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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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Hey Taylor,
Thanks for the reply. I am following the issue I had in the past (from this thread ). After a series of failures i admit i got discouraged, so I switched to diffusion toolkit (its easier to run through the GUI). The results from the diffusion tookit were better (as in there is actual tracts that make sense now). I noticed that in diffusion toolkit you can select the machine and nu
by
bit-warrior
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AFNI Message Board
Dear Afni experts,
about a while ago i was having issues running diffprep and fatproc on my dwi data. I tried using dtk and everything seems normal; the data makes sense. Is it possible to feed the siemens_64 gradient table to the 1dDW_Grad_o_Mat++ or DIFFPREP? just trying to explore if this would help.
Thanks,
-bit warrior
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bit-warrior
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AFNI Message Board
I attached the MD_FA_thr0 images, because these seem bad too. I think in this step is where things are getting messed up.
by
bit-warrior
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AFNI Message Board
You mean this image ? But this is from the good run. On the bad run, the "purple" plane on the image is not slanted.
by
bit-warrior
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AFNI Message Board
Hey ptaylor thanks for the reply,
I am going through the qc images generated, i have found this picture, which i can tell does not look right). the qc02_ref_b0 also is different; on the correct run it seems to be slanted (I don't know if this matters). The qc03_MD_FA_thr0 ( not attached) also looks bad for the bad runs
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bit-warrior
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AFNI Message Board
Dear Afni forum,
I have generated a script to run fatcat (steps as described on ). I have run the scripts on about 13 subjects, with only one set of "good" results.
This is my processing pipeline (i apologize for the amount of txt, in this script "i" refers to the subject ID, and this is all in for loops. I have 3 different scripts doing this):
#----- Converting DWIs
by
bit-warrior
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AFNI Message Board
Dear Afni experts,
I am executing the command:
fat_proc_filter_dwis -in_dwi /home/ahoxha/Desktop/dti_fatproc/dwi_nii.nii.gz -in_col_matT /home/ahoxha/Desktop/dti_fatproc/dwi_nii_matT.dat -prefix /home/ahoxha/Desktop/dti_fatproc/filt
and the program gives me error:
++ Start script version: 3.1
++ 3dinfo: AFNI version=AFNI_17.3.06 (Dec 5 2017) [64-bit]
++ Found inset DWI file: /home/ah
by
bit-warrior
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AFNI Message Board
Hey Ptaylor,
Thanks for your reply. I asked the MRI tech who gave me the data, and she confirmed that it is a DTI sequence. However, i removed the file from the directory just in case, and ran the same command. Again I get the same error message.
I have run the same command on another dataset which had the same layout as the one I am currently running.
last time i had issues with the PATH
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bit-warrior
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AFNI Message Board
Dear Afni group,
I have recently run into an issue with the fat_proc_convert_dcm_dwis. I have my DTI data in a folder (3 folders, 2 have ~65 dcm images, and one has 1 dcm image ~27MB). I have run the same command on another dataset, and that works completely fine, however when I run it on two other datasets, I get the same error message, and fat_proc_convert_dcm_dwis does not finish executing.
by
bit-warrior
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AFNI Message Board
Got it, thank you for your help, greatly appreciate it! I will fix the issue and process the rest of my data.
by
bit-warrior
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AFNI Message Board
yep now it worked fine, i just removed all the extra things from the .cshrc and re run the command, now everythings seems to have worked fine, i got my indt files as well.
however, again i get this at my .cshrc file:
set path = ( $path /home/armand/abin )
if ( -f $HOME/.afni/help/all_progs.COMP ) then
source $HOME/.afni/help/all_progs.COMP
endif
set rootdir = `dirname $0`
c
by
bit-warrior
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AFNI Message Board
Another thing, i notice also that my .cshrc file has somehow added all these to the path ( sorry for pasting this here)
setenv PATH /home/armand/Desktop/dti_fatproc/DIFFPREPV31/bin/bin:$PATH
setenv PATH /home/armand/Desktop/dti_fatproc/DIFFCALC/DIFFCALCV31:$PATH
setenv PATH /home/armand/Desktop/dti_fatproc/DRBUDDIV31/bin:$PATH
setenv PATH /home/armand/abin/DIFFPREPV31/bin/bin:$PATH
setenv
by
bit-warrior
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AFNI Message Board
I tried the command and now I have the REN nii gz files. i still get this at the beginning of the command execution:
armand-HP-ENVY-x360-Convertible:~/Desktop/dti_fatproc> @SUMA_renumber_FS ~/Desktop/dti_fatproc/anat/SUMA
setenv: Too many arguments.
++ found ./aparc+aseg.nii
++ found ./aparc.a2009s+aseg.nii
++ Renumbering FS whole brain (./aparc+aseg.nii).
however when i run the
by
bit-warrior
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AFNI Message Board
so i have it scripted :
# I/O path, same as above, following earlier steps
set path_P_ss = /home/armand/Desktop/dti_fatproc
# ID of individual subj from "tail" of path, above
set ss_id = $path_P_ss:t
@SUMA_Make_Spec_FS \
-NIFTI \
-fspath $path_P_ss/anat \
-sid $ss_id
by
bit-warrior
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AFNI Message Board
I just ran the ls command
armand@armand-HP-ENVY-x360-Convertible:~/Desktop/AFNI BOOTCAMP/AFNI_demos/FATCAT_DEMO$ ls ~/Desktop/dti_fatproc/dwi_nii/dw_dti/indt*cmd.txt
ls: cannot access '/home/armand/Desktop/dti_fatproc/dwi_nii/dw_dti/indt*cmd.txt': No such file or directory
so I get no files with indt.
I went ahead and deleted the SUMA directory to re-run the @SUMA_Make_FS. at t
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bit-warrior
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AFNI Message Board
Hey, thanks for the quick reply. I don't have the indt directory; I have no indt files/folders in my directories.
thank you !
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bit-warrior
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AFNI Message Board
I do not have that... however I think my Freesurfer conversion did not work properly; my @SUMA_Make_Spec_FS produces no REN nii gz files. this is the ls command on the SUMA directory
armand-HP-ENVY-x360-Convertible:~/Desktop/dti_fatproc/anat/SUMA> ls
aparc.a2009s+aseg.nii std.141.dti_fatproc_both.spec
aparc.a2009s+aseg_rank.nii std.141.dti_fatproc_lh.MI.1D
aparc.a2009s+aseg_rank.niml.l
by
bit-warrior
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AFNI Message Board
Hey thanks for the reply!
so I tried doing the ls command :
armand@armand-HP-ENVY-x360-Convertible:~/Desktop/dti_fatproc$ ls /home/armand/Desktop/dti_fatproc/anat/SUMA/std.141.*.gii
/home/armand/Desktop/dti_fatproc/anat/SUMA/std.141.lh.inf_200.gii
/home/armand/Desktop/dti_fatproc/anat/SUMA/std.141.lh.inflated.gii
/home/armand/Desktop/dti_fatproc/anat/SUMA/std.141.lh.pial.gii
/home/armand/De
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bit-warrior
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AFNI Message Board
Dear AFNI forum,
I have come up with an issues running the fat_proc_map_to_dti command. I have been following the tutorials provided in . I am running the following script
# I/O path, same as above, following earlier steps
set path_P_ss = ~/Desktop/dti_fatproc
fat_proc_map_to_dti \
-source $path_P_ss/anat/SUMA/brain.nii
by
bit-warrior
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AFNI Message Board