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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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Here are my analysis procedures:
3dDeconvolve -input catrunregblurob+orig -polort 2 \ catrunregblurob +orig is the Bold which has been tshifted,registered,blurred and deobliqued
-num_stimts 9 \
-stim_file 1 s_PULSE.1D -stim_label 1 "PULSE" -stim_maxlag 1 6 \ s_PULSE.1D, s_PPI.1D and s_PPI2.1D are the stimulus timing files
-stim_file 2 s_PPI.1D -stim_label 2 "PP
by
heiding66
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AFNI Message Board
I am thinking about what you said. Are you saying I should use adwarp to register my SPMs to the Native +orig space of the first scan instead of the +tlrc Volume of the first scan? Or what are you saying? Also will this be a problem for group data which I need to be in +tlrc space?
by
heiding66
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AFNI Message Board
Hi there!
Will be grateful for your advice and I believe you will know the answer.
I have two sets of data from two separate scans. The previous scan I used the Bold data in +orig space I got from preprocessing the data and I used this in a deconvolution along with a mask I obtained from 3dAutomask on the preprocessed data. The resulting SPMs were then laid on top of the tlrc anatomy with exce
by
heiding66
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AFNI Message Board
Hello Rick,
What I want is correlation between voxels of two different ROIs. What I get out of my analysis is a BRIK for a given voxel in the Rmiddle correlated to each voxel in the Insula. These BRIKs I would like to put each into an FDR giving a list which can be thresholded by q-value leaving the remaining "active" voxels- ones with significant correlations. One can then convert th
by
heiding66
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AFNI Message Board
Here is my program where I resample the ROIs into the space of the coefficient file: DeconIMGAMPPI+tlrc. Then I dump out the middle frontal coefficients
into a file called tempmiddle and subsequently transpose the matrix. Finally, I correlate every middle set of coefficients with every set in the Insula giving 1024 Briks but there were I believe 1883 coefficient sets--is 1024 a cutoff? Anyway,
by
heiding66
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AFNI Message Board
Hi there!
Hopefully this is an easy question for you. Could you use a func-bucket dataset which contains 64 coefficients (beta coefficients) the same way as a 3d+time dataset in 3dTcorr1D? How do you convert the two where the func-bucket dataset becomes a 3d+time with 64 coefficient timepoints. I want to correlate coefficients instead of timepoints unlike a normal timeseries. I also thought of
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heiding66
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AFNI Message Board
Thank you Daniel since I was confused and I am glad I am not doing anything wrong. Now I can continue with my analysis. Thanks! -Linda
by
heiding66
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AFNI Message Board
Hi ALL,
I have the problem that when I try to dump out the 64 values per voxel into a file using 3dmaskdump, the dumped values with corresponding spatial coordinates don't match when I upload the file I dumped into AFNI GUI and go to the spatial coordinate position there. The following are the commands I used:
(1) whereami -mask_atlas_region TT_Daemon:right:47 -prefix trmiddle
(2) 3dresa
by
heiding66
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AFNI Message Board
Hello AFNI folk,
I was wondering if one can create a 3D picture using an anatomical as background and add to it an ROI and individual single voxels at specific coordinates in various colors. Is there a way to have the program read in the coordinates of the specific points and of the ROI? I don't know if there is a simple way.
Thanks for your help and attention.
-Linda
by
heiding66
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AFNI Message Board
Hello, I have a quick question. What is the maximum size of a file which AFNI programs can handle fine without getting hung?
Apparently, 37GB is too BIG. thanks. -Linda
by
heiding66
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AFNI Message Board
You say a single linear model, does that mean the runs are concatenated together to create this single model? Otherwise if you have three separate runs, for example, you don't do a separate linear model for each doing 3 regression analyses (i.e. LS models) and then combine beta coefficients together from each run's linear model somehow. I know baselines can be unique to each run. But yo
by
heiding66
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AFNI Message Board
Thank You! for your attention. It turned out that the resulting Bold matrix from freesurfer is over 37GB and causes AFNI to be hung. Besides getting a better computer whose standards you can suggest, is it possible in anyway using AFNI to reduce the size by using runs instead ? However, I feel we would have a big problem with the deconvolution since we use the old version with impulse response fu
by
heiding66
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AFNI Message Board
Thanks! The AFNI commands were hung--they were just killed after a long while so I have no output. I am going to check the stuff from freesurfer .
I appreciate your help and I may get back to you in the future. -Linda
by
heiding66
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AFNI Message Board
Hello Daniel,
Specifically none of the commands worked when using the freesurfer Bold. It just maybe that my nifti file derived from freesurfer is wrong. However, does AFNI commands allow nifti files as input? or do they need to be transformed using 3dcopy to AFNI format? Even this was not possible in this case. Also do AFNI commands in general allow the use of a freesurfer MNI152 template defi
by
heiding66
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AFNI Message Board
Hi again,
I was wondering if you have to convert nifti to AFNI format in order for the output which is the Bold in standard space obtained from the freesurfer vol2vol program which follows from using mri_cvs_register to register the volumetric to the standard brain cvs_avg35_inMNI152? I try to use the .nii file in the AFNI viewer and try to do 3dAutomask on it but it gets hung. Then I tried to
by
heiding66
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AFNI Message Board
Hello there,
I have a question about if it is possible to use freesurfer programs by first doing bbregister on output from 3dvolreg and then using mri_cvs_register for coregistration of the freesurfer anatomical to a CVS35MNI152 template and then use mri_vol2vol to get the BOLD in this space. Then it was suggested to take this output and use it in 3dDeconvolve and then 3dANOVA2 etc. Is it possi
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heiding66
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AFNI Message Board
Thanks very much Rick!
I am currently looking into afni_proc.py for use for our problem.
I really appreciate your help!
by
heiding66
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AFNI Message Board
Hello AFNI folks,
All I need is some reassurance that I am doing things correctly. There is no one here I could ask and I am learning everything by myself. Ultimately, I have a group of subjects that I need to analyze first at the subject level and map their functional to surface space to get the original mesh and then transform to standard mesh space where I can do group data analysis and find
by
heiding66
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AFNI Message Board
Dear AFNI and SUMA experts:
Here is my program which I believe creates the original mesh. After concatenation of runs, removal of TPs and doing tshifting, I do the following set of commands below: I wonder if you see anything obviously wrong??? Since I use +orig space anatomical volume and SurfVol, I am guessing the surface meshes are in original space--Is that correct? I wonder how they can
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heiding66
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AFNI Message Board
Thanks for your help!!!! I just have one question. Is wm_rh_S_circular_insula_ant the anterior insula on the right hand side in surface space which corresponds to the right anterior insula in volume space? This is really what we are looking for. With great appreciation. -Linda
by
heiding66
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AFNI Message Board
Hi there!
I believe this question is easy for you but it is frustrating me. In one of Beauchamp's handouts called "UseCortSurfMod" on page 6 there is a line which I believe extracts out a specific ROI from the entire parcellation but I tried finding the .dset in my freesurfer data but all I could find were rh.aparc.a2009s.annot.niml.dset or rh.aparc.a2009s.annot.1D.{cmap or ROI}.
by
heiding66
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AFNI Message Board
Thanks much Rick!
I know so little that I didn't think you could do that probably because I thought there should be an -input ROI option in SurfClust if it were possible. sorry! Somehow I thought the surfaces were "special". I also think the coordinates corresponding to the maximum node in the brain region can be found in AFNI or volume space and averaged over subjects to get th
by
heiding66
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AFNI Message Board
Hello AFNI experts,
As I stated in the last message I am interested in using SurfClust. However I would like to use an atlas of parcellations. I am guessing other people would like to use their favorite atlas as well to define the clustering boundaries. I suppose you can convert the parcellation from Volume space to surface space and create a parcellation in cortical surface space but what would
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heiding66
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AFNI Message Board
Thanks for your comments. They helped A LOT!!!!
I have a question about program SurfClust. What I want to do is find the maximum node in a cluster in an ROI. I know you can draw ROIs in suma although I don't know how at this moment. I was wondering that it seems you can output an ROI but not input one (unless I am wrong). We were thinking about inputing a parcellation from the human brainne
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heiding66
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AFNI Message Board
Hi experts,
Are my questions too obvious or too difficult. I don't know where to find the answers directly but I could try things with suma now but could still use your knowledge and help. Appreciate you guys much.
-Linda
by
heiding66
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AFNI Message Board
Hi again,
I understand using the grey matter only reduces error and smooths better. However, I wonder if you must use afni_proc.py for a surface analysis or can you simply use ALL the regular afni commands like 3dcalc, 3dDeconvolve, FDR etc. except for the special surface commands like SurfSmooth etc. but what would you input into these commands-- will they assume a surface dataset is the same a
by
heiding66
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AFNI Message Board
Hello again,
I am wondering if one has behavioural regressors in an event-related design and you use 3dDeconvolve to find the BR coefficients and t-statistics, is it proper to transform each of these t-stats to the cortical surface using 3dVol2Surf and then continue with smoothing etc. or must you start with the +orig functional data? If this shortcut can be done do you know of any examples of
by
heiding66
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AFNI Message Board
Hello there!
I have a quick question: If you have an entire hippocampus and want to divide it into anterior and posterior sections and need the two resulting ROIs to have different ROI numbers (currently they are the same number)--What would be the easiest way of doing that? Of course we know the slice number where they separate.
Thanks for your help in advance.
-Linda
by
heiding66
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AFNI Message Board
Hi again,
I have been trying some things. I copied the .afnirc example off the internet and have been trying to add the variable : AFNI_ANALYZE_VIEW = tlrc but whenever I try to transform my +tlrc dataset to analyze format it still gives me one in +orig space. I also tried to convert the analyze format back to AFNI using 3dcopy but it gives me an error that it doesn't have any input file in
by
heiding66
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AFNI Message Board
Hi there,
I have a quick question. This is the first time I am using 3dAFNItoANALYZE. I noticed that when I apply this program to a functional image file in +tlrc space, it seems like the resulting file is in +orig space. This is a problem since I need to transform the data and it should be in +tlrc space in order to be correct. I tried using NIfTI but Analyze software doesn't seem to recog
by
heiding66
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AFNI Message Board
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