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Hi again, I guess you could OR start from the beginning having your raw images CON_101.nii.gz and re-run tbss_1 to 4 ( this really depends on whether you are patient enough to go through all steps again) or you could remove one of the "FA_" from all images in your ./FA dir (ONLY) so that instead of CON_101_FA_FA_to_target_warp.nii.gz you have CON_101_FA_to_target_warp.nii.gz etc., in which case you should be very careful when renaming. What error msg are you getting? Hope this helps. Best, Rali On 12 April 2013 17:57, Cindy Hovington <[log in to unmask]>wrote: > Thank you for your reply Rali. > > This answers my question! I will try it right now. > > Also, so if I have already went through the tbss steps for my FA > analysis and my RAW images had FA at the end (meaning that in the ./FA dir > they are name CON_101_FA_FA.nii.gz) then I should also rename them > "subject_n.nii.gz" or simply remove 1 of the 2 FA's? ) "subject_n_FA.nii.gz" > > Thanks again, > > Cindy > > > On 2013-04-12, at 12:47 PM, Rali Dimitrova wrote: > > Hi > > When you run tbss_non_FA you don`t have to change anything in the ./FA or > the ./origdata dir. What you need to do is to copy your non_FA images, lets > say your MD images, in a directory called "MD" and make sure they are named > the same way as your raw FA images. > > I would recommend that you leave out "FA" or "MD" when you name the RAW > images as the tbss_scripts (as well as the tbss_non_FA) add these for you > in the newly created images located in the ./FA dir. So you could name your > original FA images something like "subject_n.nii.gz" and your original MD > images ./MD/ "subject_n.nii.gz". > > Does this answer your question? > > Best, Rali > > > On 12 April 2013 12:14, Cindy Hovington <[log in to unmask]>wrote: > >> Just in case....here is the info from the post I am confused about. >> >> >> Subject:Re: problems with non_TBSS_FA still remains.... >> >> From:Rosalia Dacosta Aguayo <[log in to unmask]> >> >> Reply-To:FSL - FMRIB's Software Library <[log in to unmask]> >> >> Date:Mon, 4 Feb 2013 18:09:40 +0100 >> >> >> >> Thank you in advance for your help. >> >> Cindy >> On 2013-04-11, at 2:35 PM, Cindy HC wrote: >> >> > Dear Experts, >> > >> > I have been having the same issue as several people. I am a little >> confused from all the posting as to which file I need to edit when I am >> getting an error with the tbss_non_FA script. >> > >> > I would just like to confirm which files I am changing. I have gone >> through all TBSS steps and I know have 3 folders (FA, origdata and stats). >> I have added a new folder called MD...added all my MD files (named the same >> way as my FA files). From what I understand, I need to remove the "FA" at >> the end of my files. From origidata or FA? "FA" contains the FA files >> (CON_103_FA_FA.nii.gz) along with several other files obtain from TBSS step >> 2. Files in "origidata" are called CON_103_FA.nii.gz. >> > >> > Do I change the name of the files in "FA"? If so would it be from >> CON_103_FA_FA.nii.gz to CON_103.nii.gz? >> > >> > Also, after I have changed their name do I leave them in this folder? >> If I want to re-run some more TBSS analysis will the change in the name >> have an impact? >> > >> > Thank you for your advice. >> > >> > Cindy >> > > >