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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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Page 4 of 5
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Hi Rick,
Thanks for checking that!
I was wondering if you could help potentially give me starting point for how I might go about doing the following in afni.
I would like to use Roy's (2009) tactic for parcellating the amygdala with resting state data into superficial, centromedial, and basolateral subdivisions.
The following steps are:
1.) Include only voxels with a probability
by
Emily
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AFNI Message Board
Hello,
I plan on parcellating the amygdala into lateralbasal, centromedial, and superficial amygdala. I was wondering what threshold the TT_N27_CA_EZ_MPM (I will be using the MNI shifted version that Daniel Glen made). That is what % does a voxel have to reach in order for it to be considered a part of one of the subdivisions?
For example, I have seen some studies use a 50% cut off.
Than
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Emily
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AFNI Message Board
Hello,
I know that 3dRegAna is out of phase in terms of usage, but I was wondering if it was possible to enter a mask so that you can restrict your regression to certain voxels?
When I tried entering -mask maskname into the script, I got an error "unrecognized command line option -mask."
Thanks,
Emily
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Emily
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AFNI Message Board
Hello Afni Experts,
I am trying to preprocess my resting state data using example # 9 from afni proc py with the addition of Qwarp.
However, I am running into the following error: proc_sub202.Qwarp.Rest1.Pre: No such file or directory.
**error option -blur_size follows unknown arg # 31 (-tlrc_NL_warp)
Below is my script. Any idea of what I am missing?
Thanks so much,
Emily
#!
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Emily
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AFNI Message Board
Hi Rick,
Thanks so much for the clarification! I appreciate it!
Emily
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Emily
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AFNI Message Board
Hi Rick,
I was wondering if what we are doing with regard to censoring data is the same as the "motion scrubbing" technique described in Powers et al., Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion. Neuroimage, 59, 2142-2154.
Thanks!!!
Emily
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Emily
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AFNI Message Board
Hi Rick,
I slightly different but related question....I just tried 3dClust Sim on our bilateral amygdala (62 3.5x3.5x3.5 voxels) with our whole brain 3dFWHM values from afni proc and it crashed saying there were not enough voxels. This was with using the -OKsmallmask option.
Should I try resampling the data (although that means I will need to resample the data and redo the stats)? Or woul
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Emily
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AFNI Message Board
Hi Rick,
Below is my script. The output file that I asked to print to a text file gives me the x, y and z for every time point not the average. It does look like the average is on the terminal window though. Is there any way I can have the average written to a text file? I attached a sample file. I will definitely look into the proc example.
cd /home/AD/ebelleau/Desktop/nas/MRI/IRC_PTSD/R
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Emily
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AFNI Message Board
3dFWHMx - 10 years ago
Hello Afni Experts.
I am trying to do a small volume correction on the amygdala.
To do this, I am first getting the smoothness estimates from 3dFWHMx. I am using the errts files as my input and a mask of the amygdala as my mask. My out-put is a list of x,y and z values for every time point....is there a way to get a print out of the overall average for each subject, like we get in the blur
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Emily
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AFNI Message Board
Hi AFNI experts,
I had a question regarding the example number 9 of afni proc py for analyzing resting state data with banspassing and censoring.
I am trying to understand what is occuring during the censoring process and regressing out outliers?
There is a message next to the example:
Censoring due to motion has long been considered appropriate in
BOLD FMRI analysis, but i
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Emily
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AFNI Message Board
Hello,
I am interested in correlating the default mode network and the right fronto-parietal (executive) network during rest.
What I did was extract the time series of the default mode network as a whole based on a template for each subject. I did the exact same process with the right executive network using 3dmaskave.
Then I used the following 3dfim+ command to correlate the two time se
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Emily
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AFNI Message Board
Hi Rick,
My apologies. Let me clarify. I did not use the ort option in 3dfiM+ because I did already include my nusiance regressors when I preprocessed my data in afni proc py.
Thanks so much! I will try it with these parameters.
Emily
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Emily
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AFNI Message Board
Hello again,
I did try running 3dtstat with the DMN template as my mask and the whole brain correlational map for one subject as my input data set. I am getting an error that my mask and dataset are not in the same dimensions. According to 3dinfo, both are in tlrc space. Additionally I resampled the mask so that had the same voxel size as that of my correlational map. I am not sure what I am m
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Emily
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AFNI Message Board
Hello,
I am using a seed region in the PCC. I would like to isolate myself to looking only at correlations (or Z-score values as I did a Fischers Z transformation) within the DMN based on a standard DMN template that I have.
I am assuming that the first thing that I do is use 3dcalc and multiply the whole brain correlational map with the DMN mask? Although that won't retain the value
by
Emily
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AFNI Message Board
Hi Afni Experts,
I had a quick question. I processed all of my resting data using afni proc py. number 9
When I create a correlation using 3dfim, should I remove the polort since this has already been done. The reason I am using this older program instead of InstaCorr is because I am using a seed ROI.
I am using the following example from Sim Corr Ana:
3dfim+ -input EPI_subj01+tlrc \
by
Emily
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AFNI Message Board
Hello,
This question might be most appropriate for the developers of GIFT for ICA analyses but thought I would check to see if anyone had any ideas about an issue that I am having.
I have been using intensity normalization as a processing step in GIFT. When GIFT is conducting this preprocessing step along with prinicipal components analysis, for one subject, I get the following error: Input
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Emily
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AFNI Message Board
Hi Daniel,
Thanks again.
So, should I first use non-linear warp with the MNI template as the base and the T1 image as the input? But then, what would be the next step to getting the gray matter mask to align with the MNI template? I make the gray matter masks from the aseg file.
I did try directly warping the gray matter mask by using the MNI template as the base and the input file as
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Emily
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AFNI Message Board
Hi Daniel,
Thanks for the suggestions! So for the @auto_warp can I use the gray matter mask as the input directly or should I use the brain.nii first or the aseg segmentation file?
Thanks!!
Emily
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Emily
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AFNI Message Board
Hello all,
These new commands worked great for making individual grey matter masks! Thank you so much!
However, it gets a little tricky when combining them into making a group grey matter mask.
First, I averaged the masks together using 3dcalc. This looked pretty bad. Then, I simply added them, and that looked better, but a bit too inclusive. I am guessing this will probably be the bes
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Emily
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AFNI Message Board
Hello,
I just tried running Auto Centers seperately and got the following output:
$ ./Auto_Centers.tcsh
home/AD/ebelleau/Desktop/10023: No such file or directory.
$ ./Auto_Centers.tcsh
Error: base brick ./MNI_avg152T1.nii not found.
$ ./Auto_Centers.tcsh
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 22 2013) [64-bit]
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Mar 22 2013) [6
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Emily
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AFNI Message Board
Hello again,
Sorry for all the question. It appears that I still get the same errors when I try to run with Auto Centers. This is even when I tried puttingv it somewhere else to further ensure I had enough disk space. It did not come with a diskspace warning this time. Should I try running Auto Centers seperately after @_auto_tlrc?
Here is my output:
$ ./GM_Convert_to_MNI_PM.tcsh
/ho
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Emily
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AFNI Message Board
Hi Peter,
Thanks so much! Just to be extra clear. I should try warping the spgr file (NOT the aseg file from freesurfer that I used to create the GM mask). You meant the spgr when you said "original brain" correct?
Thanks so much,
Emily
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Emily
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AFNI Message Board
Hi Daniel,
Are you suggesting run @auto_tlrc without AUTO Center and then run Auto Centers by itself?
Also, does it make sense to then average the individual masks to make a group mask or is there just to much individual variability to really make an accurate group grey matter (including subcortical structures)?
Thanks so much!
Emily
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Emily
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AFNI Message Board
Hello Nick,
We actually always seem to get that error, even though there is enough space. I actually have 3.7 TB available to me.
I am not sure if -init_xform AUTO_CENTER will be the problem solver. It seems like there is still going to be a lot of individual variability.
I just tried making a group grey matter mask (by averaging all of the individual MNI warped masks) and it looked rat
by
Emily
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AFNI Message Board
Hi Nick,
Yes, 10017.GM.nii' is in '/home/AD/ebelleau/Desktop/nas/MRI/RumMR/FreeSurfer/10017/SUMA'.
Here is the full output:
$ ./Warp_Freesurfer_MNI_final
Copying NIFTI volume to ./10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 22 2013) [64-bit]
*+ WARNING: Disk space: writing file ./10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK
by
Emily
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AFNI Message Board
Hi Nick,
I talked to one of the GIFT developers. As long as I have removed the baseline for each resting session prior to putting them in GIFT, I will be able to then stack the resting state runs in GIFT.
So, to remove just the baseline in each run for afni would I just add "regress" as a block in my afni proc py script? Would I need to specify anything? This is all I want to d
by
Emily
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AFNI Message Board
Hello,
I have tried to incorporate -init_xform AUTO_CENTER into my @auto_tlrc script because my centers were off by 40 mm when I ran the script without it. I am hoping it will help better align my GM masks onto an MNI template.
This is the error message I get: Error: Anatomical dset pre../10017.GM_XYZ_OYmeqfZ3JqF7n9LNC7gDAA+orig.HEAD not found
Are there files I needed to create prior to
by
Emily
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AFNI Message Board
Hi Nick,
Thanks so much for the helpful reply.
Actually, the ICA program that I use actually will do the normalization and detrending steps. Based on what I have been told bandpassing should not be used because the ICA program benefits from all the frequency information. I did try bandpassing and did a motion regression prior to ICA, and got some strange results. Additionally, the alogrit
by
Emily
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AFNI Message Board
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Pages: 12345