Hi,
Thank you very much! I appreciate your help immensely!
Hope you are having a lovely day,
Catherine
On 10/17/12, Stephen Smith <[log in to unmask]> wrote:
> Hi - yes I guess tbss_1_preproc should be able to handle having directory
> names in the input file list - we'll look into fixing that in the future.
>
> Yes if you stick to the correct format you can edit the design.mat and
> design.con files by hand - though it's easier with the Glm / Glm_gui GUI.
>
> Cheers.
>
>
> On 16 Oct 2012, at 14:12, Nucleos P wrote:
>
>> Hi Steve,
>>
>> I reran it again with the input files NOT in folders. All went well.
>> Hopefully, all will run smoothly throughout the rest of the tbss process.
>>
>> I know we want to set up a design matrix of our own (including age and
>> sex)...so not just the regular "designttest # #" command.
>> Is there anyway to ensure it will work by adding columns to the .mat and
>> editing the .con files? Does the program understand "spaces" and 0s from
>> the docs. Any special way to set this up?
>>
>> Thanks,
>> Catherine
>>
>> On Tue, Oct 16, 2012 at 3:24 AM, Stephen Smith <[log in to unmask]>
>> wrote:
>> Hi - it looks like you have somehow got the input files listed as files
>> inside folders - can you tell us what your full original command line was
>> for the tbss_1_preproc?
>> Cheers, Steve.
>>
>>
>> On 15 Oct 2012, at 18:14, Nucleos P wrote:
>>
>>> Good day!
>>>
>>> I have been working with FSL 5.0 to run some new DTI data analyses.
>>>
>>> All of the pre-processing steps completed (e.g. eddy_correct, BET, and
>>> dtifit). All of the permissions are set to full (+rwx). I am having
>>> trouble with running tbss_1_preproc with the dti_FA.nii.gz files for each
>>> subject.
>>>
>>> When the script runs, it creates two folders: "origdata" and "FA"
>>>
>>> Within the "origdata" the process moves all of the dti_FA.nii.gz images
>>> into it.
>>>
>>> The "FA" directory turns up empty (without output images).
>>>
>>> Here is the error message I am receiving:
>>>
>>> Now running "slicesdir" to generate report of all input images
>>> -e <thr> : use the specified threshold for edges (if >0 use this
>>> proportion of max-min, if <0, use the absolute value)
>>> -S : output every second axial slice rather than just 9 ortho
>>> slices
>>> tbss_1_preproc grp3_mgi71_016945_006204
>>> processing grp3_mgi71_016945_006204/grp3_mgi71_016945_006204_dti_FA
>>> Error: failed to open file
>>> FA/grp3_mgi71_016945_006204/grp3_mgi71_016945_006204_dti_FA_FA.nii.gz
>>> Image Exception : #22 :: ERROR: Could not open image
>>> FA/grp3_mgi71_016945_006204/grp3_mgi71_016945_006204_dti_FA_FA
>>> terminate called after throwing an instance of
>>> 'RBD_COMMON::BaseException'
>>> /usr/local/fsl/bin/tbss_1_preproc: line 85: 19344 Aborted
>>> (core dumped) $FSLDIR/bin/fslmaths $f -min 1 -ero -roi 1 $X 1 $Y 1 $Z 0 1
>>> FA/${f}_FA
>>> Cannot open volume
>>> FA/grp3_mgi71_016945_006204/grp3_mgi71_016945_006204_dti_FA_FA for
>>> reading!
>>> Cannot open volume
>>> FA/grp3_mgi71_016945_006204/grp3_mgi71_016945_006204_dti_FA_FA_mask for
>>> reading!
>>>
>>> Thank you for looking at this!
>>>
>>> -Catherine Upton, RA
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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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