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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
Page 1 of 5
Pages: 12345
Results 1 - 30 of 149
Hello AFNI Experts,
I plan to merge DTI and resting state data. I will have resting state ICA networks guide the DTI tractography analysis.
I was planning to feed in the group ICA maps generated from Group Melodic in FSL into 3dROIMaker.
However, there are a lot of options to choose from in 3dROImaker and was unsure how to optimize. I was not sure what thresholding parameters to do, infl
by
Emily
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AFNI Message Board
Masks - 5 years ago
Hi AFNI experts.
I have a few striatal masks that were generated from a probabalistic atlas thresholded at 60%. Now, I want to make sure that each voxel is assigned to only one mask...so each voxel is assigned to the one that it had the highest likelihood of belonging to. I am sure this is something that I can do with a 3dcalc function/functions but was not 100% sure which function/functions m
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Emily
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AFNI Message Board
3dcalc - 5 years ago
Hello AFNI experts,
I planned to use 3dcalc to calculate the standard deviation of a bunch of correlation maps. However, I have more maps than the alphabet, and I know in 3dcalc, you specify each data set you want incorporated in your 3dcalc expression with a, b, c. Are you restricted by the letter of the alphabet? Can you go beyond 26 variables?
Thanks,
Emily
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Emily
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AFNI Message Board
Hello AFNI Experts.
I am finding that every time I try to use the Where am I tool that my AFNI Gui crashes. Any thoughts on what could be going on?
Thanks!
Emily
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Emily
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AFNI Message Board
Hello AFNI Experts,
I have done some initial preprocessing of resting state data in AFNI. Now I plan to do the rest of the denosing and 1st levels for the connectivity analysis in CONN.
I plan to use the motion regressors and censoring files that AFNI produced from my afni proc py script as first level covariates. I will importing the smoothed functional data (not the errts that would have
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Emily
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AFNI Message Board
Hi AFNI Experts,
When running resting state analyses, when you are correlated a seed with the rest of the brain, I am guessing it is best to extract the average timecourse for the seed using the unsmoothed file, to avoid spillage from other nearby brain regions. And then, correlate that timecourse with the rest of the brain (the errts file).
However, the unsmoothed data (vol reg) won'
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Emily
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AFNI Message Board
Post-doctoral Positions in Affective Neuroscience
at McLean Hospital/Harvard Medical School
Two post-doctoral positions are available within the Laboratory for Affective and Translational Neuroscience at McLean Hospital/Harvard Medical School, directed by Diego A. Pizzagalli, Ph.D.
The laboratory is part of the Center for Depression, Anxiety and Stress Research (CDASR), a vibrant research
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Emily
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AFNI Message Board
Hello AFNI experts,
I am getting back into dyanamic resting state connectivity and have a few more questions.
1.) In 3dmaskave, where I extract the time course for my seed, can I specify what subbricks I want to extract from? For example, say I wanted to extract the amygdala time course for the first 36 seconds of resting state. I have data with a TR of 2. Could I extract the amygdala time
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Emily
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AFNI Message Board
Hi Rick,
I just saw in the afni proc py note that the brain stem was incorrectly included in the white matter mask. I actually just noticed I ran some data using number 16 in the white matter mask. I am guessing I should rerun these subjects as including the brain stem will throw off the accuracy of the regression?
Thanks,
Emily
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Emily
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AFNI Message Board
Hi Daniel,
Would it be okay if I sent you my gray matter mask with the rACC overlay. It may be best just to show you. Can I private message it to you? I ultimately want to warp the rACC mask to MNI space. I thought maybe I would need to do a preliminary step of warping the gray matter with rACC mask overlay onto its gray matter mask that is still in native T1 space.
Thank you!!!!!
Emily
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Emily
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AFNI Message Board
Hello AFNI Experts,
I am working on a project that is linking MRS data with functional data.
I am trying to use the voxel that was aquired from the MRS data on each individual subject to be used as an ROI for the functional data.
In order to overlay the MRS voxel on top of each individual's gray matter mask, the physicist resampled the gray matter mask from 192 X 192 X 144 to 256 X
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Emily
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AFNI Message Board
Hello,
I am tagging onto this as I have the same issue with my data being processed in SPM and wanting to use 3dClustSim.
Just to clarify from the previous message, I should be using the square root of the RESMS file? I assume I can take the square root with 3dcalc? Would this be the equivalent of taking in afni's "errts file"?
Are there any other additional settings I
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Emily
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AFNI Message Board
Hi Gang,
Thanks so much! I am a bit confused...how would I apply the mask to the output of 3dMVM? So I have my lets say whole brain ANOVA with my main effects and interaction. Is there a way to then restrict my analyses to the mask (for small volume correction...use amygdala as a search space) in the gui? Or are you saying to just extract the parameter estimates from the entire amygdala mask?
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Emily
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AFNI Message Board
3dMVM - 7 years ago
Hi AFNI Experts,
I am running 3dMVM to model a Group (2 levels) by Emotion Task (3 levels) interaction. I am using an amygdala mask to restrict the analyses to amygdala voxels. I have successfully done this analysis using a cingulate mask.
However, when I get to the amygdala mask, it says that the model is failing. The script is exactly the same, except the mask is different.
Could it be
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Emily
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AFNI Message Board
Hi Rick,
I am actually getting an "operation not permitted" error when I try to run Dimon. Any ideas why this could be going on and how to solve?
Thanks,
Emily
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Emily
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AFNI Message Board
Hi Rick,
I am attempting to use Dimon, but am running into some errors.
My script is:
#!/bin/tcsh
foreach subject (AGS)
Dimon -infile_prefix '/Volumes/Emily/${subject}/REST1/*.dcm' -gert_create_dataset -save_details ${subject}_dcm
end
I get the following error: error: invalid option </Users/emilybelleau/Documents/AGS/REST1/IM-0001-0002-0001.dcm>
Any thou
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Emily
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AFNI Message Board
Hello AFNI Experts,
I am planning on doing a dynamic resting state functional connectivity analysis. I have a number of questions related to this, bear with me!
1.) The papers that I have read regress CSF and WM as well as bandpass, so I plan on doing example # 11 with afni proc py adding back in the bandpass. Some papers have used used the CONN tool box, which does the bandpass as a second
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Emily
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AFNI Message Board
Hi Rick,
I agree I will plan to use Dimon from now. So, I did use "alt+z" in my to3d command instead of "alt+z2". So, I am assuming this will screw up slice timing correction in afni proc py?
Emily
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Emily
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AFNI Message Board
Hi Rick,
I have been reading a bit more about Siemens scanners. I believe that for Siemens scanners, if the number of slices collected is odd, you start with the odd slices and if the number of slices is even, you start with the even slices. So the number of slices we collected was odd, I believe we need the order to be 1,3,5,0,2,4. So in this situation, should I use "alt+z2" inst
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Emily
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AFNI Message Board
Hi Rick,
Sorry to ask you likely this basic question. Is alt+z the same as saying interleaved/alternating Ascending (1,4,2,5,3,6) and alt-z the same as saying interleaved/alternating Descending (6,3,5,2,4,1)?
I am trying to have a better understanding of all of the slice order options in to3d.
From what I understand, Siemens uses Interleaved Ascending 1,4,2,5,3,6 when an odd number of s
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Emily
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AFNI Message Board
to 3d - 7 years ago
Hello all,
I am working with someone who has collected her data on Siemens Skyra 3T. Her scans are interleaved and oblique.
She found on the to 3d description: Some Siemens .ima files seems to have their EPI slices stored in
spatial order, and some in acquisition (interleaved) order. This
program doesn't try to figure this out. You can use the command
line option '-sin
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Emily
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AFNI Message Board
Thanks so much Rick! I appreciate it! What a big help!
Emily
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Emily
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AFNI Message Board
Hi Peter,
I think what is happening is that these are 3D DICOM files, such that a whole volume is contained in a single file. Would this script be able to handle something like this?
Thanks,
Emily
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Emily
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AFNI Message Board
Thanks Peter! So I am getting an error: /Users/emilybelleau/abin/@move.to.series.dirs: Argument list too long.
I used the following command: @move.to.eries.dirs Biograph_mMR-51006-20160907-103311-000700/MR*
I also have files that begin with PT (pet scan), which I plan to do in a separate script.
Any thoughts?
Thanks so much!
Emily
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Emily
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AFNI Message Board
Hello AFNI Experts,
We have recently collected some data from the Martinos Center. They way it is collected all of the scans from the entire protocol (resting state, task, DWI) are in one folder. I would like to be able to sort the dicoms into their appropriate run...so that I have a folder with the task data, folder with DWI data, etc. These were collected via a Siemens scanner I believe. At
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Emily
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AFNI Message Board
Hello AFNI Experts,
I have tried running @SUMA_Make_Spec_FS on my mac, however I keep getting this set: Syntax Error.
I have just been typing:
@SUMA_Make_Spec_FS -sid CIGU -NIFTI
Any thoughts?
Thanks,
Emily
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Emily
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AFNI Message Board
Hi Rick,
Thank you so much. I have used @SUMA_Make_Spec_FS and made the ventricle and white matter masks.
I have finished writing the number 11 afni script. One issue that I am running into is the following error: ** ERROR: erode label '/Volumes/HaleDepo/AGS/Freesurfer_SPGR_1/AGS.fs/mri/SUMA/AGS_vent' not in followers list
** ERROR: erode label '/Volumes/HaleDepo/AGS/Freesu
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Emily
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AFNI Message Board
Hi Rick,
Thank you! I understand how to make the FS_vent, and FS_white based on the Freesurfer note.
I guess the final confusion lies in the input Freesurfer anatomy. You have it labeled as " FT_SurfVol.nii" Is this equivalent to the "T1.mgz" file that is created by Freesurfer?
Also, Freesurfer creates an "fsaverage" folder and a "${subject}.fs folder.
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Emily
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AFNI Message Board
Hi Rick,
Okay the ${subject}.fs is a directory. That directory contains a mri folder with the aseg files. I assume I should be using the aseg files coming from the ${subject}.fs and not the fsaverage folder, then mri?
Sorry for all the questions and confusion. Still no _rank file though. I assume the T1.mgz is the input anat file we would need from freesurfer?
Emily
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Emily
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AFNI Message Board
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Pages: 12345