Hi,
No, you don't need to redo those stages. As long as the FA images as
produced in the FA directory by tbss_1_preproc all look fine (make
sure they do) then that's fine.
If the .msf files are empty and you didn't delete those before trying
tbss_2_reg again then it won't have done anything - delete all
the .msf files and try tbss_2_reg again? Watch your computer (e.g.
with "top") to see if the registrations actually run?
Cheers.
On 25 Feb 2009, at 12:53, Hanne Antila wrote:
> Yep,
>
> I did indeed start from the beginning of tbss after updating and the
> result was the files I mentioned below. Should I also redo the
> eddy_correction and dtifit?
>
> Hanne Antila
> [log in to unmask]
> 0500-563674
>
> ----- Original Message -----
> From: Steve Smith <[log in to unmask]>
> Date: Wednesday, February 25, 2009 11:03 am
> Subject: Re: [FSL] problem with TBSS/tbss_3_postreg
> To: [log in to unmask]
>
>> Hi - if you have just upgraded then I suggest starting from
>> scratch.
>> It sounds like your registration never completed. for some reason.
>> Cheers.
>>
>>
>>
>> On 25 Feb 2009, at 06:45, Hanne Antila wrote:
>>
>>> Hi,
>>>
>>> I thought about that and updated to the newest version.
>> Unfortunately> this didn'n help and the problem remains the same.
>> So I guess the
>>> registration is then the issue here and now when I think about
>> it, the
>>> registration did finish really fast. It isn't the data anyway,
>> since I
>>> already tried with different dataset.
>>>
>>> The FA file contains these kinds of files
>>>
>>> Best.mfs
>>> Subject_FA.nii.gz
>>> Subject_FA_mask.nii.gz
>>> subject_FA_to_target_warp.mfs
>>> target.nii.gz
>>>
>>> Those subject_FA_to_target_warp.mfs -files are size 0 bites and
>> empty> when viewed in gedit. Does someone has any pointers? All
>> help will be
>>> appreciated!
>>>
>>> Hanne Antila
>>> [log in to unmask]
>>> 0500-563674
>>>
>>> ----- Original Message -----
>>> From: Steve Smith <[log in to unmask]>
>>> Date: Tuesday, February 24, 2009 10:36 pm
>>> Subject: Re: [FSL] problem with TBSS/tbss_3_postreg
>>> To: [log in to unmask]
>>>
>>>> HI - are you maybe mixing up FSL versions? *_FAi images are from
>>>> the
>>>> old version. Either that or the registrations didn't complete
>>>> correctly.Cheers.
>>>>
>>>> On 24 Feb 2009, at 12:53, Hanne Antila wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm a rookie in TBSS and I have run it successfully twice.
>>>> However,
>>>>> now I
>>>>> ran into some problems.
>>>>>
>>>>> I first ran tbss_1_preproc *.nii.gz and tbss_2_reg -T as
>>>> recommended
>>>>> and
>>>>> everything seemed ok, no error messages.
>>>>>
>>>>> The problems emerged, when I ran tbss_3_postreg -S. The error
>>>>> messages are
>>>>> below. Has someone had similar problems? My data consists of 30
>>>> FA-
>>>>> images.
>>>>>
>>>>> hanne@gyrus:~/DTI_Irina/TBBS$ tbss_3_postreg -S
>>>>> using pre-chosen target for registration
>>>>> transforming all FA images into MNI152 space
>>>>> dti_FA_C01_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C01_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C01_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C01_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C01_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C01_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C02_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C02_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C02_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C02_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C02_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C02_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C03_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C03_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C03_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C03_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C03_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C03_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C04_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C04_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C04_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C04_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C04_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C04_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C06_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C06_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C06_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C06_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C06_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C06_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C07_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C07_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C07_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C07_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C07_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C07_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C09_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C09_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C09_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C09_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C09_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C09_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C10_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C10_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C10_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C10_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C10_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C10_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C12_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C12_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C12_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C12_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C12_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C12_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C13_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C13_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C13_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C13_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C13_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C13_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C14_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C14_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C14_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C14_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C14_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C14_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C15_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C15_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C15_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C15_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C15_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C15_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C16_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C16_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C16_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C16_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C16_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C16_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C17_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C17_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C17_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C17_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C17_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C17_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_C18_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_C18_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_C18_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_C18_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_C18_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_C18_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P01_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P01_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P01_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P01_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P01_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P01_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P02_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P02_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P02_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P02_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P02_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P02_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P03_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P03_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P03_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P03_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P03_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P03_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P04_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P04_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P04_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P04_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P04_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P04_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P05_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P05_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P05_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P05_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P05_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P05_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P06_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P06_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P06_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P06_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P06_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P06_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P07_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P07_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P07_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P07_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P07_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P07_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P08_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P08_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P08_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P08_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P08_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P08_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P10_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P10_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P10_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P10_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P10_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P10_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P11_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P11_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P11_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P11_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P11_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P11_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P12_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P12_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P12_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P12_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P12_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P12_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P13_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P13_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P13_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P13_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P13_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P13_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P14_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P14_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P14_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P14_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P14_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P14_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P15_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P15_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P15_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P15_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P15_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P15_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> dti_FA_P16_FAi
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>>> 'dti_FA_P16_FAi_to_target_nonlinear'
>>>>> ** ERROR: nifti_image_open(dti_FA_P16_FAi_to_target_nonlinear):
>>>> bad
>>>>> header info
>>>>> Error: failed to open file dti_FA_P16_FAi_to_target_nonlinear
>>>>> ERROR: Could not open image dti_FA_P16_FAi_to_target_nonlinear
>>>>> Image Exception : #22 :: Failed to read volume
>>>>> dti_FA_P16_FAi_to_target_nonlinear
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> merging all upsampled FA images into single 4D image
>>>>>
>>>>> 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_FA'>>> ** ERROR: nifti_image_open(all_FA): bad header info
>>>>> Error: failed to open file all_FA
>>>>> Error:: FslCloneHeader: Null pointer passed for FSLIO
>>>>> creating valid mask and mean FA
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>> 'all_FA'>>> ** ERROR: nifti_image_open(all_FA): bad header info
>>>>> Error: failed to open file all_FA
>>>>> Cannot open volume all_FA for reading!
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>> 'all_FA'>>> ** ERROR: nifti_image_open(all_FA): bad header info
>>>>> Error: failed to open file all_FA
>>>>> Cannot open volume all_FA for reading!
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>> 'all_FA'>>> ** ERROR: nifti_image_open(all_FA): bad header info
>>>>> Error: failed to open file all_FA
>>>>> Cannot open volume all_FA for reading!
>>>>> skeletonising mean FA
>>>>> ** ERROR (nifti_image_read): failed to find header file for
>>>> 'mean_FA'> ** ERROR: nifti_image_open(mean_FA): bad header info
>>>>> Error: failed to open file mean_FA
>>>>> ERROR: Could not open image mean_FA
>>>>> Image Exception : #22 :: Failed to read volume mean_FA
>>>>> terminate called after throwing an instance of
>>>>> 'RBD_COMMON::BaseException'
>>>>> Aborted
>>>>> now view mean_FA_skeleton to check whether the default threshold
>>>> of
>>>>> 2000
>>>>> needs changing, when running:
>>>>> tbss_4_prestats [threshold]
>>>>> hanne@gyrus:~/DTI_Irina/TBBS$
>>>>>
>>>>
>>>>
>>>> -----------------------------------------------------------------
>> ---
>>>> -------
>>>> Stephen M. Smith, Professor of Biomedical Engineering
>>>> Associate Director, Oxford University FMRIB Centre
>>>>
>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>> +44 (0) 1865 222726 (fax 222717)
>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>> -----------------------------------------------------------------
>> ---
>>>> -------
>>>>
>>>
>>
>>
>> --------------------------------------------------------------------
>> -------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> --------------------------------------------------------------------
>> -------
>>
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
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