Show all posts by user
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
Page 3 of 4
Pages: 1234
Results 61 - 90 of 119
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
Dear AFNI experts,
I just tested the new version of animal_warper. Everything works fine, but I just find something not normal when the bain mask is produced at the end. I guess it is based on the skullstriped anatomical image in the template space that is sent back into the subject space? It seems that the mask is cut when compared to the previous version. In consequence, in macaque, I am losi
by
Doughboys
-
AFNI Message Board
Hi AFNI expert,
is it still not possible to performed VBM with AFNI?
if not, can I use (SPM, ANTS, or something else) to calculate the voxel-wise volume ratio changes after using @animal_warper?
Thanks a lot!
Clément
by
Doughboys
-
AFNI Message Board
Hi -pt,
Sorry to come back with this old topic but my new problem is actually related to the co-registration of these animals.
By having a deep look at the co-registrated functional images and extracting some signal with the D99 atlas, I finally understand why the correlation coefficients were not great.
It seems that a slight section of voxels in the grey matter (edge) of the functional
by
Doughboys
-
AFNI Message Board
Salut pt,
No problem I will send you that straight away.
Tks!
Clément
by
Doughboys
-
AFNI Message Board
Hello AFNI experts
I would like to use a macaque atlas that is in the F99 template space.
In order to do that, I would like to send the atlas in the nmt template.
To do so I used:
@animal_warper -input nmt_1.2/NMT_SS.nii.gz -base Human_macaque_equivalent/F99_with_skull.nii.gz -atlas RM_inF99.nii.gz -outdir Human_macaque_equivalent/InD99 -skullstrip Human_macaque_equivalent/F99_with_sku
by
Doughboys
-
AFNI Message Board
Dear AFNI expert,
I am trying to coregistrate fMRI images to their anatomical and then to a Template for another species (mouse lemur) and with afni_proc.py
To do so, I applied the exact same script as described here for macaques:
I am using a template that we published:
In order to use the script and afni_proc.py, I had to change the template space name to NMT but I guess that is
by
Doughboys
-
AFNI Message Board
Hi, Pt-
First, thank you for your answer,
I have done the analysis and:
Re. "Since I increase the number of regions and so the number of subdivisions in each atlas I may expect a relatively linear increase of the mean ReHo for each atlas?"*
Re. "Does this will really identify an atlas that could be 'ideal' for a correlation matrix analysis?"
--Yes, the incre
by
Doughboys
-
AFNI Message Board
Hello AFNI expert,
I would like to compare the ability of different atlases to extract a homogeneous BOLD signal in each ROI.
I created different atlases based on ICA. I built one atlas per component number (for ex: from 5 to 30 components so I have 25 atlases).
I was thinking of using 3dReHo with -in_rois one each atlas and calculating the curve of an increase of ReHo per atlas.
Since I
by
Doughboys
-
AFNI Message Board
Hi Gang,
Thank you again for your answer,
For the record, here is the new command:
3dLME -prefix /3dLME_glt.nii.gz \
-jobs 8 -model "gender*age" -qVars "age" -ranEff '~1+age' \
-num_glt 5 \
-gltLabel 1 '05MF' -gltCode 1 'gender : 0.5*M +0.5*F age :' \
-gltLabel 2 '1MF' -gltCode 2 'gender : 1*M -1*F age :' \
-gltL
by
Doughboys
-
AFNI Message Board
Hi Gang,
Thank you again for your help!!
As advised, I ran the command:
3dLME -prefix 3dLME_.nii.gz -jobs 8 \
-model "gender*age" \
-qVars "age" \
-ranEff '~1+age' \
-dataTable
Subj age Sexe InputFile
Oliver 1128.0 M /Oliver2019_02_02_ztest.nii.gz \
Oliver 1247.0 M Oliver2019_06_01_ztest.nii.gz \
Oliver 1353.0 M Oliver2019_09_15_ztest.nii.gz \
Oliv
by
Doughboys
-
AFNI Message Board
Hi Gang,
Thank for your answer!
The subjects were not measured exactly at the same age but within the same session. The effect of interest is the age and I am looking to observe a correlation with the modification of the connectivity strength. As an example, I previously did an extraction of the ALLF signal with an atlas and then calculated the Repeated measures correlation coefficient within
by
Doughboys
-
AFNI Message Board
Hello AFNI experts in statistics,
I would like to measure the effect on age on a longitudinal fMRI resting-state dataset (4 repeated measures at a different age) with covariate such has gender.
I already performed the seed base analysis on each subject and now I want to regress the age on each statistical maps in order to observe the age related variation of the DMN connectivity (with gen
by
Doughboys
-
AFNI Message Board
Hi AFNI expert,
I finally found the solution and I will probably be able to be more clear.
Two things were impacting the results of this analysis and fixing it has tremendously improved the quality of the coregistration:
1. Deobliquing the data prior to @afni_proc.py can be dangerous if like in my dataset the EPI and the anatomical images have different FOV orientations.
3drefit
by
Doughboys
-
AFNI Message Board
Hi --pt,
So sorry for the confusion,
1. The first group of monkeys (including the image that I send to you) has successfully ended. All the images are well aligned with the template (thank you again!) using the protocol that I describe here:
2. I have a second group of monkey that has been scan with another coil. For almost all these 8 monkeys, the coregistration between the functional
by
Doughboys
-
AFNI Message Board
Page 3 of 4
Pages: 1234