Dear AFNI forum,https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fatcat_prep/Postprocessing_II.html . I am running the following script
set path_P_ss = ~/Desktop/dti_fatproc
fat_proc_map_to_dti REN .nii.gz .gii .niml.dset .spec
and what i get from terminal is :
I also checked to make sure that I do have the required files and with a simple ls command i get:
I also updated AFNI to the latest version and it does not seem to fix the problem. Any help is appreciated, thank you
Howdy-
OK, I just tried running that command on my computer, and it ran OK for me (same version number of the program. I think the problem might be that your surfaces are not *gii files, but instead in a different format.
That would be why in this list of “found” dsets, there are no *gii, even though you specified some:
++ User has listed 15 followers_NN dsets
++ User has listed 8 followers_niml dsets
++ User has listed 3 followers_spec dsets
So, for you, what is the output of:
ls $path_P_ss/anat/SUMA/std.141.*.gii
?do have for the surfaces. The *gii surfaces are made if, when running @SUMA_Make_Spec_FS , you use the “-NIFTI” option. We recommend using this-- if you see the “running FreeSurfer” part of the fat_proc documentation, that should be done.
Assuming that this actually is the root of the problem here , then I would recommend rerunning your @SUMA_Make_Spec_FS command with the “-NIFTI” option. (Alternatively, you could also just specify the kind of surfaces you do have for the fat_proc_map_to_dti call; however, we recommend converting FreeSurfer results with “@SUMA_Make_Spec -NIFTI”, anyways.)
–pt
Hey thanks for the reply!
so i have about 14 .gii files , for some reason it does not read them. I did process it according to tutorial using @SUMA_Make_Spec_FS with -NIFTI option.
Weird. Can you paste the contents of the *cmd.txt file that gets made, echoing the command that was run?
Thanks,
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
Not sure how I would proceed further, re-run freesurfer maybe? I have no *.nii.gz files in my SUMA directory, although i do provide the -NIFTI command
Hi-
Can you please check for a file called:
–pt
Hey, thanks for the quick reply. I don’t have the indt directory; I have no indt files/folders in my directories.
thank you !
Hi-
So, just to sure-sure, this doesn’t list any file out?
ls ~/Desktop/dti_fatproc/dwi_nii/dw_dti/indt*cmd.txt
That is odd that your @SUMA_Make_Spec_FS didn’t make any *nii.gz files. Would you want to run that again and check about any error messages there?
Thanks,
I just ran the ls commandcmd.txt 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 the end of the execution on the terminal i get:
++ Going to make renumbered ROIs now.@SUMA_renumber_FS -help’ for description.
setenv: Too many arguments.
@SUMA_Make_Spec_FS … finished
I think this could/must/gotta be the issue.
ptaylor
November 6, 2017, 4:40pm
10
Ah, yes, that is badness. What is your @SUMA_Make_Spec_FS command?
–pt
so i have it scripted :
set path_P_ss = /home/armand/Desktop/dti_fatproc
set ss_id = $path_P_ss:t
@SUMA_Make_Spec_FS
ptaylor
November 6, 2017, 5:57pm
12
What happens if you run the @SUMA_renumber_FS command, which is the last thing run by @SUMA_Make_Spec_FS , on your SUMA/ directory:
@SUMA_renumber_FS ~/Desktop/dti_fatproc/anat/SUMA
? Does that make REN nii* files there?
–pt
I tried the command and now I have the REN nii gz files. i still get this at the beginning of the command execution:
armand-HP-ENVY-x360-Convertible:~/Desktop/dti_fatproc> @SUMA_renumber_FS ~/Desktop/dti_fatproc/anat/SUMA
setenv: Too many arguments.
however when i run the other script fat_proc_map_to_dti i get just these two lines:
Another thing, i notice also that my .cshrc file has somehow added all these to the path ( sorry for pasting this here)
setenv PATH /home/armand/Desktop/dti_fatproc/DIFFPREPV31/bin/bin:$PATH
if ( -f $HOME/.afni/help/all_progs.COMP ) then
setenv PATH /home/armand/Desktop/dti_fatproc/DIFFPREPV31/bin/bin:$PATH
ptaylor
November 6, 2017, 6:39pm
15
Umm, something has gone horribly wrong with that path setup-- judging by the name, that is something from when installing TORTOISE v3.1? Can you copy that file somewhere else and try with a cleaned version? That might be causing path-oddities.
–pt
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
set rootdir = dirname $0pwd
echo ‘setenv PATH’ $abs_rootdir’/DIFFPREPV31/bin/bin:$PATH’ >>! ~/.cshrc
setenv PATH /home/armand/Desktop/dti_fatproc/DIFFPREPV31/bin/bin:$PATH
ptaylor
November 6, 2017, 7:48pm
17
Glad things are working now.
I think the reason you get soooo many of those “setenv …” lines is that you have an echo statement in the ~/.cshrc file:
echo 'setenv PATH' $abs_rootdir'/DIFFPREPV31/bin/bin:$PATH' >>! ~/.cshrc
echo 'setenv PATH' $abs_rootdir'/DIFFCALC/DIFFCALCV31:$PATH' >>! ~/.cshrc
echo 'setenv PATH' $abs_rootdir'/DRBUDDIV31/bin:$PATH' >>! ~/.cshrc
So, every time your ~/.cshrc file is sourced (which is done when a tcsh script is executed), then another trio of lines gets put in.
Therefore, you should also move out this ~/.cshrc file, and clean out the repeated setenv commands, and make sure you don’t have the following lines in that file:
echo 'setenv PATH' $abs_rootdir'/DIFFPREPV31/bin/bin:$PATH' >>! ~/.cshrc
echo 'setenv PATH' $abs_rootdir'/DIFFCALC/DIFFCALCV31:$PATH' >>! ~/.cshrc
echo 'setenv PATH' $abs_rootdir'/DRBUDDIV31/bin:$PATH' >>! ~/.cshrc
–pt
Got it, thank you for your help, greatly appreciate it! I will fix the issue and process the rest of my data.