Hi Gwenaëlle,
I have many errors when i'm running fslvbm_2_template -n
The first one is :
** ERROR (nifti_image_read): failed to find header file for
'01_CON_002_S_0295_M06_struc.nii.gz_brain'
My files are of this form 01_CON_002_S_0295_M06_struc.nii.gz
02_CON_XXX__XXXXX_XXX_struc.nii.gz
etc
It seems that one of fsl scripts during the fslvbm_2_template run, adds this
prefix { _brain} in the end of the file that should be read without renaming
the actual file.So the script can't read a file that doesn't exist. Why this
happens?
I've noticed also that the names' files of some new created files are
really strange with added big prefixes in the end of the file's name. For
instance 01_CON_002_S_0295_M06_struc.nii.gz_GM_to_T_init_warp.msf
I'm sending you the structure of my files in the folder where the analysis
takes place+ the error messages that aroused during it.
I would really appreciate once more your help
Thank you
Antonios-Constantine Thanellas
On Tue, 26 Aug 2008 17:42:44 +0000, Gwenaëlle DOUAUD
<[log in to unmask]> wrote:
>Hi Antonios,
>
>now the pre-processed data are in a directory called struc/ (instead of FAi/).
>You need to do exactly the same thing as previously, apart from the fact
that there is no need for you to run tbss_1 anymore, and fnirt can deal with
compressed nifti images (instead of analyze).
>
>
>So it boils down to:
>- rename your betted images: exam00X_struc_brain.nii.gz
>- have in your struc/ directory corresponding files *without* the _brain
suffix, so in this case: exam00X_struc.nii.gz (no matter what they are, so
for you, empty files would just be fine: touch exam00X_struc.nii.gz).
>
>Cheers,
>Gwen
>
>
>--- En date de : Lun 25.8.08, Antonios - Constantine Thanellas
<[log in to unmask]> a écrit :
>
>> De: Antonios - Constantine Thanellas <[log in to unmask]>
>> Objet: [FSL] following different order on VBM analysis steps
>> À: [log in to unmask]
>> Date: Lundi 25 Août 2008, 17h05
>> Hello fsl users,
>>
>> I want to ask the same question that i've done one
>> month ago, but for the
>> newer version of FSL 4.1 this time.
>>
>> How can I avoid the first step of VBM analysis
>> (fslvbm_1_bet) on FSL 4.1
>> since i have my data already "beted" from a
>> previous analysis step?
>>
>> Gwenaelle gave me an answer (it is attached in the end of
>> this e-mail) that
>> worked fine with fsl 4.0.4 but since now i've upgraded
>> fsl to 4.1 i have the
>> same problem again.
>>
>> Thank you once more
>>
>> On Mon, 21 Jul 2008 14:20:23 +0000, Gwenaëlle DOUAUD
>> <[log in to unmask]> wrote:
>>
>> >Hi Antonios,
>> >
>> >absolutely. The only thing that is required is to
>> present the data as if
>> they'd been processed in the right order...
>> >
>> >If, say, you've named your various brain extracted
>> exams:
>> exam00X_brain.nii.gz, then after running tbss_1_preproc,
>> you'll have in your
>> FAi/ directory all your images called exam00X_brain_FAi.hdr
>> and .img.
>> >
>> >So you then just need to rename them
>> exam00X_FAi_brain.hdr and .img.
>> >
>> >One additional requirement (for nomenclature purposes)
>> is that you need to
>> have in your FAi/ directory corresponding files *without*
>> the _brain suffix,
>> so in this case: exam00X_FAi.hdr and .img (no matter what
>> they are, so for
>> you, empty files would just be fine: touch exam00X_FAi.hdr
>> and .img).
>> >
>> >Hope this makes sense,
>> >Gwenaelle
>> >
>> >
>> >--- En date de : Lun 21.7.08, Antonios - Constantine
>> Thanellas
>> <[log in to unmask]> a écrit :
>> >
>> >> De: Antonios - Constantine Thanellas
>> <[log in to unmask]>
>> >> Objet: [FSL] following different order on VBM
>> analysis steps
>> >> À: [log in to unmask]
>> >> Date: Lundi 21 Juillet 2008, 12h23
>> >> Dear fsl users,
>> >>
>> >> I want to analyse my data (controls-patients)
>> using
>> >> fsl's VBM.
>> >>
>> >> All my data (whole heads) have been brain
>> extracted with
>> >> BET beforehand in
>> >> another analysis part.
>> >>
>> >> So instead of "beting" my data again
>> (2nd step of
>> >> VBM analysis) can i just
>> >> modify the already extracted brains with
>> tbss_1_preproc
>> >> (1st step of VBM
>> >> analysis) and omit the second step?
>> >>
>> >> Thank you in advance
>> >> Antonios-Konstantinos Thanellas
>>
>>
>>
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