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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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Thanks, will check out the new 3dTortoisetoHere program.
Also, I found out from Tortoise developers that their bmatrix format (in 2.01 version) is actually xx xy -xz yy -yz zz. So the bmatrix and vectors will always need a Z flip when exporting to AFNI. I heard that they may work on incorporating this into a newer version, such that their export to AFNI function will take care of the reorderi
by
akwl
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AFNI Message Board
Hello again,
The flipping did work! I did a z-flip on eigenvector 1 from Tortoise. The resulting map for a corpus callosum ROI looks as expected, and very similar to the one using AFNI generated FA/V1 on the same dataset.
Thank you so much for you help!
-akwl
by
akwl
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AFNI Message Board
I just put together a rudimentary script and it seems to work. Please let me know if there a better way to do it. Thank you!
#3dcalc -a "DTI/${name}_V1+orig[0]" -expr "a" -prefix "DTI/${name}_V1_0+orig"
#3dcalc -a "DTI/${name}_V1+orig[1]" -expr "a" -prefix "DTI/${name}_V1_1+orig"
#3dcalc -a "DTI/${name}_V1+orig[2]" -expr &
by
akwl
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AFNI Message Board
Thank you very much for your reply.
I'm going to try flipping the vector components one at a time to see if it works.
In 3dcalc, is there an option to select a specific subrik for calculation while keeping the other subrik unchanged? Or do I need to separate the vector file into 3 different files, do the calculation, and merge them back as one?
by
akwl
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AFNI Message Board
FATCAT - 10 years ago
Hello experts,
I have been following the FATCAT algorithm in analyzing a DWI dataset, but ran into problems when using Tortoise generated tensors and scalar metrics for tractography on AFNI. However, I heard that this pipeline has been tested extensively and worked well during the AFNI bootcamp. So I'm wondering if I am missing something.
For example, I ran a simple deterministic trac
by
akwl
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AFNI Message Board
Hello,
I read from the program help that 3dDWItoDT requires bmatrix to be in xx, yy, zz, xy, xz, yz format, whereas 3dDWUncert expects xx, xy, xz, yy, yz, zz. Is that correct? If yes, is there a program to convert the bmatrix accordingly?
The 1dDW_GradOrMat has a 2* factor for the off diagonals. Is there a way to skip that? or shall I convert to gradient?
Thanks!
-akwl
by
akwl
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AFNI Message Board
Dear experts,
I'm trying to run tractography with 3dTrackID using a ROI map in tlrc space, but my DWI and all another scalar maps are in subject space (they are all output from TORTOISE).
Would you recommend warping the ROI map to the individual subject space, or transforming the DWI etc to Talairach space? For the latter, how can I rotate the Bmatrix or gradient files along with the
by
akwl
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AFNI Message Board
Thanks for your help. I'm sharing your suggested solution here:
*****************************
if I convert your input file to be floats instead of scaled shorts, then I don't get an error:
$ 3dcalc -a rs_map+tlrc -expr 'a' -prefix rs_map_FLOAT -float
$ 3dROIMaker -inset rs_map_FLOAT+tlrc. -inflate 2 -prefix TEST2 -skel_thr 0.2 -skel_stop -thresh 1 -wm_skel subject_FA+
by
akwl
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AFNI Message Board
It does work when I remove the skeleton option. It also work when I use a Z-map instead of a T-map. Am I not supposed to use a T-map?
It would great you can look at my data set. Where shall I sent it?
Thanks!
by
akwl
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AFNI Message Board
Yes I've run Do_03 and it worked just fine. I also just updated the binaries to yesterday version, but still get the same error.
That make me wonder if there is something wrong with my data set.
by
akwl
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AFNI Message Board
Hello,
I received the following error when running 3dROIMaker using an one-sample t-map from a RSFC analysis. Could you let me know what went wrong? Thank you!
# 3dROIMaker -inset ${name}_rsfc_tmap+tlrc"[0]" \
# -thresh 4.966 -volthr 184 -inflate 2 \
# -wm_skel DT/${name}_FA+tlrc \
# -skel_thr 0.2 -skel_stop -mask ${name}_MASK+tlrc \
# -prefix ${name}_ROI -overwrite
++ V
by
akwl
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AFNI Message Board