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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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Hi Dr. Paul, thanks for your prompt reply.
My AFNI version is AFNI_16.0.18 and Tortoise version is 2.5.1.
I use calcvm to export AFNI and yes, I got DWI.nii and BMTXT.txt. (I do not have IDL, so I use prepvm and calcvm; the titles of the windows are DIFF_PREP and DIFF_CALC).
Issuing the command 3drefit -orient to DWI.nii: RPI -128.000000 100.251221 -85.367073, far away from yours.
Be
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JoJo
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AFNI Message Board
Hi AFNI/FATCAT experts, Sorry that after construction of my analytic pipeline, I encountered an unexpected problem. I found that the Tortoise output by AFNI Export has (0,0,0) coordinate at the bottom left of the image, not in the center of volume (AFNI convention). It seems that 3dwarp (adding translation to volume) and vecwarp (adding constants to gradient file) could serve as a quick fix. Howe
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JoJo
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AFNI Message Board
Hi Dr. Taylor, sorry that I found another question w.r.t bmtxt file.
The Tortoise "DTI_DMC.bmtxt" has perfect correspondence with AFNI export "BMTXT.txt", both with 6 columns.
Assume that a particular row in DTI_DMC.bmtxt is:
I found the correspondent row observed in AFNI export BMTXT.txt is:
Given diagonal-first order (AFNI) is: Bxx, Byy, Bzz, Bxy, Bxz, Byz, while
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JoJo
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AFNI Message Board
Dr. Molfese, thank you very much for the comments: Align T2 when approaching the edge and leave DWI to Tortoise. Got you. JoJo ~
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JoJo
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AFNI Message Board
Dr. Taylor, Thank you very much. The FATCAT demo is fantastic, and enables me to enjoy more about AFNI and Suma. JoJo ~
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JoJo
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AFNI Message Board
Dear Peter, thanks for your quick response. It works like a charm ~
Forgive me that I have two minor questions:
a. I have 12 T2 (B0) and I did not average them before importing to Tortoise. The results returned only 1 B0. I guess Tortoise recognized that there could be more than 1 B0 and handled all the average work for me. Since the Status console showed that the B0 and DWI images were alig
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JoJo
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AFNI Message Board
Hi Dr. Taylor and AFNI Gurus,
I've gone through your tutorial of FATCAT. I'm now trying pre-processing of DWI by Tortoise. I've 12 T2 and 64 DWI. The program seems work well (revealed by real-time console).
I've got 6 folders (DTI_up_rpd_corims, DTI_up_RAWFLOAT, DTI_up.list_deformation_field_output, DTI_slices, DTI_DMC_noise_info and DTI_DMC_corims) and a bunch of file
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JoJo
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AFNI Message Board
Dear AFNI experts,
Does anybody happen to know that whether 3dReHo and 3dLocalPV(SVD) can be applied to *.dset?
I've tried both wihout error but with some confusing message.
As to 3dReHo:
++ Final vox neighbood: ellipsoid with Nneigh=19 and radii (1.700,1.700,1.700).
++ ReHo (Kendall's W) calculated.
Although no error, "ellipsoid" with x,y,z radii seem not reason
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JoJo
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AFNI Message Board
Hi SUMA Gurus,
May I ask 3 questions about SUMA? I cannot find the answers in the tutorial and this message board.
First, I’m still confused whether we need to perform e2a or a2e in the preparatory step?
In the suma tutorial, p42 first line: functional data are assumed to be in register with experiments' anatomical
second line: align anatomical to EPI using: align_epi_anat.py
but
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JoJo
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AFNI Message Board
Hello, I'm not sure whether it's suitable to post my query of FDR here. Sorry if it's not.
Suppose that I used to set q=0.05 for a single statistical image. But now, I have ten statistical images to analyze. They are related in some sense but not the same.
Should I choose q = 0.05 or q = 0.005 for multiple comparisons of these ten statistical images?
Thanks for any quick r
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JoJo
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AFNI Message Board
Hi AFNI Guru,
Suppose that I have used 3dClustSim and 3drefit to apply to all the contrasts images. May I ask how to batch statistical calculations with masks/tables as outputs?
For example, if I have 50 statistical compraisons and I do not want to abuse the GUI 50 times, how can I use command line to set p threshold, cluster size threshold, do clusterization, then output the result images
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JoJo
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AFNI Message Board
Thanks Paul, I'm trying them.
Btw, may I ask does current 3dDWItoDT incorporate gradient matrix adjustment by movement (maybe from the header)? Or we have to calculate the transformed gradient matrix by something like @rotategraddirs.csh before hand?
JoJo~
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JoJo
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AFNI Message Board
Hi Bob, Could you please explain the last sentence for us?
Say, if we hope to see the characteristics of slow 4 (0.027 to 0.08 Hz) with TR 2 s in resting fMRI, which bandpass filter serves this purpose better?
JoJo~
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JoJo
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AFNI Message Board
Hello Dr. Taylor, may I have a quick question?
Is the ALFF in your code divided by global mean ALFF value? (Zang et al., 2007)
JoJo
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JoJo
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AFNI Message Board
Hi Dr. Taylor, thanks for your quick response. Either is fine with me. Cheers, JoJo
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JoJo
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AFNI Message Board
Hi Dr. Taylor,
Do you think it's feasible to add an option based on ROIs rather than each single voxel or neighboring voxels (9 or 27...)? For example, ReHo of a particular Brodmann area/brain region, etc.
If you think this feature request is reasonble, 3dROIstats could be a good template since it handles all the ROIs (indicated by different values) in one execution.
JoJo~
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JoJo
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AFNI Message Board
Thanks, Daniel. It works as cool as this winter.
Best wishes for the new year, JoJo~
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JoJo
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AFNI Message Board
Dear AFNI guru,
I’d like to ask how to obtain the mean coordinates of each 115 (or 116) ROIs in the CA_N27_ML template; MNI system would be better, TT is also fine. This information would be useful for network illustration of neural nodes.
Any suggestion is greatly appreciated. Thanks in advance, JoJo.
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JoJo
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AFNI Message Board
Hi Rick,
I've gone through the processes and got goog results on defauld mode network. I'd like to extend my analyses to other seed regions.
Could you provide batch mode example(s)? I cannot find them in the help file.
Happy New Year, JoJo
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JoJo
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AFNI Message Board