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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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Dear experts,
I have a couple questions about the NT parameter from the 3dTrackID *.grid output file.
- I believe streamline count is another term used synonymously with number of tracts (NT), correct?
- Given one subject, if NT = 0 for a region, should all other indices (i.e. FA, MD, RD, etc) also be 0?
- Am I correct that NT and PV should be strongly correlated?
- Related to the above
by
eji
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AFNI Message Board
Ok great, understood.
btw, yesterday I ended up creating a python script that extracts the OR-logic values of FA from MD for each subject into a concatenated csv. Made more sense to just do that. So, no need for you to look at the data I emailed you yesterday for FAT_MVM or tableize.
Looks like I finally made it to the end of my AFNI journey, at least for this project - with a lot of assist
by
eji
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AFNI Message Board
ok, so it seems like a solution could be to use the "-unionize" option in order to have a table including ALL available data from the 318x318 rois, and then replace zero values by "NA" ?
(just wanting to confirm that you are using "zero values" and "missing data" synonymously in your message above)
by
eji
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AFNI Message Board
Hi pt,
ah, I didn't know about FAT_MVM_DEMO but yes that is also suitable.
Oddly, while fat_mvm_prep.py completed for me, not all the roi connections were extracted into _MVMtbl.txt. As I have 318 rois, there should be 318x318 connections including AND and OR-logic. However, only 34 roi connections were extracted:
048__159
058__104
070__071
by
eji
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AFNI Message Board
Hi,
I'm glad I stumbled upon fat_mat_tableize.py, which should make things easier. I'm trying to extract the FA and MD only, from the .grid output of 3dTrackID PROB.
Here is the command I am using:
fat_mat_tableize.py \
-in_csv tableize_CSV.csv \
-in_listfile tableize_LIST.csv \
-prefix tableizeoutput \
-pars FA MD
Questions:
1. What does this error suggest that I receiv
by
eji
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AFNI Message Board
Hi Paul,
Thanks for your suggestion that it could be a memory issue. The test you proposed results in a syntax issue for me because I can't include single quotes within the nohup command (a single quote ends the command).
However, I monitored the memory usage of one subject using htop (it continuously grew... to 48GB by the end... yikes!). Is it possible that there is a bug in the code w
by
eji
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AFNI Message Board
I'm receiving Fatal Signal 11 (SIGSEGV) when I run 3dTrackID PROB in parallel.
It works fine when I run one subject at a time or even a for loop, however I much prefer to run them in parallel to save time.
I have run all commands leading up to this (e.g. 3dDWItoDT and 3dDWUncert) in parallel with no problem, therefore I believe the error is related to AFNI. Any ideas what might be causing
by
eji
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AFNI Message Board
fat_proc_align_anat_pair \
-in_t1w ./T1.nii.gz \
-in_t2w ./data.nii.gz'[0]' \
-out_t2w_grid \
-prefix t1_al
@djunct_overlap_check -ulay data.nii.gz'[0]' -olay t1_al.nii.gz -prefix IMAGE
aiv IMAGE.jpg
by
eji
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AFNI Message Board
Hi pt,
I am now sure that fat_proc_align_anat_pair is not working/aligning on my end. I even went back to the Box drive and downloaded the T1 and T2 I uploaded for you to be sure that we were running it on the same subject. I also tested fat_proc_align_anat_pair for other subjects and each time, the output is not aligned to the T2.
Attached are screenshots from the subject data we both proc
by
eji
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AFNI Message Board
thanks, looking at the 0th volume def helped and it took 2 min to complete.
However, the top is still cut off for me. I've attached what I see when I view t1_aligned_NEW in freeview and also when I align it with data.nii.gz using @djunct_overlap_check.
The t1_aligned_NEW didn't seem to be cut off for you if I saw/understood correctly... or were you suggesting that the EPI distort
by
eji
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AFNI Message Board
Happy new year pt!
Just following up on my previous message: in the case that the T1 and T2 are very far apart to start with (I attached an image before), is there a solution to the problem that fat_proc_align_anat_pair cuts off part of the T1?
Thank you!
by
eji
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AFNI Message Board
ok we have updated our AFNI version
Attached is the screenshot from @djunct_overlap_check with the T1 and T2 data. Does it seem problematic?
Is there a solution to the issue of the aligned T1 (output of fat_proc_align_anat_pair) being cut off? I hope!
Additionally, the command itself (fat_proc_align_anat_pair) takes several hours per subject, even on a 32 core machine!
by
eji
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AFNI Message Board
Hm, I'm getting:
@djunct_overlap_check: command not found
We have Version AFNI_20.1.06 'Otho'.
by
eji
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AFNI Message Board
Hm, so the alignment trims off part of the T1 and it seems to be related to square surrounding the dwi, thus limiting the area (photo attached)
fat_proc_align_anat_pair -in_t1w $SUBJECTS_DIR/$subj/mri/T1.nii.gz -in_t2w $dtipath/$subj/data.nii.gz -out_t2w_grid -prefix t1_aligned
I'm not sure if the output is informative but I am pasting it here:
++ Start script version: 1.2
++ Found i
by
eji
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AFNI Message Board
ok thank you. so basically I could:
Run fat_proc_align_anat_pair to align T1 to T2 and then create the mask from the aligned T1 using 3dSkullStrip and 3dAutomask.
by
eji
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AFNI Message Board
Hi, I would like to create a binary mask of the brain from dwi. I thought the following two steps should be ok:
1) 3dSkullstrip -input data.nii.gz -prefix data_skullstripped.nii.gz
2) 3dAutomask data_skullstripped.nii.gz -prefix data_masked.nii.gz
My questions:
1) Is there any reason I should perform 3dcalc afterward or should my mask be ready as is?
2) The output of 3dAutomask did not a
by
eji
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AFNI Message Board
Yes please, I would feel better if you could take a look at it to double check. Thank you!
by
eji
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AFNI Message Board
so I just ran 3dDWUncert with a binary mask.
Without the mask it took 5 hours for a single subject. With the mask it finished in less than a minute.
I'm shocked by the drastic decrease in processing time.
by
eji
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AFNI Message Board
Hi pt,
I have been checking and it is using all 32 cores on our 32-core virtual machine, with one subject being run on each core at a time. Basically, the memory is being maxed out.
I have a binary mask - would that help?
bval = 1000, 47 gradient directions, 2mm voxel size.
If it comes down to it, could I decrease the # of iterations to an acceptable #, per your suggestion? thoughts?
by
eji
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AFNI Message Board
Hi (probably pt) :)
Per your suggestion, I changed the number of iterations from 50 to 300 for 3dDWUncert. I guess it makes sense that this would now extend the processing time of this command. However, I'm wondering what a *reasonable* amount of time would be. For instance, I am running our subjects (n=330) in parallel across 32 cores. After 3 days, I have gone in to check and it's
by
eji
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AFNI Message Board
Hi pt, yes we obtained T1, T2 and dwis. I don't think T2 was used in any step of the process and tbh I'm not sure if dwis were dual phase encoded.
On a related note, I now left out 3dWarp -deoblique and then ran 3dInfo to look at the data necessary for 3dTrackID:
3dinfo \
> -is_oblique \
> -obliquity \
> -same_grid \
> -n4 \
> -ad3 \
> -prefix \
> $dtip
by
eji
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AFNI Message Board
Hi pt,
The reason I applied 3dWarp -deoblique is because I believe the dwi is oblique. A few weeks ago you asked me to check that the data used for 3dTrackID are on the same grid using 3dInfo (because I was encountering an error when running 3dTrackID). 3dInfo revealed that data weren't on the same grid (see our thread ).
Basically, for some subjects, the angle from plumb for dwi is 6.
by
eji
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AFNI Message Board
Hello, I realized that some of our diffusion data are oblique, therefore I used 3dWarp to deoblique. I then checked the output using 3dinfo. While the angle from plumb is now 0, it appears that the matrix size has changed. It would be helpful if someone could explain why this happened and confirm whether this should be fixed. Thanks!
Below I pasted the input commands of 3dWarp and 3dInfo and
by
eji
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AFNI Message Board
Hi pt.
I finally figured out why some of those files were on different grids. When I transformed the freesurfer file to AFNI, I used the transformation matrix based on oblique dwi data rather than the de-obliqued (3dWarp) data. Thus, this should solve my problem.
It seems like you suggest that I should not use 3dAllineate. Ok.
Further, our collaborators sent their pipeline for dwi pre-proc
by
eji
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AFNI Message Board
Hi pt,
The .annot parcellation was actually sent to us by another group, and is based on the fs_average template, which is why I executed a series of commands to transpose the parcellation onto each individual's surface and then convert to nifti. Am I understanding correctly that your suggestion re @SUMA_Make_Spec_FS should replace mri_aparc2aseg in our pipeline? (to clarify, I never prev
by
eji
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AFNI Message Board
That would be fantastic! I've pasted it below. Hopefully it makes sense.
Steps 1-5 should *theoretically* be the equivalent of fat_proc_map_to_dti I think.
################################################################################
# set path for Freesurfer data
export SUBJECTS_DIR="/home/eji/projects/spins/preproc/freesurfer/subjects/w0"
# set path for diffusion data
by
eji
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AFNI Message Board
To add to my last message: I do indeed have one processing script for everything. I performed each step in batch/parallel for all subjects from beginning to end, minus the very beginning (conversion of dicoms). That is, the converted niftis, bval, bvec etc were given to me. Which is why I'm wondering if the mismatched matrices/datasets is related to the dicom conversion.
by
eji
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AFNI Message Board
Ok I'll investigate. But basically what you're saying is that if the datasets are on diff grids within-subject, it suggests an error during the conversion of the raw dicom files? It wouldn't have happened later during the various freesurfer/AFNI steps?
by
eji
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AFNI Message Board
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