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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 Rick,
While describing to your my task design, I realized the stim_dur is actually fixed....it's the total trial duration and ITI that are randomized. I was able to generate condition.1d file after fixing the "bug".
I have been following the steps here:
Will study the PPI example you provided.
Thank you very much for your help!
Kitty
by
kittyzxu
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AFNI Message Board
Hi Rick,
Thank you so much for your reply! Really appreciated!
I have three trial types (all mixed in one run), but within each trial type, there are different events 1) initial fixation on, 2) target appears on the periphery, 3) subject makes a response with a fixed response window(this response window is the same for all trials), and while subject was making a response 4) another stimulus
by
kittyzxu
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AFNI Message Board
Hi AFNI expert,
After reading through timing_tool.py I am still stuck with making condition.1D file for PPI analysis.
This is the stimulus_timing.txt file (each row is a run)
10.5 34 78 102 109 115 167.5 192 214 224.5 274 315.5 323 382 395.5 428
32.5 44 88 95 102 114 173 192.5 254 280 298.5 329.5 390 396 414 446.5
38.5 59 76 115 147.5 184.5 230.5 279 284.5 292.5 343 361.5 376 402 408 4
by
kittyzxu
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AFNI Message Board
Hi Afni experts,
I am trying to do PPI analysis and am stuck at step 4 (see below)
4. Obtain the interaction regressor
First create a 1D (one column) file, conditionA.1D, with 0's (at those TR's where condition A does not occur), 1's (at those TR's where condition A occurs).
My condition files are two separate .txt. files.
sub_conditionA1: 78 102 109 115 274 3
by
kittyzxu
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AFNI Message Board
Hi Rick,
I checked the data structure over the weekend and found a mistake of choosing the right data sets.
3dinfo -prefix -n4 -d3 sl_result_27BD_aw+tlrc sl_result_28KX_aw+tlrc sl_result_29LG_aw+tlrc. sl_result_30CG_aw+tlrc.
sl_result_27BD_aw 80 95 75 1 2.000000 2.000000 2.000000
sl_result_28KX_aw 80 95 75 1 2.000000 2.000000 2.000000
sl_result_29LG_aw 80 95 75 1 2.000
by
kittyzxu
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AFNI Message Board
Hi Rick,
These data sets are accuracy maps from searchlight analysis using PyMVPA. Individual's accuracy map was obtained on original space, and was later warped into Talairach space using auto_warp.py. I then used autoMask for each individual's dataset, and then used 3dcalc (amongest) to make a union of all subjects' mask (i.e. group mask). 3dttest++ was used to attempt to do g
by
kittyzxu
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AFNI Message Board
Hi Rick,
Sorry for the confusion. Here are examples of 4 datasets
3dinfo -prefix -n4 -d3 sl_result_27BD+tlrc sl_result_28KX+tlrc sl_result_29LG+tlrc. sl_result_30CG+tlrc.
sl_result_27BD 88 88 47 1 -2.400000 -2.400000 3.000000
sl_result_28KX 88 88 48 1 -2.400000 -2.400000 3.000000
sl_result_29LG 88 88 47 1 -2.400000 -2.400000 3.000000
sl_result_30CG 88 88 46 1 -2.
by
kittyzxu
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AFNI Message Board
Hi Rick,
subject 88 88 47 1 -2.400000 -2.400000 3.000000
Thank you!
by
kittyzxu
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AFNI Message Board
Hi Gang,
Thank you for your quick reply.
Follow your suggestion, i did this:
3dttest -set1 subj1+tlrc subj2+tlrc subj3+tlrc subj4+tlrc subj5+tlrc subj6+tlrc -mask mask_sl -base1 0.5 -prefix sl_stats
got the following msg:
3dttest: AFNI version=AFNI_2011_12_21_1014 (Sep 25 2015) [64-bit]
++ For most purposes, 3dttest++ should be used instead of 3dttest!
** FATAL ERROR: unrecognized o
by
kittyzxu
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AFNI Message Board
Dear AFNI experts,
I am trying to do a t test using a group of 6 datasets, within a group mask (mask_sl), against a single value 0.5. The voxel number for each subject is different, and the mask_sl is a UNION of all 6 subjects' datasets.
i have the following script
3dttest++ -singletonA 0.5 -setB subj1+tlrc subj2+tlrc subj3+tlrc subj4+tlrc subj5+tlrc subj6+tlrc -mask mask_sl -prefix
by
kittyzxu
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AFNI Message Board
Hi Daniel,
Thank you for your reply. And i did this and it worked!
auto_warp.py -base TT_N27+tlrc. -input subjectdata.nii -skull_strip_input no -warp_dxyz 2 -output_dir subjectdata -affine_input_xmat ID
Just a side note, this is what says on the auto_warp.py manual, and my interpreation of "-skull_strip_input" is "Do not skullstrip input dataset", and by choosing yes
by
kittyzxu
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AFNI Message Board
Hi again!
How could I ran auto_warp.py with @auto_tlrc at the same time? The auto_warp.py script repeatedly bugged out at the affline aligment error (where 3dWarpDrive was being executed), so I called the 3dWarpDrive separetely so I could increase the -maxite to 500. Then 3dWarpDrive ran though, but I don't know what's next step. I looked up the auto_warp.py script to see if I could
by
kittyzxu
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AFNI Message Board
Hi Daniel,
Thank you for your quick reply!
both my dataset and the tlrc template I am using are WITHOUT skulls.
(i thgoutht "-skull_strip_input yes" means no skull stripping...am I wrong?)
I tried @auto_tlrc, and it worked, but I thought the reason to use auto_warp.py instead of @auto_tlrc is because the former does non-linear warping, while the later uses linear warping (less p
by
kittyzxu
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AFNI Message Board
Dear afni supporting staff members:
I am trying to execute the following command to warp a brain image from +orig to +tlrc
auto_warp.py -base TT_N27+tlrc. -input subjectdata.nii -skull_strip_input yes -warp_dxyz 2 -output_dir subject_folder
I have done the procedure with a few subjects successfully, but with one subject, i kept getting error messages (see below).
Here is the error mes
by
kittyzxu
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AFNI Message Board
Hi,
I know I asked this question earlier regarding transforming group ROI back to individual space. But I realized the solution that was proposed before dealt with anatomically defined ROI. How can I transform a group ROI (which is defined functionally) back to individual functional scan (instead of anatomical scan)?
Thank you!
Kitty
by
kittyzxu
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AFNI Message Board
Hi,
I used 3dQwarp to do non-linear warping during the initial preprocessing. Now, I am trying to transform group ROI back to the original individual space so I can do MVPA analysis on an individual basis.
I read this:
Example of warping +tlrc results back to +orig space of some subject
(get xform matrix, apply it, tell dataset it is not in orig space):
cat_matvec subj1_anat+tlrc:
by
kittyzxu
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AFNI Message Board
Hi AFNI friends,
I was trying to use uber_subject.py for running my analysis and I ran into a problem with volume registration.
uber_subject.py offers three options: volreg base string (first/third/last) . However, I don't know how to apply this to my specific case because I have 6 functional run plus one structural run. The structural one is in the middle, that is, i have 3 functional r
by
kittyzxu
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AFNI Message Board