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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 1 - 30 of 32
Dear Prof.Glen,
Thanks for your greatly useful answer, are there any reference paper of this brodmann atlas in MNI space by Juergen Mai and Milan Matajnik? Only one related book was found.
Best wishes,
Peng
by
Peng Ren
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AFNI Message Board
Dear AFNI experts,
I am trying to calculate spatial correlation between single subject PET and MRI with 3ddot, which i think is the proper command to use, right? the output seems to only contain one single r value, are there any way to get proper p value with such large DOF? I've seen spatial permutation test(spin test) in surface based analysis, but not appliable to my case, are there an
by
Peng Ren
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AFNI Message Board
Dear experts,
It is solved with -cm option, no worries.
Best,
Peng
by
Peng Ren
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AFNI Message Board
Dear AFNI experts,
I am trying to coregister FDG PET image and MRI image acquisied in two different site , beginning with @Align_Centers, while it failed to move them roughtly together, or even they didn't appear in the same AFNI view when using underlay-overlay mode, are there any good suggestions?
The example PET and MRI file is uploaded to the cloud.
Best wishes,
Peng
by
Peng Ren
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AFNI Message Board
Dear Peter,
HaHa, you are so great and you will be magician after having coffee, Let me try 3dttest++ first and ask more questions if there is some problems, after you becoming a magician.
Best wishes,
Peng
by
Peng Ren
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AFNI Message Board
Dear Peter,
Here is what's in the covariates.1D file, i think there is no intercept, right? And also, do you mean that df should be the same across voxels?
Subject Score
Sub1 74.7
Sub2 57.0
Sub3 58.6
Sub4 58.2
Sub5 72.5
Sub6 68.0
Sub7 74.9
Sub8 65.5
Best wishes,
Peng
by
Peng Ren
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AFNI Message Board
Dear Peter,
Thanks for your kind reply, just follow what you've suggested, i check the information of the result of following code, while i get a little trouble in finding the DF information, would you mind helping me with that?
3dttest++ -prefix corr_result \
-setA allSubs \
Sub1 CA3-DG_P3_1_z_left+orig \
Sub2 CA3-DG_P3_2_z_left+orig \
Sub3 CA3-DG_P3_3_z_left+orig \
Sub4 CA3-DG_
by
Peng Ren
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AFNI Message Board
Dear Peter,
Great thanks for this helpful instruction, i found there is no voxel-wise output option for DF of t-test, which is needed in this conversion.
would you mind giving me further instructions?
Best wishes,
Peng
by
Peng Ren
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AFNI Message Board
Dear Gang,
Thanks for your immediate reply, as far as i know, 3dttest++ is usually used for one sample or two sample ttest, which takes Group into GLM model and shows if Group effect is significant, while i am not quite clear how to conduct correlation with the behavior test score (can also be implemented by GLM), which is a continuous variable, would you mind giving me some instructions?
by
Peng Ren
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AFNI Message Board
Dear all,
I am trying to use 3dRegAna command for multiple linear regression according to an online doc wrote by B. Douglas Ward in 2006, here is the script:
3dRegAna \
-rows 134 \
-cols 1 \
-xydata 90.0 NC_002_S_0295_ROI_z+tlrc \
-xydata 81.5 NC_002_S_0413_ROI_z+tlrc \
-xydata 94.7 NC_002_S_0685_ROI_z+tlrc \
-xydata 75.1 NC_002_S_1280_ROI_z+tlrc \
-xydata 72.9 NC_002_S_4262_ROI_z+tl
by
Peng Ren
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AFNI Message Board
Dear rick,
Great thanks for help me solving this long-standing confusing problem!!!
Hope all barriers been removed in your way!
Best wishes,
Peng
by
Peng Ren
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AFNI Message Board
Dear rick,
It's the first step to run dcm2niix from MRIcron to convert dicom files to a single NIFTI file, nothing has done except this, is it okay?
Best,
Peng
by
Peng Ren
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AFNI Message Board
Dear rick,
Here are the Information from 3dinfo:
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
which seems to be I to S on the disk, I think it should be alt-z according to your post above, am i right?
Best wishes,
Peng
by
Peng Ren
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AFNI Message Board
Dear afni experts,
I'm doing slice timing correction for data from GE MR750 machine.
Up to now, i get the interleaved scan order from engineer, and find some interesting tags from DICOM header:
First scan Direction: Superior
First scan Location:75.135
Last scan Direction: Inferior
Last scan Location: -91.658
And I've checked that these two slice are the highest and lowest
by
Peng Ren
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AFNI Message Board
Dear rick,
I'm quite sorry for my mistake, i confuse the output from several test, you are right, the output is exactly 3mm.
Then, can i take -dxyz option as the new voxel size for output specificed? and this is exactly what the grid spacing means? I don't want to change the resolution, is it proper to specify -dxyz as the same resolution as input? for here, it's 3.312mm.
by
Peng Ren
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AFNI Message Board
Dear rick,
I think i'd better reexplain my question:
when i check the output from the following command, i found that the grid spacing specified by dxyz option make no difference on the grid of the input, which is also shown below. What's the effect of this command and where's the corresponding information?
adwarp -resam Cu -dxyz 3 -apar 10-anat-ns_shft_alBOLDEC_shft+tlr
by
Peng Ren
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AFNI Message Board
Dear,
There are two terms called grid and grid spacing, which makes me confused. I found it when using adwarp command with -dxyz option. Here are the situation:
anat+tlrc: voxel size=2x2x2, grid=91x109x91
epi+orig: voxel size=3.312x3.312x3.312, grid=64x64x48
epi+tlrc: voxel size=3.312x3.312x3.312, grid=64x64x48
As far as i know, grid spacing should be the spacing between grid lines in
by
Peng Ren
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AFNI Message Board
Dear,
I am conducting oblique correction for EPI data in resolution of 3.125x3.125x4.50 with 3dWarp, which coming out an image in resolution of 3.125x3.125x3.125. I'm curious of whether this upsampling is alright cause it may involve more noise relative to downsampling? am i right?
To put it a general word, are there any principles we can rest on when we need to conduct resampling? Are
by
Peng Ren
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AFNI Message Board
Dear,
I am just curious of the details of this warning, why it's saying surface self intersecting? would you mind show more details about this?
Thanks for your great patience and kindness!
Best,
Peng
by
Peng Ren
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AFNI Message Board
Dear ptaylor,
It does product the anatomical image after skull stripping and the final output of preprocessing for participant 1, but with several successive warning like this for this participant.
I am just curious of what's happening to make sure it's been properly operated.
Best,
Peng
by
Peng Ren
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AFNI Message Board
Dear Glen,
I only have two subjects with oblique images, to reduce processing of the other subjects' images, i want to remain the original grid of these two oblique images, is it reasonable?
I'm not sure why you need the grid to be the same as another dataset when clearly this is in a different space.
Besides, i am not quite clear for "this is in a different space" you
by
Peng Ren
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AFNI Message Board
Dear,
I am conducting skull stripping with 3dSkullstrip, with warning as below:
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 84, avoid_vent -1
It's difficult for me to figure out what happens to my data, could you give me some idea?
Best,
Peng
by
Peng Ren
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AFNI Message Board
Dear,
Thanks for your immediate reply!
Is it possible for me to get the same grid as the original image? the default option of 3dWarp will output same voxel size in all three dimensions, while what i want is the original one (3.125 x 3.125 x 4.50) .
Moreover, it's seems to have no effect to make adjustment for severely oblique image with both 3dWarp and some other warp commands, are th
by
Peng Ren
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AFNI Message Board
Dear,
I'm conducting preprocessing on resting state fMRI data and make alignment for anatomical and resting state fMRI data, with warning:
If you are performing spatial transformations on an oblique dset,
such as ./101-BOLD-EC-volreg-lp-dt_temp+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on t
by
Peng Ren
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AFNI Message Board
Dear Paul,
Great thanks for your reply, I will try it again!
Best wishes,
Peng
by
Peng Ren
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AFNI Message Board
Dear all,
I want to find the difference of voxel-wise connectivity strength between group1 and group2,with 58 subjects in group1 and 24 subjects in group2.
To do this, i tried 3dttest++ with covariates, 3dttest, and 3dMEMA with covariates, with all the findings failed to pass the cluter size threshold, with p equals 0.001, 0.01 and 0.02 in turn.
i find a concept c
by
Peng Ren
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AFNI Message Board
Dear rick,
Thanks for your immediately reply, I get the difference between 3drefit and 3dresample, but get confused by "leaves the brain in the same location in space, but changes it on disk", could you explain further?
As I known, there are four attributes in afni related to orientation:
1.the -orientation option showed by 3dinfo
2.R-L extent ... option showed by 3dinfo
3.th
by
Peng Ren
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AFNI Message Board
Dear ptalylor,
Thank you for your immediate reply.It helps me a lot with this problem, I just express your explanation again in my words for confirmation: the "x,y,z extent" information in the header is just preference of showing 3D volume in afni, so it won't change with 3dresample. if i want to change the orientation of the dataset, 3dresample -orient should be used. Is
by
Peng Ren
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AFNI Message Board
Dear,
when I look at 3dinfo's output for a dataset, I just get a little confused by the conflicting orientation, just like this:
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -102.774 -to- 105.914 -step- 3.312 mm [ 64 voxels]
A-to-P exte
by
Peng Ren
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AFNI Message Board
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Pages: 12