Dear Jesper
the dataset ID is 345841
I have included the mprage from the 4 subjects and the description of
what I did to the data .
I would be much obliged if you could take a look at the data and comment on
the processing chain.
Thank you very much for your help
Lazar
On 12/3/12, Lazar Fleysher <[log in to unmask]> wrote:
> Dear Jesper
>
> Thank you very much for your comments
> I used --imprefm=0 --impinm=0 switches becuase I thought
> the switches mean that the image value of zero means that there
> is no tissue there, where is if I set them to 1, it says there is
> tissue there, but
> it was not measured. Since zeros should happen outside the brain, I thought
> this
> was the correct choice.
>
> As to the upload of raw data, I would like to upload it to fsl service
> so you could have a better look, but I do not know how. The only
> reference is
>
> https://www.fmrib.ox.ac.uk/internal/support/computing/user-guides/data-management/data-sharing
>
> which requires some sort of password. Shold I ask for some sort of
> account to upload the data?
>
> Thank you very much for your kind help
>
> Lazar
>
>
>
> On 12/3/12, Lazar Fleysher <[log in to unmask]> wrote:
>> I am trying to prepare data for a voxel-based analysis.
>> for this purpose, I have to coregister all data to a template.
>>
>> For now I am using MNI_T1_2mm template provided by FSL
>>
>> Thus, I have used this script to coregister MPRAGE to T1 template
>> (this is based on FNIRT manual):
>>
>>
>> mpr=`$FSLDIR/bin/remove_ext $1`
>> mpr_brain=`$FSLDIR/bin/remove_ext $2`
>>
>> flirt -dof 6 -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -in
>> ${mpr_brain} -omat ${mpr_brain}_transf.mat -out ${mpr_brain}_flirted
>>
>> fnirt --in=${mpr} --aff=${mpr_brain}_transf.mat
>> --cout=${mpr}_nonlinear_transf
>> --ref=$FSLDIR/data/standard/MNI152_T1_2mm --imprefm=0 --impinm=0
>> --config=T1_2_MNI152_2mm
>>
>> applywarp --ref=$FSLDIR/data/standard/MNI152_T1_2mm --in=${mpr}
>> --warp=${mpr}_nonlinear_transf --out=${mpr}_warped
>>
>> Attached is a result from 4 subjects
>> There is a lot of "play" in different brain areas. Is this the best
>> what can be done or I did something wrong or I missed something?
>>
>> Thank you very much for your help
>>
>> Lazar
>>
>
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