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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
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I'm consistently encountering a 3dvolreg error for a subset (N=3) of my subjects, the crash log contents are provided here:
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 m
by
Dan
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AFNI Message Board
Hi,
After looking through the afni_proc.py script, it appears that the default FD threshold is set to 0.3mm, though from this twitter post (https://twitter.com/AFNIman/status/977622189712211968), reducing it further to 0.2mm is desirable. Fortunately I have a fMRI task study with a cohort of healthy adults, so I wanted to see if setting the FD threshold somewhere in the range of 0.2-0.5mm seem
by
Dan
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AFNI Message Board
Hello,
I am trying to analyze data from a task consisting of two conditions where reaction times varied greatly: ranging from 1-30 seconds. To alleviate this, I've put trials into bins (2-sec) for each condition, and am trying to incorporate this into my design matrix. By binning my trials, I run into situations where some bins contain little data, so an example timing file may be as spar
by
Dan
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AFNI Message Board
Yes, the tissue-based regressors are applied per run.
Thanks for the help!
by
Dan
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AFNI Message Board
Hello,
I'm running into the following error when I try running to3d to convert my DICOM files to NIFTI
to3d -prefix dan_test -time:zt 72 276 1000 FROM_IMAGE *_-0002*.dcm
++ to3d: AFNI version=AFNI_16.3.00 (Oct 10 2016) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
*+ WARNING: TR expressed in milliseconds will be converted to TR=1.000000s
++ Cou
by
Dan
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AFNI Message Board
Hello,
I have extracted WM and CSF signal prior to scaling my data, which I plan to use in 3dDeconvolve. Currently, the CSF units are in the 4400 units range, and the WM is in the 5500 units range. Given that the signal of my scaled data is around 100 units, would the large discrepancy in signals cause any potential issues? I noticed this thread (https://afni.nimh.nih.gov/afni/community/board/
by
Dan
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AFNI Message Board
Hi Gang,
Sorry for the late reply. I'm performing an ROI time-series analysis where I don't want to assume the shape of the signal. The direction I've taken (for now) is to just extract the ROI BOLD time-series from the preprocessed data (after spatial smoothing and intensity normalization). From there I've been using the timing files to match the BOLD time-series to each
by
Dan
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AFNI Message Board
Hi Gang,
There is some varied duration across across trials in the same stimulus category. I've looked a little into dmUBLOCK, but it seems very similar to dmBLOCK, which assumes a canonical hemodynamic response function, which I'm trying to avoid with an FIR. If the best way then is to model each trial separately, does that mean that I need to re-order my stimulus timing files so t
by
Dan
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AFNI Message Board
Hello,
I've been going back and forth on deciding on what 3dDeconvolve options to use for my data, and wanted to see if I could get an expert opinion on the matter (I apologize if this is a lot). What I want to do is select a model that does not assume a canonical HDR model, but instead models with a Finite Impulse Response. It seems to me that CSLPIN will do this, but I wanted to double
by
Dan
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AFNI Message Board
I'm running AFNI and SUMA on my university's HPC, so I'm not entirely sure off the top of my head if there are any special graphics/video drivers ( I can ask one of the admins though). Since I don't have root privileges, I wouldn't be able to install mesa-utils and libgl1-mesa-glx myself, but I'll them about it first to see how to proceed.
Thanks,
Dan
by
Dan
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AFNI Message Board
Hi,
The output from afni_system_check.py is:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-862.11.6.el7.x86_64
version: #1 SMP Fri Aug 10 16:55:11 UTC 2018
distribution: Red Hat Enterprise Linux Server 7.5 Maipo
number of CPUs: 24
apparent l
by
Dan
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AFNI Message Board
Hi,
I'm doing a surfaced-based analysis on my data, and am trying to use SUMA for visualization purposes. I ran Freesurfer's recon-all on my data, then used @SUMA_Make_Spec_FS to create the SUMA directory and files. Once I finished preprocessing my data, I tried using SUMA with the command suma -spec ${subj}_lh.spec -sv ${subj}_SurfVol+orig. &
The output from the command line
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Dan
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AFNI Message Board
Hi Rick,
I'm a little confused regarding Freesurfer's usage here. I had run Freesurfer prior to @SUMA_Make_Spec_FS, where Freesurfer was used to reconstruct surfaces from T1w/T2w structural images, and the the motion-corrected functional series (after resampling to T1w space) is sampled to the surface. In total, Freesurfer is generating surfaces in the subjects' native space, an
by
Dan
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AFNI Message Board
Thanks Rick,
I reorganized things, and now it runs smoothly using this code:
hemi=(lh rh)
runs=`ls $data_dir/*run*preproc.nii* | wc -l`
for r in `seq 1 $runs`
do
r=0$r
for h in ${hemi[*]}
do
if [ ! -f $data_dir/sub-${s}_run-${r}_${h}_v2s.niml.dset ]; then
3dVol2Surf \
-spec $freesurfer_dir/std.60.${s}_${h}.spec \
-surf_A smoothwm
by
Dan
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AFNI Message Board
Hello,
I am planning to perform an ROI analysis, and want to project the volumetric data to the surface for better viewing. It seems like AFNI's 3dVol2Surf is what I need to use, but this is my first time using the command, so I wanted to make sure that I am using it properly. I used @SUMA_Make_Spec_FS beforehand to create a SUMA directory with the SUMA-specific files. Then I use 3dVol2Su
by
Dan
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AFNI Message Board
Hello,
I have been pre-processing my data using FMRIPREP, which incorporates FSL's mcflirt for volume alignment rather than AFNI's volreg. As such, I can't use volreg's -1Dfile option to create the motion parameters. Foruntately, fmriprep provides a confounds.tsv file for each EPI run, which includes motion parameters. What I've done is concatenate all the confounds.ts
by
Dan
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AFNI Message Board
I re-ran everything where I requested one core (job), 20gb of virtual memory, and a wall time of 2 hours. I was able to get the output from the -x1D, -x1D_uncensored, -cbucket, and -bucket commands, but not the -errts output due to this error:
Fatal Signal 15 (SIGTERM) received
Last STATUS: convert to p-value
mri_fdrize
mri_fdr_curve
THD_create_one_fdrcurve
THD_create_a
by
Dan
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AFNI Message Board
Thanks Rick,
Since it seems that modeling attenuation is a bit difficult (particularly since I don't have a great idea of when or how it would affect the response amplitude), would it be more sensible to focus on duration modulation instead? If so, I can switch the stim_times lines to the following:
-stim_times_IM 1 $data_dir/$s/derivatives/Timing_Files/AM/mut.txt 'dmBLOCK(1)'
by
Dan
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AFNI Message Board
Hi Rick,
Thank you for your response. Correcting the last parameter in the -concat option did indeed resolve the 2nd set of warning message I was getting.
Regarding the timing files, this is related to a previous question I posted earlier (https://afni.nimh.nih.gov/afni/community/board/read.php?1,159421,159421#msg-159421), where I provided one of my timing files, which only has duration mo
by
Dan
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AFNI Message Board
Hello,
I am noticing some warning message that I don't fully understand, and am worried are affecting the output. I run 3dDeconvolve after using 3dTcat to combine the functional runs (following intensity normalization) into one file. The 3dDeconvolve command I'm using is:
3dDeconvolve \
-input $data_dir/$s/fmriprep/sub-${s}/func/*smooth_scale_all*
by
Dan
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AFNI Message Board
Hello,
I am trying to perform duration and amplitude modulation together, and according the the 3dDeconvolve help file, the best option for this is the -stim_times_AM2 option. My main question is in relation to the ordering of the stim_times files when I specify this part of the 3dDeconvolve command:
-stim_times_AM2 1 Timing_Files/Cond1.txt 'dmBLOCK(1)' -stim_label 1 Cond1 \
-sti
by
Dan
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AFNI Message Board
I actually just came across this thread:
It seems that I would need to run "3dresample" or "3dWarp -deoblique" in order to adjust the orientation?
by
Dan
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AFNI Message Board
Hello,
I have a NIFTI file that I converted from the raw DICOMS, and when I checked the orientation with 3dinfo, this was the output:
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -92.188 -to- 98.312 -step- 1.500 mm [128 voxels]
A-to-P extent: -132.969 -t
by
Dan
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AFNI Message Board
Hi Peter,
I just realized that the issue was that I was using the wrong repetition time. I was using the time from the anatomical and functional DICOMS, but the spin echo TR is different. I should've noticed that when I kept getting the message "** max slice time 15725.0 outside TR range [0.0, 2200.0]"
Thank you for your help.
by
Dan
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AFNI Message Board
The command I'm using is: to3d -prefix data1.nii.gz -time:zt 84 2 2200 FROM_IMAGE -session $dest_dir *.dcm
I'm converting spin echo DICOM files to NIFTI, and I've run this before on my local machine with no issues at all, so I'm unsure by why this issue is occurring on the linux cluster that I'm working from.
by
Dan
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AFNI Message Board
I'm running to3d from the command line, but the to3d GUI keeps popping up and forcing me to continue manually. Is there a way to prevent this from occurring?
by
Dan
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AFNI Message Board
Hello,
I have been doing some skull stripping on an MNI template; however, I am still getting some extra non-brain tissue. I was wondering if there is an AFNI tool that would allow me to manually remove the voxels of the extraneous tissue?
by
Dan
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AFNI Message Board
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