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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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Thanks Rick. So, if I want to do analysis of haemodynamic response for each condition, should I use tent function for blocked design? Also what is the difference between the beta weights and -iresp output for tent function?
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udaykurkure
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AFNI Message Board
Hi,
How to interpret the output of -iresp (Impulse response) option in 3dDeconvolve if I use a BLOCK function instead of a TENT function?
Also how the number of time-points in -iresp option are computed for a block of 30 seconds: BLOCK(30,1)? AFNI gives me 24 time-points (volumes).
Best,
Uday
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udaykurkure
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AFNI Message Board
Hi,
I want to understand the positive/negative values in the output of GLT and SVM. Please let me know if I have understood it correctly.
If I give a contrast [+condA -condB] in 3dDeconvolve, the coefficients brik will have positive values where condA's coefficient were greater than those of condB. Is that right?
If I give label 1 for condA and label 0 for condB, the SVM output (wei
by
udaykurkure
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AFNI Message Board
Hi
This is related to the thread:
I am trying to transform the space from orig->tlrc of be bucket1 (result of glm containing about 50 briks) and bucket2 (result of svm containing a single brik).
When I apply adwarp to bucket1:
- The clusterization didn't work.
- The min-max range is not updated in the new space. It showed the range from bucket1+orig.
- 3drefit -redo_bstats d
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udaykurkure
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AFNI Message Board
Hi there,
I am going through to understand q-values.
Can someone briefly explain what the columns in the .HEAD file under FDR Curve correspond to?
Uday
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udaykurkure
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AFNI Message Board
Thanks Daniel. This is exactly what I was trying to figure out. (by aligning mask I meant to align anat to epi and use the transformation to transform mask to epi space).
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udaykurkure
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AFNI Message Board
Hi,
I created a mask using whereami from TT_Daemon atlas. But when I overlay it on TT_N27 data, it doesn't match well with the region of interest (based on my limited knowledge of anatomy) and also falls outside the brain. What am I doing wrong here?
Thanks,
Uday
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udaykurkure
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AFNI Message Board
Thanks. Here we are assuming that anat (or mask) is aligned to epi (after deoblique), so we can use the function 3dWarp - card2oblique directly to oblique the mask/anat. Don't we need to first align the mask to epi_card and then oblique it?
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udaykurkure
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AFNI Message Board
Sorry but that is still confusing to me.
Let's say I have a mask in cardinal space as my anat+orig. The epi is oblique. How do I transform the mask to epi space (oblique) with the correct header information?
by
udaykurkure
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AFNI Message Board
Thanks. I am using the 2nd option. Here I guess we assume the oblique as cardinal and vice-versa. Is it?
Also, the reoblique data's header still contains "plumb" in "data axes tilt". Isn't that should be oblique?
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udaykurkure
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AFNI Message Board
Hi,
If my mask has many different regions (all have value 1), is there a method in afni where I can get a output mask with only the single largest region?
Thanks,
Uday
by
udaykurkure
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AFNI Message Board
Thanks for the examples.
Quick questions regarding obliquity:
- When I do dry_run for "align_epi_anat.py -epi2anat...-ex_mode dry_run", I observed that it finds obliquity 'Spacing for anat to oblique epi alignment is 1.234567' and later computes the mat.aff12.1d. However, when I test my epi and anat data using 3dinfo for 'is_oblique' and 'obliquity', i
by
udaykurkure
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AFNI Message Board
Thanks for your reply. I am a newbie with afni, so pardon my ignorance.
I would like to avoid aligning stats and anat as it adds another step of interpolation. Is it possible to concatenate the warp from epi->anat->tlrc and then apply it directly to stats+orig?
I had tried to compute and concatenate the transformation matrices (epi->anat->tlrc) and then use 3dAllineate on stats
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udaykurkure
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AFNI Message Board
Hi,
I have 3dDeconvolve results in native fmri space that I need to transform to tlrc space. Either the stats can be directly aligned to the epi atlas TT_EPI or 3dAllineate could be used with a concatenated transformation matrix (al_tlrc). Are there other ways to do this? Which one is recommended? How to evaluate between different transformation results?
Also, should FDR-curves be computed
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udaykurkure
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AFNI Message Board
In the following partial script created by afni_proc, how the mask_anat is being created? Is the 3dmask_tool also creates a mask in addition to perform operations on masks?
Will this mask be different from the anatomy mask created by 3dautomask and resampled to epi grid?
# ================================== mask ==================================
# create 'full_mask' dataset (u
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udaykurkure
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AFNI Message Board
I have not yet. I was thinking of using '3dWarp -oblique2card' but it seems that I can do analysis in the native space directly without deoblique(ing) it. Is that right?
Still it would be good to know the solution for this case.
Thanks.
by
udaykurkure
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AFNI Message Board
Hi there,
For an oblique dataset, if I create a ROI mask after deoblique(ing) the original dataset, how can I transform the mask data to native oblique space?
Thanks,
- Uday
by
udaykurkure
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AFNI Message Board
Hi there,
I am new to AFNI. I want to create a functional ROI from a single fmri run using a statistical test and contrast definition (ROI from functional clusters). Can someone point me to the series of steps and afni commands that I should follow to achieve this?
Thanks.
by
udaykurkure
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AFNI Message Board
Made significant progress with AFNI realtime. I have a few questions:
- What kind of registration cost function is used for motion correction (is it based on position info from headers or image similarity metrics such as correlation etc.)?
- Is there a way to align epi with anatomical in real time?
Thanks.
by
udaykurkure
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AFNI Message Board
Hello Rick,
Thanks for the info. I was able to run some demo with existing data & code.
Where can I find more info on the real-time afni plugin?
-uday
by
udaykurkure
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AFNI Message Board
Hello,
I am new to AFNI and seem to be getting comfortable with the analysis commands and options.
I want to know if we can use it in our rt-fMRI pipeline. I have gone through the previous messages on this board: .
- We will be using a Seimens scanner (mosaic epi).
- I will have access through the network to the shared folder in which the dicom images arrive but I cannot install anyth
by
udaykurkure
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AFNI Message Board