Show all posts by user
History of AFNI updates
Page 2 of 4
Pages: 
1234
Results 31 - 60 of 104
Ok no problem, I see that the discussion is expending a little too much =)
by
Doughboys
-
AFNI Message Board
For the Jacobean, you certainly *don't* want the global translation and rotation included (those are the rigid body parts of the transform).
Sure this is what I thought, but I was confused when you said: If in subject space... no issues.
do you want the global shear and scaling from the affine, as well as the local displacements from the WARP, or just local displacements themselves?
by
Doughboys
-
AFNI Message Board
Update,
I actually still have the problem (a few co-registration misalignments) of macaques anatomical T1 to the template (out of 90 success, not bad!)
to resume:
- something not normal with aff_move_opt. It seems that you can only use one option and not combine multiple ones.
- _shft.nii.gz = far from the BASE. The orientation (mostly in SI axis in my case) is not correct (not sure actual
by
Doughboys
-
AFNI Message Board
Hello,
So, I actually find that the mistake was coming on my side (my study template was not centred on 0).
Animal_warper seems to have worked without problems on 90 macaques images... I still need to validate that precisely =)
Note that, I previously skullstrip and centred on 0 my original anatomical images before passing them into animal_warper
Just to clarify my previous question,
by
Doughboys
-
AFNI Message Board
Hello AFNI team,
I would like to use a WARP in tlrc_NL_warped_dsets the has been created using 3dNwarpCat.
This WARP originated from multiple .1D and WARP files and works perfectly when used with 3dNwarpApply.
The problem is that if I only input 1 WARP (and the anat file) in volreg_tlrc_warp, it doesn't work because volreg_tlrc_warp needs 3 files.
Can I add a .1D file with just 0?
by
Doughboys
-
AFNI Message Board
thanks, Paul!
I was using the shft_WARP provided by animal_warper, so I should use _shft_base2osh_WARP (this is the only WARP in the indiv space) instead in 3dNwarpFuncs? and then send the Jacobian in the template space?
I am trying to identify more precisely what is wrong with @animal_warper, I will give updates if I managed to find it, do you have any suggestions?
I just find somethin
by
Doughboys
-
AFNI Message Board
Hello,
I am also facing the same problem
I will try your fix tomorrow, thank you
As far as I remember this recent modification was made to automatically recenter the anatomical image to the template
Something might be wrong with it.
Also, I was wondering if the scaling or shearing performed in align_epi_anat.py would modify any volume quantification performed when using VBM with on the ext
by
Doughboys
-
AFNI Message Board
Hello AFNI team,
It seems that the option -qw_opts in @animal_warper doesn't work.
I systematically got:
** unknown option -qw_opts
when trying to use it.
I am working on 'Version AFNI_21.2.03 'Nerva''
Clément
by
Doughboys
-
AFNI Message Board
Hello Pawel,
exactly
3dSkullStrip, -skullstrip_opts -monkey and cost lpa+ZZ did the trick (I also used -resample off).
Happy to help you!
by
Doughboys
-
AFNI Message Board
Yes, I think that this one has MION (I need to ask...)
However, my guess was good!
lpa+ZZ associated with the option -monkey did the trick for those who it didn't work previously!
by
Doughboys
-
AFNI Message Board
Hello pt!
Thank you for your answer that will really help!
Here is an example of the kind of image that I am working with:
Indeed, I was already using -cost lpa+ZZ that is actually working fine on half of the images. lpc+zz and nmi doesn't work at all.
I am confident that changing the epi strip parameters might help!
I will let you know
Thank you for explaining align_epi_strip_
by
Doughboys
-
AFNI Message Board
Hello AFNI team,
I would like to "classically" co-registrate a BOLD image to a template using the movement parameters of the anatomical image, in a primate, with afni_proc.py.
for a typical command please see:
I would like to know if there is a way to modify the "3dSkullStrip or "3dAutomask" parameters in -epi_strip of afni_proc.py?
For example, if I would like
by
Doughboys
-
AFNI Message Board
Hello,
Still stuck with that problem.
Any idea of what I could do to fix it?
Thanks!
by
Doughboys
-
AFNI Message Board
Hello,
>Thank you, I was not sure about this. I replaced it but it did not change anything on the error message.
Thank you for your help!
Clément
by
Doughboys
-
AFNI Message Board
Hello AFNI team,
I have a problem concerning the use of RetroTS.py:
I managed to convert SCANPHYSLOG data (from Phillips) in BIDS using:
If anyone knows a better way?
I tried to run the command:
/abin/RetroTS.py -phys_file SCANPHYSLOG20210420091530.tsv.gz \
-v 1 -n 600 -prefix physio_regressors.1D -phys_json SCANPHYSLOG20210420091530.json
my .json looks like:
{
&quo
by
Doughboys
-
AFNI Message Board
Hello Daniel,
Sorry to jump on this subject.
I was actually looking for a human 3D Brodmann atlas. Do you think that I can use that one (https://afni.nimh.nih.gov/pub/dist/atlases/Brodmann_MM/) for publication?
Is there a publication that I can read/site associated with this atlas?
By any chance, do you know an atlas that I can use to complete this one with subcortical, brainstem and cerebe
by
Doughboys
-
AFNI Message Board
Ok, sry. I thought that I have done something wrong with my script but it appears that your surprise made me think that maybe it was the viewer (ITK-snap)?
And the answer is yes...
Thank you for your anwer!
Clément
by
Doughboys
-
AFNI Message Board
Thank you Gang,
In what sense those 4 sub-bricks are empty? All zeros in the brain? Are sub-bricks 5, 7, 9 and 10 fine?
== Yes, they are just filled with 0 and 5, 7, 9, 10 are fine.
Also, I have tried with other images and I have got the same result.
by
Doughboys
-
AFNI Message Board
Hello Gang,
I am sorry to come back to that question.
There are a few things that are not clear yet on my side.
Here is the last update of the script:
3dLME -prefix 3dLME_glt.nii.gz -jobs 20 -mask brainmask_nolr_func.nii.gz \
-model "Sexe*age" -qVars "age" -ranEff "~1+age" -num_glt 4 \
-gltLabel 1 "05MF" -gltCode 1 "Sexe : 0.5*M +0.5*F age
by
Doughboys
-
AFNI Message Board
Hello pt,
The results of the QC has been sent.
Here is the command:
@animal_warper -input dset_anat_deob -base studytemplatebrain -atlas Brain_label.nii \
-outdir ouput_dir_a_id -ok_to_exist -align_centers_meth OFF -cost nmi -skullstrip mask_brain.nii.gz
afni_proc.py -subj_id a_id -script ouput_dir_a_id + /proc. + a_id -scr_overwrite -out_dir ouput_dir_a_id + / + a_id + .resul
by
Doughboys
-
AFNI Message Board
Hello AFNI expert,
I am trying to interpret the quality check of the output of afni_proc.py in order to see if one or multiple metrics could help me to understand the quality of my results in resting-state fMRI in dogs. I basically tested 4 sequences, 1 SE EPI and 3 GE EPI. I co-registrate all the BOLD to a template and performed a seed base analysis.
Then, it appeared that the SE EPI gave m
by
Doughboys
-
AFNI Message Board
Hello pt,
Thank you for these clear explanations!
Typically, the range of censored time point fractions is around 5 on 275-time points. One subject is around 34 but it never goes up to 20%.
I am a little bit concern by the raw ALFF and fALFF images produced with this analysis, to my knowledge, high ALFF values are essentially around the DMN. However, I do not observe that here.
assuming
by
Doughboys
-
AFNI Message Board
Hi pt,
I followed your advice,
I tested my human dataset with 'scale' and without and I not obtain the same results, especially for the comparison of aged versus young.
With 'scale', the difference of ALLF in the DMN seems to not be less important.
Since I am not sure how scale would affect the results, do you think that scaling is recommended for comparison between group
by
Doughboys
-
AFNI Message Board
Hi pt,
#1 no worries, in my second message I found that the TR (for an unknown reason, this dataset comes from another lab) was detected in a millisecond instate of a second. Fixing that TR in the header did actually solve my problem.
#3 for mALFF, I am not sure why, but the reproducibility in my lemurs gave me good and meaningful results that allowed me to characterize some interesting ch
by
Doughboys
-
AFNI Message Board
Thank you for your answer!
1) It was 100% linked to the resolution, now it is more about 20min/run...
2) 2.800003 2.799999 2.799998 80 80 42 280 Rest_BOLD.nii.gz
2) It is 24 for me
3) mALFF should be a voxelwise value... so I don't understand this statement:
"Also, to calculate mALFF, the result is strongly dependent on the mask used. Is there a way with afni_proc to add th
by
Doughboys
-
AFNI Message Board
Problem solved,
the program died with
3dDeconvolve -input pb05.imapt1s080.r01.scale+orig.HEAD -mask full_mask.imapt1s080+orig -ortvec motion_demean.1D mot_demean -ortvec motion_deriv.1D mot_deriv -polort 4399 -float -num_stimts 0 -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -fitts fitts.imapt1s080 -errts errts.imapt1s080 -x1D_stop -bucket stats.imapt1s080
++ 3dDeconvolve extending num_stimts f
by
Doughboys
-
AFNI Message Board
Hello AFNI experts!
I have two basic and quick questions,
I am not used to working with human datasets and I am surprised with the processing time with afni_proc.py
I have human BOLD images at a resolution of 2.8 and afni_proc.py takes more than 5h per subject and my computer has good characteristics.
Is that normal?
afni_proc.py -subj_id imapt1s080 -script Imapt1s080/proc.imapt1s080
by
Doughboys
-
AFNI Message Board
Hi pt,
Thank you for the update!
I was not aware of this new version. The new atlases that come with it are going to be extremely useful! This paper is really interesting!
I send to you one of the anatomical images that doesn't work. I think that it might be interesting to see why it used to work with my previous version of animal_waper and now it doesn't? On my side, I will try the
by
Doughboys
-
AFNI Message Board
Salut pt!
The problem occurred when changing from
Version AFNI_20.1.06 'Otho'
to
Version AFNI_20.2.12 'Aulus Vitellius'
the version of the nmt is 1.2
and my command was:
@animal_warper -input /Oliver2019_02_02/anatT1_deob.nii.gz -base /nmt_1.2/NMT_SS.nii.gz -atlas /nmt_1.2/D99_in_NMT_with_WM.nii.gz -outdir
/7_animal_warper/Oliver2019_02_02 -ok_to_exist
th
by
Doughboys
-
AFNI Message Board
Page 2 of 4
Pages: 1234