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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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I wanted to also add that I tried using the following:
align_epi_anat.py -anat mni_template.nii.gz -epi ZHRTS1.nii.gz -epi_base 0 -master_epi mni_template.nii.gz -epi2anat -giant_move
And it sort of works, however, the FOV for the mni_template.nii is larger than the one for the ZHRTS1 image volumes so it is not clear to me how to get the FOVs to match.
All I am wanting to do is to ali
by
maitra
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AFNI Message Board
Hi,
I have a set of 12 structurals images (T1-weighted being the first one) and I am trying to get them registered to a template. The template file is called mni_template.nii.gz and the 12 structurals are in ZHRTS1.nii.gz.
I tried the following:
3dvolreg -twopass -twodup -heptic -clipit -rotcom -verbose -verbose -prefix S3.2nd.REG -base 'ZHRTS1.nii.gz[0]' mni_template.nii.g
by
maitra
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AFNI Message Board
Rick,
Thanks very much for this clarification. I had forgotten about the ACF blur parameters, thank you!
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
I have been running 3dClustSim using the following:
3dClustSim -mask mask.nii.gz
and I get:
$ 3dClustSim -mask mask.nii.gz
++ 3dClustSim: AFNI version=AFNI_20.2.08 (Jul 31 2020) [64-bit]
++ Authored by: RW Cox and BD Ward
++ 31596 voxels in mask (45.04% of total)
++ Startup clock time = 0.1 s
++ Using 8 OpenMP threads
Simulating:0123456789.0123456789.0123456789.0123456789.0
by
maitra
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AFNI Message Board
Hi,
I am a statistician and AFNI still continues to be new to me, after 4-5 years of using it intermittently (sorry if the answers are obvious).
So I am trying to redo the results on the datset in:
The authors used AFNI but are cut off from their code (at work) because of the pandemic so can not send me their AFNI code/scripts. But these are general questions (I think) and I think that
by
maitra
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AFNI Message Board
Rick,
Thanks, very much for looking into this. I am really grateful. Unfortunately, the dataset is made available here: http://www.ccbi.cmu.edu/Suicidal-ideation-NATHUMBEH2017/Just-NatHumBeh2017-data-and-code.html
It just has the values stored as an array, and they say it is in NMI space so that is what we have proceeded with. I guess that the infomation is not enough for spatial display then
by
maitra
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AFNI Message Board
Rick,
Thanks very much! I had originally tried what you suggested, but my activation regions are coming to be outside the brain. This is a mismatch. (I have attached the figure.)
Here are the parameters that I used while saving (in R):
y <- nifti(x, pixdim = c(3,3.5,3.5,6), qform.code = 4, sform.code = 4, intent.code = 5, xyzt.units = c("mm", "mm", "mm"
by
maitra
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AFNI Message Board
Rick,
Thank you, I was putting the sform_code to be 4 (because as per the authors of the dataset, the coordinates are in MNI space).
Btw, if I save the sform and qform codes to be 0 then I do not get anything to show up at all on SUMA. However, the slices are activated, as in the attached screenshot.
With AFNI and SUMA, I used:
afni -niml&
suma -spec suma_mni/N27_both.spec -sv
by
maitra
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AFNI Message Board
I guess Rick already sent me details and I have uploaded the file in the location asked.
by
maitra
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AFNI Message Board
Rick,
Yes, of course, I am happy to send it to you. Let me know where.
Here is the output of nifti_tool:
$ nifti_tool -disp_hdr -infile Bstand2-int-FAST-death-negative.nii.gz
N-1 header file 'Bstand2-int-FAST-death-negative.nii.gz', num_fields = 43
all fields:
name offset nvals values
------------------- ------ ----- ------
sizeof_hdr
by
maitra
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AFNI Message Board
HI,
I am sorry: this may be a straightforward question but I can not figure out why 3dinfo is crashing with a segmentation fault.
This file is an activation map obtained by the FAST-fMRI algorithm in our R package (RFASTfMRI). What RFASTfMRI does is creates an activation map and as an array. We have multiplied the activation map with the Z map to only have the Z map wherever there is activa
by
maitra
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AFNI Message Board
Thank you for your response and your example!
It works as advertised.
However, from what I understand, in your example, you use the -geomparent on TT_N27_junk_8.nii.gz to get the slice thickness, etc for the file to be created. I do not have this file. I only have my ascii files and I know that my values are correlations and of dimensions 50 x 61 x 23 with voxel dimensions : 3.5 x 3.5 x 6
by
maitra
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AFNI Message Board
Hi,
I have been given a 3D image volume after normalization in MNI space. The dimensions of the image volume are (in MNI space, 3.125x3.125x6 mm voxels, 50x61x23 voxels) as per the README file.
It is a correlation functional image volume in text format. I would like to display this image volume overlaid on an anatomic image (the standard MNI anatomic image, since I did not get a separate an
by
maitra
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AFNI Message Board
Bob Cox Wrote:
-------------------------------------------------------
> I see -- you are new to AFNI.
>
> Always look at the data. Just because a data was
> put on a Web repository doesn't mean it is OK. We
> have seen things where images were oriented
> incorrectly, "skull stripped" images still had the
> skull on, and so forth. AFNI is good for look
by
maitra
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AFNI Message Board
RWCox Wrote:
-------------------------------------------------------
> That EPI dataset looks kind of small (in space).
> Only 71 mm in extent from L-R (half the brain
> width, roughly) and also in A-P, and only 35 mm in
> I-S. If you look at these two datasets in AFNI, do
> they properly overlap? That is, if the EPI
> dataset is the underlay and the brain mask dataset
by
maitra
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AFNI Message Board
Hi,
I am a statistician: please pardon the naivette in asking this question but I am trying to use AFNI to massage my functional data in anatomic space.
I have an anatomic mask in registered space of the following dimensions, according to 3dinfo:
$ 3dinfo highres001_brain_mask.nii.gz
++ 3dinfo: AFNI version=AFNI_16.2.18 (Sep 19 2016) [64-bit]
Dataset File: highres001_brain_mas
by
maitra
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AFNI Message Board
Rick,
Thanks! So, there is no published reference yet, I guess?
Btw, as an aside, does not the use of the mixture of the Gaussian and mono-exponential create issues with using the 3d FFT? (This mixture can not be decomposed for each dimension.) Is the result very different (in terms of fitting) if a mixture of the Gaussian and monoexponential (with the same parameters) were fit in each dime
by
maitra
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AFNI Message Board
Hi,
I tried it, using the default 3dclustsim values but the result does not appear to change (in the SUMA rendering) if I change the number of voxels so I was not sure that I was doing this correctly. Since you say it should be possible, I will try this again.
Btw, I was reading:
and there is this statement:
"Notably, real FMRI data does not actually have a Gaussian-shaped ACF, so t
by
maitra
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AFNI Message Board
Hi,
I have a t-statistic image stored in nifti format. This is obtained from a non-AFNI source. Is it possible to perform cluster-thresholding and display this image in AFNI? If so, how?
Many thanks and best wishes,
Ranjan
by
maitra
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AFNI Message Board
Thanks! I thought my NumLock key does not do much but I will keep track of it. This is another aspect that I was unaware of, so thanks again for point this out to me.
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hi,
Just wanted to mention that an update to the binary (I had last updated earlier this year) appears to have solved my issues with printing for now.
Thanks again for all the help!
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
QuoteWhile the cursor is over the SUMA window, hitting 'ctrl + r' should 'r'ecord/save an individual image (in a subdirectory called SUMA_Recordings/.
Thanks! Hitting ctrl-r or even just r does not what you say it should and what it used to. Instead what I get is that small notification window and the following similar message at the prompt:
++ Notice SUMA_R_Key (SU
by
maitra
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AFNI Message Board
Hi,
I have a strange problem. I get suma working and then I press "r" a window (Nice SUMA_R_Key: Oversampling now set to 2" appears. In the past, I thought I had to press shift-D and I get a window which would allow for saving to different file formats. Nothing of the sort happens now for me.
Any suggestion on how to print the SUMA images?
Many thanks and best wishes,
Ran
by
maitra
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AFNI Message Board
Dan,
Thanks again for the clarification! How are the percentiles calculated? Are they raw percentiles of the test statistic,or is there something more sophisticated than that?
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Thanks! What does the "%" next to the "autoRange" do?
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hi,
I am still new to AFNI, but I think that I should ask about the scale for the display on the AFNI viewer. So, I have a display viewer viewing my functional images overlaid on the anatomical images. I have checked and my t-statistics range from -4.65 to 5.35. However, the "OLay" runs from -7.64777 to 7.485167. Interestingly, this is also what 3dInfo on the file says.
$ 3di
by
maitra
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AFNI Message Board
Thanks: but I have only one subject. Sorry, but my issue was that the display (in AFNI) is giving me maps that also show activation outside the brain. So, I was asking if there was a way to get these outside activation areas out without doing the calculations separately: unless I am misunderstanding, your response seems to indicate not. '
Thanks again!
Best wishes,
Ranjan
by
maitra
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AFNI Message Board
Hello,
I have used AFNI (uber_subject.py) to create my statistics datasets which are stored in stats.Imag_anat2epi_REML+tlrc. But I notice that in the display, I get "activation" using FDR even in the background region. I do have a few masks stored in there: full_mask.Imag_anat2epi+tlrc and mask_epi_extents+tlrc.
I was wondering: is it possible to use these masks in the display? I
by
maitra
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AFNI Message Board
Hello,
I have used AFNI (uber_subject.py) to create my statistics datasets which are stored in stats.Imag_anat2epi_REML+tlrc. But I notice that in the display, I get "activation" using FDR even in the background region. I do have a few masks stored in there: full_mask.Imag_anat2epi+tlrc and mask_epi_extents+tlrc.
I was wondering: is it possible to use these masks in the display?
by
maitra
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AFNI Message Board
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Pages: 12345