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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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Thank you for all your responses and clarifications!
3dTcat solution worked well.
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daisyburr
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AFNI Message Board
I converted a BRIK and HEAD file to nifti using 3dAFNItoNIFTI. The resulting .nii file is more than 4 dimensions and can't be read by some standard softwares, resulting in errors such as "Input data has incompatible dimensionality: Expected dimension is 4D and you provided a 5D image". Is there a way to restrict the dimensions in the conversion or modify the header so it is 4D (x,
by
daisyburr
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AFNI Message Board
Yes, right, thank you. Just wondering if you guys have a built in way to relabel the labels (stim 0...136) with the actual stim labels bc it is different order per subject? Thanks!!!!!!!
by
daisyburr
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AFNI Message Board
Here is the full output of
3dinfo -verb stats.A001240.results+tlrc
(note that each subjects stim order is randomized)
3dinfo -verb stats.A001240.results+tlrc.
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Nov 1 2015) [64-bit]
Dataset File: stats.A001240.results+tlrc
Identifier Code: XYZ_RXBgwhDOmyaI5hujC5Tmdw Creation Date: Tue Jan 30 19:19:22 2018
Template Space: MNI
Dataset
by
daisyburr
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AFNI Message Board
Okay, that clarifies my confusion, thank you.
For extracting and relabeling post hoc, what order will the files be in? How do you know what coefficient # corresponds to?
by
daisyburr
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AFNI Message Board
Okay, thanks. It isn't resting state so i looked further, and I discovered this issue:
I have 136 regressors, so I used _regress_stim_types IM, entered all 136 regressor labels, and one block regressor (see script):
foreach subject (A001240)
afni_proc.py \
-subj_id $subject.$label \
-dsets $subject/run1+orig \
$subject/run2+orig \
$subj
by
daisyburr
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AFNI Message Board
Sorry to post so much today...I am dealing with a very different type of design and computer than what I have typically encountered.
I have a similar error to this chain. When running the preprocessing script, everything runs smoothly until:
if ( -e @ss_review_basic ) ./@ss_review_basic
tee out.ss_review.A001240.results.txt
./@ss_review_basic
./@ss_review_basic: Permission denied
Th
by
daisyburr
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AFNI Message Board
Is there any update on "BIDS-ification of AFNI scripts"?
by
daisyburr
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AFNI Message Board
Just switched to a new high performance cluster and forgot to update binaries in my profile...now I have:
/opt/afni/2017_10_2/afni
Thank you very much! this worked. now the output is:
set OutlierCheck =
set OutPrefix = OutBrick
to3d -prefix OutBrick_run_005 -@
++ to3d: AFNI version=AFNI_17.2.16 (Jul 8 2015) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon pro
by
daisyburr
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AFNI Message Board
Hey Rick,
Sorry for the delayed response!
Here is the output you requested:
afni -ver
Precompiled binary linux_openmp_64: Nov 1 2015 (Version AFNI_2011_12_21_1014)
which tcsh
/bin/tcsh
ls -l GERT_Reco_dicom_005
---------- 1 dburr rc-DBIC 315 Jan 30 08:41 GERT_Reco_dicom_005
head -n 3 GERT_Reco_dicom_005
#!/bin/tcsh
# This script was automatically generated by 'Dimon
by
daisyburr
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AFNI Message Board
Hi,
I am trying to convert my raw data using the dimon conversion package, which I have never had issues with in the past.
Both
Dimon -infile_pattern '005*/*.dcm' -gert_create_dataset -gert_write_as_nifti
(from outside the anatomical folder)
and
Dimon -infile_prefix 000 -dicom_org -gert_create_dataset
(inside the anatomical folder)
produce this error:
++ writing dimon f
by
daisyburr
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AFNI Message Board
Hey Rick,
Script with this command:
-regress_stim_types IM ONSETS/unlabeled.txt \
It is thinking IM is a text file and outputting:
** A1D: failed to read data file IM
** failed to load stimulus timing file 'IM'
by
daisyburr
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AFNI Message Board
Oops. nevermind. Just understood this all. Thanks for pointing me toward IM.
by
daisyburr
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AFNI Message Board
Okay, thanks. I just want to clarify though, that is a block design, not event-related. So I am confused how this would output a beta weight for each condition without knowing the timing of each block for each run? The existing onsets files only have onsets for condition, not block. So I was assuming I would need to revise the onsets to be like:
example onset 1:
18 #run 1 block 1
* #run 2
by
daisyburr
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AFNI Message Board
Thank you! I will look into that now. But I still need to recreate all the onset files and include those in the generating script, right?
So it would look like:
set label = ulab_block
foreach subject (A000442 A000443 A000452 A000453 A000454 A000455 A000479 A000484 A000485 A000487 A000488 A000493 A000498 A000500 A000522 A000526 A000580 A000581 A000582 A000583 A000584 A000585 A000587 A000
by
daisyburr
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AFNI Message Board
Hello,
I am figure out how to re-preprocess my data in order to extract out stats and nifti files for each block, instead of each run or each condition within a run. For example, in my initial preprocess, my generating script (below) resulting in stats files that I could 3dBucket into to extract nifti files that were an average beta weight for entire condition (unlabeled in the below):
af
by
daisyburr
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AFNI Message Board
With the advanced version, are the commands to get the ISI stats from ID files different?
For basic version, I used:
timing_tool.py -multi_stim_dur 5 5 5 -multi_timing stimes.0001_*.1D -multi_show_isi_stats
by
daisyburr
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AFNI Message Board
Precompiled binary linux_openmp_64: Apr 27 2017 (Version AFNI_17.1.02)
by
daisyburr
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AFNI Message Board
Also, I had someone else recopy, save and run the script and they get the same error...
by
daisyburr
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AFNI Message Board
Hi Rick,
No...I still get:
0000nums: Subscript out of range.
It looks like this line is not properly saving:
-save_3dd_cmd cmd.3dd.$iter \
Meaning this line searches and finds nothing, leading to an error and it not iterating:
set nums = ( `awk -F= '/'"$pattern"'/ {print $2}' out.3dD.${iter}` )
But I do not know why it is not saving! I checked fo
by
daisyburr
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AFNI Message Board
Thanks, Rick. Almost working! There is one error that I have gone over and over am not fixing.
0000nums: Subscript out of range.
It looks like this line is not properly saving:
-save_3dd_cmd cmd.3dd.$iter \
Meaning this line searches and finds nothing, leading to an error and it not iterating:
set nums = ( `awk -F= '/'"$pattern"'/ {print $2}' out.3dD.${
by
daisyburr
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AFNI Message Board
The full script script intended for uniform rest with no average, min, or max is here:
#!/bin/tcsh
set iteration = 100 # number of iterations to compare
set outdir = stim_results_uniform # directory that all results are under
set LCfile = NSD_sums # file to store normal standard dev sums (root mean square of the measurement error #variance for each conditi
by
daisyburr
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AFNI Message Board
Hi Rick,
Thanks so much for this really helpful response.
I will check with my group about the 11 sec average rest, that does seem like a lot. Thanks for pointing that out. But actually, we don't want an average rest at all.
In terms of trying one with the uniform_rand dist:
# execution parameters
set iteration = 100 # number of iterations to compare
set outdir
by
daisyburr
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AFNI Message Board
Actually i fixed this, I just needed to execute it in tcsh.
So the output of sorting:
sort -n stim_results/NSD_sums | head -1
0.247900 = 0.0822 + 0.0820 + 0.0837 : iteration 0076, seed 1234643
Does this mean iteration 76 had the highest efficiency?
Output of:
timing_tool.py -multi_stim_dur 5 5 5 -multi_timing stimes.0001_*.1D -multi_show_isi_stats
is this:
ISI statistics (3 element
by
daisyburr
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AFNI Message Board
Thanks, Rick. This is really clear and very helpful program. I fixed that # but am still getting an error in the same location:
afni_make_randomtiming_3dDeconvolve: line 70: syntax error near unexpected token `('
afni_make_randomtiming_3dDeconvolve: line 70: `foreach iter (`count -digits 4 1 $iterations`)'
I also tried replying the "0000" with "100" to match t
by
daisyburr
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AFNI Message Board
Hi,
I am trying to use the @stim_analyze script to simulate a design for optimal ITI efficiency.
The experiment has:
-3 stimuli classes: pos, neg, neu
-135 stims (45 in each class)
-15 stim reps per run
-1s TR
-5 sec stim duration
Does it make sense to run the below script utilizing make_random_timing input for 3dDeconvole to optimize efficiency?
This is the modified script:
#
by
daisyburr
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AFNI Message Board
Hi Rick,
Actually, I didn't use timing_tool.py yet, but thought there may be capability within the program to assist here, which is why I included it in the title.
At the moment, I am away from my lab computer with the timing files, but it is actually just a simple .xls Excel file that is output based on my Python script (which is executed for stimulus presentation via PsychoPy) for
by
daisyburr
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AFNI Message Board
Hi Rick,
I am getting ready to analyze a study where the ISI and onset timing files are unique to each subject (totally randomized). I am going to direct my preprocessing script to each subjects txt files using {$subj} in the proc. But I am dreading manually creating each subjects files in gedit on Dartmouth's server from the Excel files on my local computer, especially because copy and
by
daisyburr
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AFNI Message Board
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