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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 moderator,
I performed cortical thickness analysis as below
1. cortical parcellation using freesurfer
2. perform @SUMA_Make_Spec_FS
3. peform mris_convert -c lh.thickness lh.white lh.thickness.asc
4. perform 1dcat lh.thickness.asc'[4]' > rh.thickness.1D.dset <- what's mean the [4] ?
5. perform MapIcosahedrone -overwrite -ld 90 -fix_cut_ssurfaces -dset_map lh
by
leetaey
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AFNI Message Board
Hi,
After performing 3dTrackID, when I load the tract.lt.thal.mpfc_000.PAIRMAP+orig on AFNI (not on SUMA), I just see the monocolor result only.
How can I set the AFNI option for visualize coloful results?
by
leetaey
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AFNI Message Board
Hi, Paul
thank you for all of our nice reply.
When I drew the tracktography, I used a netrois containing two ROIs.
I wonder if it is possible to apply an exclusion mask when performing 3DTrackID?
How can I do?
by
leetaey
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AFNI Message Board
Thank you very much for all of your nice and gentle reply!
Lastly, I'd like to know full name of abbreviation in grid file
NT ?
fNT ?
PV ?
fNV ?
NV ?
FA - fractional anisotropy
sFA - s?
MD - mean diffusivity 1+2+3/ divide 3
sMD - s?
L1 - direction 1
sL1 - s?
RD - radial diffusivity 2+3/ divide 2
sRD - s?
L2 - direction 2
sL2 -s?
L3 - direction 3
sL3 -s?
by
leetaey
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AFNI Message Board
# FA
4.130704e-01 4.096045e-01
4.096045e-01 3.369234e-01
..
Then, what should I write the FA value on the paper?
is it 0.409..?
by
leetaey
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AFNI Message Board
Thank you for nice reply!
I have one more question.
I drew a minip tractography.
I made a netrois file, which is made with two roi files.
However, when I view the output grid file, it contains the following:
leetaeyui-Mac-Pro:1001 leetaey$ cat tract.r.tha-ofc_000.grid
# 2 # Number of network ROIs
# 17 # Number of grid matrices
# WITH_ROI_LABELS
001 002
by
leetaey
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AFNI Message Board
I just want to get a outline of the brain (brain.nii in freesurfer/mri folder)
by
leetaey
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AFNI Message Board
Hi, everyone
I have one problem about make a gii file
When I conduct 3dSkullStrip command, I can get a gii file with -o_gii option
However, I wonder how can I control the stripping threshold.
If I use the already stripped brain image from freesufer's parcellation process, 3dskullstrip make the overstripped result.
So, I'd like to know the exact script to make a gii file
by
leetaey
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AFNI Message Board
Hi afni expert!
I have a question about surface image.
After conducting 3dSkullstrip command, I could get a brain surface gii file with -o_gii option
however, when I use a already skullstripped file from recon-all in freesurfer, how can I make gii surface file without re-skullstrip 3dSkullStrip command?
I'm looking forward you reply!
by
leetaey
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AFNI Message Board
Hey afni experts,
I have two question about these lovely scripts on how to rotate gradient vectors for DTI data.
1.
Currently we collect our DTI data oblique, then we have been using 3dWarp -oblique2card to deoblique it.
Therefore we need to rotate our bvecs accordingly. Is there anyway to modify this script based on header attributes from 3dWarp?
2.
It is same as described ab
by
leetaey
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AFNI Message Board
Thank you for your nice advice!
it was well done!
I'd like to ask one more question.
I used to get the FA values using trackvis program through inconvenient manual method (overlap trk file and FA file)
But, after draw tractography from 3dTrackID, how get I get the tracts' FA value?
by
leetaey
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AFNI Message Board
Hi all,
I'd like to ask one question about the make -netrois ROI.nii for 3dTrackID
when I conduct to draw mini-probabilistic tracktography with 3dTrackID, it was conducted pretty well with whole brain mask image
. 3dTrackID -mode MINIP -dti_in DT -mini_num 7 -uncert UNCERT_UNI+orig <some details..> -netrois whole_brain_mask.nii -logic OR -prefix o.MP -dt_trk_out o.MP
howev
by
leetaey
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AFNI Message Board
In deterministic tractography using 3dTrackID, AFNI uses FACT algorithm.
But, I found the tensorline algorithm make better image than that of FACT when I conducted this with diffusion_toolkit.
Do you have the plan to upgrade the 3dTrackID for better options of tractography algorithm such as kutta, fact, factid, tensorline etc..
by
leetaey
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AFNI Message Board
When I perform skulls tripping, I use 3dSkullStrip command,
and, in order to get a gifti file, I write additional option -o_gii as below
>> 3dSkullStrip -input anat+orig. -prefix anat_ns -o_gii anat_ns
In this situation, if I want to use pre-skullstripped anatomical file from FreeSurfer
How can I get gifti file from FreeSurfer anatomical file without AFNI's skullstripping
by
leetaey
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AFNI Message Board
thanks for nice answer, but I have one more quetion.
While I used 3dDWItoDT command, it produce FA and MD, and I also made RD from L2 and L3 data
however, MD and RD value is higher than about 100 - 1000
Many paper showed that MD and RD values are not much than 1
How can I calculate the raw values of MD and RD to modified(?) values which are not exceed 1
Could you give some advic
by
leetaey
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AFNI Message Board
Hi, I have one question.
While I perform 3dDWItoDT commands
It provide the several result files such as DT, FA, MD, L1, L2, L3, V1, V2, V3 ..
In trackvis, however, it needs tensor.nii, e1, e2, e3, v1, v2, v3, adc, ...
how can I change my AFNI result files to trackvis format? Is DT is same with tensor.nii?
by
leetaey
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AFNI Message Board
Thank you !!!
I have one more question.
If I want to extract specific threshold mask image
(just like in FSL : fslmaths original.nii -thr 10 -uthr 10 mask.nii AND fslmaths mask.nii -bin binary.nii)
Could you tell me about exact syntax of 3dCalc?
by
leetaey
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AFNI Message Board
I have several 4D dwi.nii images
I'd like to extract a b0 image from 4d DWI image using 3dcalc of AFNI
but, I don't know exact syntax (just like in fsl "fslroi original.nii extract.nii 0 1")
Is there anyone who know well the syntax of 3dcalc in AFNI?
by
leetaey
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AFNI Message Board
Thanks for your helpful answer!
but, I have one more question.
How much is the optimal number of -mini_num in mini-probablistic tractography command?
I'm always wonder about these issues for decision points
TaeYoung
by
leetaey
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AFNI Message Board
Hi. I'm newbie in AFNI
Recent days, I have some trouble with 3dDWUncert
3dDWUncert command needs exact iterantion number
Below is example
3dDWUncert \
-inset TEST_FILES/DTI/fin2_DTI_3mm_1+orig \
-prefix TEST_FILES/DTI/o.UNCERT \
-input TEST_FILES/DTI/DT \
-grads TEST_FILES/Siemens_d30_GRADS.dat \
-iters 50
In above command, -iters 50 is de
by
leetaey
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AFNI Message Board