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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 3 of 5
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Hi again,
Man I am having a heck of a time with this. Changing the color scheme did not work. I basically just have the same axial FA image with the gdset. I am running out of things to try. Is is a settings issue or how it is loading the files?
Also, should afni and suma be talking to each other?
Again sorry for the back and forth,
Emily
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Emily
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AFNI Message Board
Hi Paul,
Yes, I am running full probabilistic tractography. So, I should still be able to see the voxels of white matter connecting the basolateral amygdala with the ventromedial prefrontal cortex right?
*Right now, even when I went into Object Controller, selected All Objs and then toggled to NET_000_ROI_001_002+orig and pressed the v under volume rendering, I still just get the same image
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Emily
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AFNI Message Board
Hi Paul,
Yes, I am running full probabilistic tractography. So, I should still be able to see the voxels of white matter connecting the basolateral amygdala with the ventromedial prefrontal cortex right?
*Right now, even when I went into Object Controller, selected All Objs and then toggled to NET_000_ROI_001_002+orig and pressed the v under volume rendering, I still just get the same image o
by
Emily
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AFNI Message Board
Hello,
I was able to update my afni binaries to the latest afni. I did go into Object Controller and press All Objs. button. I then used the switch button to toggle to the NET_000_R01_001_002+orig. I then clicked on the v button under volume rendering controls.
I am still unable to view the tract. Is there perhaps I color scheme I need to change?
So I am loading in the following:
$sum
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Emily
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AFNI Message Board
Hi Paul,
It actually looks like I don't have that option. I have the latest afni version (AFNI 2011_12
_21_1014), but not the latest precompiled binary (which appears to be just a recent update January 23, 2015), mine is from June 19 2014.
So, I am guessing this is a quite recent addition to SUMA?
Thanks so much again for your help!
Emily
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Emily
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AFNI Message Board
Hi Paul,
So when I type in the command I showed you above I get the FA image (at least I believe that is what I am seeing) and on top of the FA image it says in white letters "N000:R0" and "N000:R1" Then when I move the image around I see a small yellow dot with a bunch of colorful lines through it that is not connected to the image.
Is it a matter of changing some setti
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Emily
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AFNI Message Board
Hi Paul,
Okay so now I am down to one error message. I had some naming convention/directory issues. I don't think that this next error message is a result of these issues.
Error Message:
++ 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
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Emily
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AFNI Message Board
Hi Paul,
Yes, I am running probabalistic tractography.
I discovered the error.....my rois were badly warped to diffusion space. I fixed that and got all of the necessary files created and it said on the the terminal that a pairwise connection was found.
However, I tried loading in the NET_000_ROI_001_002 and the DT_FA file and ran into the following error:
++ Environment variable = al
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Emily
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AFNI Message Board
Hi Paul,
To visualize my tract (basolateral amygdala to vmPFC, with the centromedial amygdala as an exclusion mask, I used the following:
$ suma -vol PAIRMAP_NAME[0] -gdset o.PR_000.niml.dset -vol FA_FILE
However, I ran into the following error: Error SUMA_LoadDsetOntoSO_eng (SUMA_Color.c:10118):
Could not find network_file "o.PR_000.niml.tract" on disk for dset
The o.PR_
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Emily
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AFNI Message Board
Hi Paul,
Excellent, that makes sense. I was wondering if you would mind giving me some additional guidance on visualizing the tracts in SUMA.?
So I made a tract from the basolateral amygdala to the ventromedial prefrontal cortex using full probabilistic tractography.
Would I be looking at o.PR_000.niml.dset or the o.PR_000_PAIRMAP.niml.lt? Also I assume that an anatomical image (spgr) for
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Emily
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AFNI Message Board
Hi Paul,
When I tried incorporating "-logic AND", it said that I can't use that when in Prob mode. So I guess I can't use that option when doing full probabilistic tractography?
Thanks,
Emily
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Emily
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AFNI Message Board
Hello,
I am reviving this conversation. I have an issue where I have a cluster that runs through portions of the posterior cingulate cortex, parahippocampal gyrus, and the cerebellum.
* I know it is not optimal to break this cluster up, but for interpretation purposes it might be the better route to go.
My data is in MNI space, 1x1x1 voxels.
Should I then use the b-mask and o-mask op
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Emily
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AFNI Message Board
Hello,
I used the following command:
time 3dTrackID -mode PROB \
-netrois /media/larson_buffalo/MRI7/KAward/Conditioning_From_Cluster/K_dti/sub238/sub238_add_rois.nii.gz \
-uncert /media/larson_buffalo/MRI7/KAward/Conditioning_From_Cluster/K_dti/sub238/dmri/DTI/o.UNCERT_UNC+orig \
-dti_in /media/larson_buffalo/MRI7/KAward/Conditioning_From_Cluster/K_dti/sub238/DTI/DT \
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Emily
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AFNI Message Board
Hello again,
I am now at the stage of running full probabilistic tracking on my data (using script 10 of the FATCAT demo). I am running into the following error:
++ Tracking mode: PROB
++ Number of ROIs in netw[0] = 2
++ No refset labeltable for naming things.
++
++ SEARCHING for files with prefix '/media/larson_buffalo/MRI7/KAward/Conditioning_From_Cluster/K_dti/sub238/DTI/DT
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Emily
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AFNI Message Board
Hello,
I am in the process of running the second script (3dDWItoDT) from the FATCAT Demo adapted to my data. I am running into the following error: data set must have number of sub-briks equal to one more than the number of gradient vectors.
I realize that in order to get around this I will need to average the 3 b0s in my dwi data set. I know how to average the three sub-briks using 3dcalc
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Emily
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AFNI Message Board
Hello Afni Experts,
I have some questions regarding diffusion tensor imaging analyses. I am quite new to this, so I appreciate your patience.
I have done all of the initial preprocessing steps (convert DWI to nifti files, eddy current correction, create a brain mask from low-b diffusion images) as well as bedpostx (Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniq
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Emily
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AFNI Message Board
Thanks Peter!!! Yes, I had to redo 3dFWHMx because I resampled the data after preprocessing in afni proc py, so needed the blur estimates based on the resampled data.
Emily
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Emily
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AFNI Message Board
Hello AFNI experts,
I planned to use 3dFWHMx since I resampled my data and will need to get the new blur estimates.
It is resting state data, so I planned to use the errts file as the input into 3dFWHMx. The data was processed using afni proc py, example number 9 for resting state data.
Do I need to use any additional options in 3dFWHMx such as demed, unif, or detrend?
Then I would us
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Emily
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AFNI Message Board
Hello,
I was wondering if there is any way I can covert a seed mask to diffusion space within afni? I plan to use the amygdala as a target mask and track to the vmpfc. I need to get both of these seeds in diffusion space.
I have been struggling to do this in FSL prior to running probtractx and was wondering if there was anything contained with afni, which I know much better.
Thanks!!
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Emily
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AFNI Message Board
Hi Rick,
That appears to have resolved the issue...looks like some information must have gotten lost/altered when the file was converted to nifti. When I look at it in afni, it does appear to look like it was in MNI space and just needed the header information changed.
Thanks,
Emily
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Emily
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AFNI Message Board
Hello Rick,
The researcher that gave this to me said it was in MNI-152 space, but when I did a 3dinfo on it, it said the mask was in original space. Additionally, when I tried to look at it on the afni gui with the MNI-152 brain as the underlay and the mask as the overlay, I was not able to because they appeared to be in different spaces.
I have attached the file, if you would not mind taki
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Emily
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AFNI Message Board
Hello AFNI experts,
I recently got a mask of the anterior midcingulate from another researcher that was developed from the Harvard-Oxford Probablistic atlas.
This mask is in original space and I would like to convert it to MNI space. Any ideas on how best to do this?
I at first took a quick pass and tried FSL's flirt through the gui, but that did not work well at all, so I assume do
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Emily
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AFNI Message Board
Hi Gang,
Yes, I was referring to modeling the stimulus of 8 s duration. Thanks for the other suggestions.
Emily
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Emily
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AFNI Message Board
Hello,
I was wondering about the best strategies for modeling the hemodynamic response in my task.
We are using a traditional fear conditioning paradigm, with two stimuli (a CS+ paired with a shock and a CS- not paired with a shock). The stimuli are presented for 8 secs and are followed by a jittered 12-20 sec ITI. Our TR is 2sec.
In our lab, we generally use tent functions. We have prev
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Emily
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AFNI Message Board
Hi Jon,
I use GIFT, developed by Vince Calhoun. It is a matlab based program.
Emily
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Emily
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AFNI Message Board
Hello all,
This question may be out of bounds but I wanted to ask it because I noticed we had some DTI experts.
I have extracted FA statistics for all of my subjects: the statistics include an Average FA (average over the entire support of the path distribution), Weighted FA (weighted average over the entire support of the path distribution), and Center FA (average over highest-probability
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Emily
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AFNI Message Board
Hi Rick,
Thank you. I generally just use the errts file for my resting state functional connectivity analysis.
I am trying to picture when one uses this file? The reason I ask is that my lab mate is working on combining both tools from afni and fsl for our preprocessing pipeline. He noticed that his script crashed when trying to make this file. So he had asked me if I would ever need this f
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Emily
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AFNI Message Board
Hello afni experts,
I was wondering what the file gmean.errts.unit.1D file that is an out-put file from afni proc py?
Does it have anything to do with global signal (in case you wanted to regress that out of your data from some reason)?
Thanks,
Emily
by
Emily
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AFNI Message Board
Hello afni experts,
I plan on doing a local probabilistic tractography analysis with the basolateral amygdala as a seed and the vmPFC as a target region. I have read some papers and saw that some people "grow or dilate" their seeds into the white matter (about 2mm or so).
Would it be possible to do this step in afni? I just generated these masks using 3dcalc and had planned on us
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Emily
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AFNI Message Board
Hello,
I was wondering if anyone could provide any guidance on parcellating the amygdala into superficial, centromedial, and laterobasal subdivisions with resting state data using 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 onl
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Emily
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AFNI Message Board
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Pages: 12345