Ok thanks. I think I will re-run the analysis with the files correctly named. It seems like the best option. This is the error I get:

This is what it says for each subject:

PNS_299

** ERROR (nifti_image_read): failed to find header file for '../-help/PNS_299'

** ERROR: nifti_image_open(../-help/PNS_299): bad header info

Error: failed to open file ../-help/PNS_299

ERROR: Could not open image ../-help/PNS_299

Image Exception : #22 :: Failed to read volume ../-help/PNS_299

terminate called after throwing an instance of 'RBD_COMMON::BaseException'

Aborted

merging all upsampled -help images into single 4D image

Then, after it has given me this error for each subject it gives me this at the end:

Usage: fslmerge <-x/y/z/t/a> <output> <file1 file2 .......>

     -t : concatenate images in time

     -x : concatenate images in the x direction

     -y : concatenate images in the y direction

     -z : concatenate images in the z direction

     -a : auto-choose: single slices -> volume, volumes -> 4D (time series)

** ERROR (nifti_image_read): failed to find header file for 'all_-help'

** ERROR: nifti_image_open(all_-help): bad header info

Error: failed to open file all_-help

Cannot open volume all_-help for reading!

projecting all_-help onto mean FA skeleton

** ERROR (nifti_image_read): failed to find header file for 'all_-help'

** ERROR: nifti_image_open(all_-help): bad header info

Error: failed to open file all_-help

ERROR: Could not open image all_-help

Image Exception : #22 :: Failed to read volume all_-help

terminate called after throwing an instance of 'RBD_COMMON::BaseException'

Aborted

now run stats - for example:

randomise -i all_-help_skeletonised -o tbss_-help -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V

(after generating design.mat and design.con)

Thanks for your help!

Cindy

On 2013-04-12, at 1:24 PM, Rali Dimitrova wrote:

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