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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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Pages: 12
Results 31 - 50 of 50
Hi all,
I just ran 3dMVM on a dataset. However, I now need to threshold the data. I want to use 3dClustSim, but now the -acf option has changed to take a, b, and c parameters.Also, when I load in the dataset, the FDR values are not showing up. Are there any suggested values for these? Is there a way to estimate them? I don't want to fall back to the fwhm option. Also, i there a refit comma
by
Matthew Hoptman
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AFNI Message Board
Thanks, and also thanks for creating a new subject for the post. I will give this all a try.
by
Matthew Hoptman
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AFNI Message Board
PS. It seems to work for version FreeSurfer 6.0 and the final version of 5.3 (I'd been using 5.3 beta for some prior work)..
However, now I have a different question. I am using FATCAT and mappng my T1 images and freesurfer brain.mgz images to DTI space. How do I map files like lh.smoothwm.gii to DTI space? This would allow me to examine the tracts generated in FATCAT on the surfaces
by
Matthew Hoptman
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AFNI Message Board
Hi all,
I'm having the same problem running AFNI_17.2..05 and Linux MInt 17.2 on a 64-bit platform.
Running the @SUMA_Make_Spec_FS program gives me the error
-- running 'mris_convert lh.smoothwm lh.smoothwm.asc
Segmentation fault (core dumped)
-- Error ConvertSurface (SUMA_ConvertSurface.c:589):
if_name lh.smoothwm.asc not found.
failure: could not create surface lh.smoot
by
Matthew Hoptman
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AFNI Message Board
Hi,
Thanks, that makes sense. I'll have to give this some more thought.
Best,
Matt
by
Matthew Hoptman
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AFNI Message Board
Hi,
Thanks, this is very helpful.
Maybe I'm missing the point, somehow. I thought 3dROIMaker could take an image and make clusters of different integer values, but I'm seeing that this isn't what's going on.
I'm struggling with how to be sure the networks are split into the same number of pieces for each subject. i guess I could use 3dcluster, perhaps? The numb
by
Matthew Hoptman
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AFNI Message Board
Hi Paul,
See my replies in caps (sorry for appearing angry LOL)
Re:
As to registration, I am using a multibrik image as input, but when I use 3dAllineate, which I confess, I'm not that familiar with. I tried with:
3dAllineate -final NN -base masked_mean.nii -automask -cost mi -prefix Yeo_EPI /afs/cabi.rfmh.org/usr/hoptman/scripts/Yeo2011_FSlib_LPI.nii.gz
What is the 'source
by
Matthew Hoptman
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AFNI Message Board
Hi Paul,
Thanks,
Re: multiple brik's, I realized that eventually, LOL
As to registration, I am using a multibrik image as input, but when I use 3dAllineate, which I confess, I'm not that familiar with. I tried with:
3dAllineate -final NN -base masked_mean.nii -automask -cost mi -prefix Yeo_EPI /afs/cabi.rfmh.org/usr/hoptman/scripts/Yeo2011_FSlib_LPI.nii.gz
Previously, I had u
by
Matthew Hoptman
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AFNI Message Board
Hi all,
I am trying to use FATCAT across a number of subjects. As regional maps, I'm using parcellations from Yeo et al., 2011. I am registering each of the 7 networks to each participants' mprage space (which is the space the DTI are in).
I'm coming up against two problems:
1) when I use 3dROIMaker, I get different numbers of ROIs for different subjects (21 DMN subROIs i
by
Matthew Hoptman
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AFNI Message Board
Good news. I got it to work. Not sure why, but it is fine now.
by
Matthew Hoptman
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AFNI Message Board
Hi all,
I've successfully run 3dMVM, but when I try to add the results of 3dClustSim, it doesn't work as it has in the past.
I ran:
3dClustSim -mask intermask.nii.gz -prefix CStemp -niml -fwhm 8
Followed by:
3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:CStemp.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:CStemp.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:CStemp.NN
by
Matthew Hoptman
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AFNI Message Board
PS. For small regions, 3dTcorrMap is actually quite fast. My DMN is only 3820 voxels.
by
Matthew Hoptman
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AFNI Message Board
Hi Rick,
As an example, using the DMN mask, for the 3dTmapCorr command and the -Mean option, I get 0.188434. For the @compute_gcor command, I get 0.188676.
Are these values generally reasonable? In a sample of 45 control subjects, I get a mean of 0.30 +/- 0.09 for the DMN.
Thanks,
Matt
by
Matthew Hoptman
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AFNI Message Board
Hi all,
I am interested in pulling out a global connectivity measure for a given network mask. I'm using some resting state network templates from Stanford (available at Stanford resting state network maps.
I've tried doing it two ways:
1) I took preprocessed resting state data and used the 3dTCorrMap and then extracted out the value form that map:
e.g., 3dTcorrMap -mask &l
by
Matthew Hoptman
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AFNI Message Board
Hi Gang,
I'm still getting the error below. Any thoughts?
Best,
Matt
> if (length(grep('tlrc', Model[1, "InputFile"]))==1) outView <- "tlrc"
> if (length(grep('orig', Model[1, "InputFile"]))==1) outView <- "orig"
>
>
> # initialization
> IData <- array(data=NA, dim=c(dimx, dimy, dimz, NoF
by
Matthew Hoptman
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AFNI Message Board
Hi,
I am getting the following message (below) when I use 3dICC.R. I've carefully checked my model.txt file (attached) to verify that I have even numbers of datasets from session 1 and session 2, so I'm not sure what has gone wrong. Files are in afni format, so that shouldn't be the problem.
Any suggestions would be helpful.
Thanks,
Matt
Error message:
> #!/usr/b
by
Matthew Hoptman
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AFNI Message Board
Hi Daniel,
This is very helpful! However, to be clear, do I not need to do any obliquity steps prior to running uber_subject.py? I should note that when I ran 3dWarp -deoblique on the MPRAGEs and EPIs, I got very nice registrations.
On another note, I noted that for one subject, I ran 3dWarp -deoblique on my input EPIs (2 runs) and got different output dimensions for them. I assume it is o
by
Matthew Hoptman
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AFNI Message Board
Hi all,
I have a dataset for which both MPRAGE and EPI were acquired obliquely. I see the common warning about obliquity.
Do I need to deoblique the datasets to get valid results? If so, do I just need oblique the EPI (using -oblique2card), or should I deoblique all datasets (using -deoblique) or is none of this necessary? My sense was I could just do:
3dWarp -deoblique <EPI>
3
by
Matthew Hoptman
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AFNI Message Board
Hi all,
I notice minor differences between the afni I'm currently using (AFNI_2011_12_21_1014; Jan 8 2014) and previous results from Aug 15 2013. However, I'm trying to replicate precisely the earlier results. Is there any way to get the older binaries?
Thanks
Matt
by
Matthew Hoptman
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AFNI Message Board
Hi all,
I am trying to use the afni_restproc.py program, but it is crashing early on. The problem appears to be a simple one, namely that the output of the convert to float program is in AFNI format, whereas the program appears to expect nifti format. Is there a way to set the default AFNI output to nifti format?
Thanks,
Matt
by
Matthew Hoptman
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AFNI Message Board
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