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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 46
Hi Daniel,
At the last step of inverse processing, we copied the attribute IJK_TO_DICOM_REAL from the original dataset to the reobliqued dataset using:
3drefit -atrcopy OriginalAnatomy+orig. IJK_TO_DICOM_REAL reoblique+orig
And the Afni GUI didn't give an angle difference warning anymore.
But just now, I find the help files of 3drefit say the option -atrcopy can't really ch
by
Zhang Yu
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AFNI Message Board
I am very sorry for so many questions. But now I have only the last two questions to verify:
1. The inverse matrix, NOT the forward matrix is outputted to the terminal by 3dWarp -verb?
2. I can change the deobliqued dataset to match the original dataset perfectly using the following codes?
#3dWarp -oblique2card -prefix card OriginalAnatomy+orig.
cat_matvec -ONELINE card+orig::WARPDRIVE_MATV
by
Zhang Yu
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AFNI Message Board
Hi Daniel,
Thank you!
I seem to have found an easy way to do the inversion:
As mentioned before, I got the deobliqued dataset using the code:
3dWarp -oblique2card -prefix card OriginalAnatomy+orig.
When I open the card+orig.HEAD file now, I find two new attributes that are different from the attributes in OriginalAnatomy+orig.HEAD:
type = float-attribute
name = WARPDRIVE_MATVEC_FO
by
Zhang Yu
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AFNI Message Board
Hi AFNI experts,
The anatomy dataset had been deobliqued using 3dWarp for each subject firstly:
3dWarp -oblique2card -prefix card OriginalAnatomy+orig.
And then many ROIs were drawn on card+orig.
Now I want to transform these cardinal ROIs back to match the original oblique dataset (OriginalAnatomy+orig) perfectly.
And I have tried the method like this:
3dWarp -card2oblique OriginalA
by
Zhang Yu
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AFNI Message Board
Hi Daniel,
Thanks a lot for your answers!
The transformations from EPI to T1 and from T1 to tlrc space were calculated firstly in my processing. And these transformations were catenated and applied later. So the skull stripped output was used here.
Yu
by
Zhang Yu
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AFNI Message Board
Hi AFNI experts,
I had done the following preprocessing to the T1 image:
3dWarp -oblique2card -prefix T1_de T1+orig
#new anat just be intermediate, stripped; transformation is not applied.
align_epi_anat.py -anat2epi -anat T1_de+orig \
-save_skullstrip -suffix _al_junk \
-epi epi+orig -epi_base 0 \
-epi_strip 3dAutomask \
-v
by
Zhang Yu
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AFNI Message Board
Thank you!
So the average of the 'tpattern' values is the default reference time.
But I am not sure what is the exact meaning of "the average of the 'tpattern' values".
The timing correction code is :
3dTshift -tpattern seq-z -quintic -prefix pb01.sub1.r01.tshift pb00.sub1.r01.tcat+orig
And the TR is 2 s in my experiment.
So I guess the average of the 'tp
by
Zhang Yu
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AFNI Message Board
Hi Rick,
Thank you!
The only different fields are ‘pixdim’ and 'slice_duration' if I choose some other EPI files for comparison:
nifti_tool -diff_hdr -infiles ver1.nii ver2.nii
name offset nvals values
------------------- ------ ----- ------
pixdim 76 8 1.0 1.5 1.5 1.49995 4.0 0.0 0.0 0.0
pixdim 76 8 1.0 1
by
Zhang Yu
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AFNI Message Board
Hi AFNI experts,
The dicom files in my fMRI experiment were transformed into the .nii format by MRIconvert firstly before preprocessing.
I found some fields in the .nii files generated by different versions of MRIconvert are different, though the inputted data are exactly the same.
nifti_tool -diff_hdr -infiles ver1.nii ver2.nii
name offset nvals values
---------------
by
Zhang Yu
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AFNI Message Board
Hi experts,
The block durations in my experiment with the bock design were 12.5167 s. I wonder whether 3dDeconvovle can work well with these decimal durations?
I am not sure whether these commands for de-convolving are appropriate or not in AFNI:
...
-local_times \
-stim_times 1 stimuli/exp.1D 'BLOCK(12.5167,1)'
by
Zhang Yu
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AFNI Message Board
Hi afni experts,
I need a group mask of superior colliculus in TT_N27 space. Do you know which atlas includes superior colliculus in afni?
Thanks
Yu
by
Zhang Yu
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AFNI Message Board
Hi Rick,
Thanks a lot!
Besides the ISIs, the post stimuli rests are also too long. Are there any parameters in make_random_timing.py to make the rest at the end of each run changing at a specific range (e.g. from 10 to 16s)?
Yu
by
Zhang Yu
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AFNI Message Board
Hi Rick,
Thanks for replying me!
I thought the longer ISIs the better the deconvolved results. And I thought we needed a slow event design to get better signal change curve of each stimulus. So the long rests were expected. But I am not sure about this. I thought the distribution of events should look evener but some ISIs are too small and the others are too big.
I also tried to reduce run_len
by
Zhang Yu
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AFNI Message Board
Hi afni experts,
I have three conditions in my new event-related fMRI experiment: exp1,exp2 & control. I am interested in two t-test pairs among these conditions: exp1-control & exp2-control. So I search the best experiment sequence use the method provided by @stim_analyze: generating sequence using make_random_timing.py, calculating NSD using 3dDeconvolve and choosing the sequence usi
by
Zhang Yu
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AFNI Message Board
Hi afni experts,
I need an optimal experimental sequence for my event-related fMRI experiment. And I found two scripts on the internet to do this: @DesignSearch and @stim_analyze. These two scripts look different. I want to know which one of them is better?
Besides,
Thank you!
Yu
by
Zhang Yu
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AFNI Message Board
Thank you, Peter!
The average is the default to the '-tpattern' option. But the default of '-slice' option is not provided in the help link. We don't know which option is activated preferentially if the reference slice is not inputted. If the '-slice' option is activated in this situation, I need to know its default reference.
by
Zhang Yu
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AFNI Message Board
Hi AFNI experts,
My fMRI data were acquired with 26 slices in descending sequence. I used the code below for timing correction before:
3dTshift -tpattern seq-z -quintic -prefix pb01.sub1.r01.tshift pb00.sub1.r01.tcat+orig
Now I need report the timing correction parameters in my manuscript. But I am not sure what is the reference slice used in my code.I have checked the usage of 3dTshift and f
by
Zhang Yu
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AFNI Message Board
Dear Daniel, I appreciate what you did! The compatible version of Brainnetome atlas is pretty good. But the transformed Brainnetome atlas for TT_N27 template seems not to be so good because some regions are not a whole. That is, some tiny parts of a specific brain region are away from the main region cluster. Finally, I would use TT_desai_ddpmaps you mentioned.
Thank you!
by
Zhang Yu
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AFNI Message Board
The values in the mask generated using TT_desai_ddpmaps atlas are not fractions or percentages. These values range from 0 to 255. I don't know how to change probability threshold with specific percentage or fraction into the threshold values corresponding to the values stored in this mask. Because I don't know what the unit of the values stored in the mask is. I guess value '0'
by
Zhang Yu
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AFNI Message Board
Hi Daniel,
I think your suggestions are very helpful. But I also have two kinds of questions:
1. I have tried to use the TT_desai_ddpmaps atlas.
1.1 Many regions are included in this atlas:
whereami -show_atlas_code -atlas DD_Desai_PM
++ Input coordinates orientation set by default rules to RAI
Atlas DD_Desai_PM, 150 regions
----------- Begin regions for DD_Desai_PM atlas---------
by
Zhang Yu
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AFNI Message Board
Thank you, Daniel!
I am interested in the activities of different insular subregions recently. I find the available atlases of insular subregions on the Internet are all in MNI space. For example, The atlases which include 5 subregions provided in this site (Faillenot, I., Heckemann, R. A., Frot, M., & Hammers, A. (2017). Macroanatomy and 3D probabilistic atlas of the human insula. NeuroImag
by
Zhang Yu
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AFNI Message Board
Hi Afni experts,
Because my fMRI data were normalized to the TT_N27 template before, I have some questions when drawing anatomical ROI:
1)Can I use these MNI atlases (CA_..._MNIA) to generate ROI?
I don‘t think these MNI atlases should be used because my fMRI data is in Talairach space.
2)Which atlas can I use?
TT_Deamon or CA_N27_LR? Are they in Talairach space?
3)How to transform the a
by
Zhang Yu
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AFNI Message Board
Thank you!
The OLay and Thr volumes are really beta coefficients and corresponding t-statistic in my case. I found the results (voxels survived) would become exactly same if the p-value threshold in the "Pos button" condition was set to two times bigger than that in the "Pos Only" popup condition. That is, if the p-value threshold is set to 0.05 in the "Pos button"
by
Zhang Yu
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AFNI Message Board
Hi afni experts,
The results of the two methods to see positive value only are very different although the same threshold is used:
1.Use the button "Pos?".
2. Change the chooser from "Pos & Neg" to "Neg only" on the popup menu called by right-clicking on the label at the top of the threshold slider.
Why? And what is the relationship between these two met
by
Zhang Yu
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AFNI Message Board
Thank you, Bob!
I notice that the parameter d is omitted in your code (TWOGAMpw(4,5,0.2,12,7)). Do you think the duration should be set to 0 in my case though the stimuli duration is 2s?
By the way, the "TWOGAMpw" option is still unavailable although my afni binaries were updated using "@update.afni.binaries -defaults" this morning (at 18:00 on Wednesday evening 10 Jan 2018
by
Zhang Yu
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AFNI Message Board
Hi Bob,
I am very very appreciated for what you did!
I don't know how these parameters of the two gamma function specified in SPM or BrainVoyager, so I have some more questions:
1) Is the variant d the time duration of stimuli or not? If each event lasts 2s in my event-related experiment, the d should be set to 2?
2) To set these parameters of TWOGAMpw correctly, the signal change
by
Zhang Yu
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AFNI Message Board
Hi afni experts,
I am interested in the superior colliculus (sc) and sc has an optimised HRF with a 4s peak (Wall, M. B., Walker, R., & Smith, A. T. (2009). Functional imaging of the human superior colliculus: an optimised approach. Neuroimage, 47(4), 1620-1627.). The optimised HRF used in the reference is the standard HRF which is a synthetic function produced by combining two gamma functio
by
Zhang Yu
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AFNI Message Board
Thank you, Daniel! I am very appreciated for your new answer!
by
Zhang Yu
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AFNI Message Board
Hi Daniel,
The largest font name is "-sony-fixed-medium-r-normal--24-230-75-75-c-120-iso8859-1" on my Ubuntu. The font package xorg-x11-fonts-misc can't be installed on Ubuntu. Do you know other font packages with large font size?
The XXXfontA, B, C options are pretty good but I have to add these options and some very long font names following the command “afni" in the ter
by
Zhang Yu
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AFNI Message Board
Hi afni experts,
Afni is installed on my laptop which has a screen with very high resolution. The words and buttons on the afni controller are too small to read and operate on. This problem can't be solved by using the option " -XXXfontA fontname " . The fontname is the name of the largest font given by this command:
"xlsfonts | grep -e '--' | grep -e '-i
by
Zhang Yu
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AFNI Message Board
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