDeconvolve model prior to conducting a PPI, I had both the fear acquisition run and my
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Emily
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AFNI Message Board
Hello,
I am running into the following error when I try to launch suma:
*We recently updated to the most recent afni binaries and was wondering if that had something to do with it.
++ Environment variable = already set to 'SUMA_SUMA_TESSCON_AutoScale'. Value of 'NO' from /home/AD/ebelleau/.sumarc is ignored.
To kill such warnings Set AFNI_ENVIRON_WARNINGS to NO
SUM
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Emily
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AFNI Message Board
Hi Peter,
Sorry to Pester! It is looking like registering the DWI to a T2 is improving things. I tried your rotation script and had it run all night and it still is not doing anything. Does it take several days to process or perhaps it is just not working for me. I did not get any errors though.
I was not sure how to modify things. Should the script just be able to run as is off of the cog
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Emily
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AFNI Message Board
Actually one more thing, would I also need to use your script to rotate vectors if I use option number 2?
Thanks,
Emily
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Emily
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AFNI Message Board
Hi Peter,
I think I will try option number 2. Do you think there are additional benefits to doing this extra step beyond DTI Prep? I was just wondering if aligning to an anamtomical further takes care of any other possible baseline inhomogeneity and increases accuracy of alignment.
If I do number 2 would I just change epi2anat to anat2epi and then just keep everything else in the command t
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Emily
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AFNI Message Board
Hi Peter,
I used the following command also taken from the cog neuro blog.
align_epi_anat.py -anat /media/larson_buffalo/MRI7/KAward/Conditioning_From_Cluster/K_dti/sub238/sub238_DTI_Prep/sub238_T2_ns.nii.gz -epi /media/larson_buffalo/MRI7/KAward/Conditioning_From_Cluster/K_dti/sub238/sub238_DTI_Prep/sub238_dwi_cleaned.nii -epi_base 0 -suffix _al2anat -epi2anat -anat_has_skull no -giant_mov
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Emily
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AFNI Message Board
Hi Peter,
Thanks for the quick reply.
Yes, I am using DTIPrep, so my data has already had slice intensity/interlace artifacts removed, data was iteratively aligned to the average baseline image, and baseline corrected.
I wanted to do a quick experiment to see if aligning the DWI to a T2 further improves quality control.
Would you be willing to guide me in terms of what piece of the sc
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Emily
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AFNI Message Board
Hello AFNI experts,
I have registered my DWI images to a T1 (a T1 that was made to look like a T2 thanks to a script from Paul Taylor) using align_epi_anat.py.
Now, I would like to rotate the bvecs.
I found on a website that I could use: @rotatevectorsallx1 volreg_dset bvec.1D
However, this @rotatevectorsallx1 does not exist in my afni version ( I have the latest compiled afni).
W
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Emily
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AFNI Message Board
Hi all,
I was wondering if anyone could give me some advice on whether or not to denoise DTI data. In DTIPrep (an extension through Slicer), you can either do a Rician LMMSE and/or a Joint Rician LMMSE on the DTI data on top of another of quality control steps (eddy current correction, epi distortion corrections......which I have done). I am sure this is largely dependent on the quality of th
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Emily
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AFNI Message Board
Hello Afni experts,
I am currently looking into a program that does a more thorough quality control check of DTI data. I will then plan to feed the data back into afni once this is done.
However, this program converts the data to NRRD format ( a popular file format for dMRI data, capable of storing all diffusion information within an ASCII readable file header). Is there a way in afni to co
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Emily
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AFNI Message Board
Hello,
I had a quick question. After doing resting state analysis and regressing out psychophsyiological regressors using afni proc py, should I be using the regular errts file that is produced during the regression (3dDeconvolve) or the errts file that is produced after 3dtproject following the regression (errts.tproject) for group analysis?
Thanks,
Emily
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Emily
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AFNI Message Board
Hi Rick,
I sent you a message via email. I am curious what your opinion as to why the script is not producing a stats file.
Thanks so much,
Emily
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Emily
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AFNI Message Board
Hello all,
I am starting to run another analysis this time incorporating physio regressors (made from McRetroTS) into the resting state analysis using afni proc py, Example 5C.
I saw the following on the command window: ERROR: Can't open dataset stats.sub202+orig
++ 3drefit processed 0 datasets
But it seemed to proceed with the rest of the steps and I have an errts data set.
I als
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Emily
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AFNI Message Board
Hi Paul,
Okay I think this is a great idea. However, it looks like I can only attach bmp, gif or jpg files. Is there perhaps another address I could attach the files too?
Thanks,
Emily
by
Emily
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AFNI Message Board
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