Hi Susanne
I don't know enough about FSL to tell you. If you change the orientation
of the image so that our process of putting it in coronal slices
("conforming") changes, or you interpolate the image before giving it to
recon-all it will certainly change the results a bit. ALso, when you send
command lines, you need to send the entire one and the screen output,
otherwise it's not possible to know what you did.
cheers
Bruce
On Fri, 15 Jan 2016, Schell, Susanne wrote:
> Dear Bruce,
>
> thanks for answering. What we did to transform the original dicom files in
> nii.gz files is the following freesurfer command:
>
> mri_convert
>
> the nii.gz files to standard oriented and cut files are the following
> commands in FSL:
>
> fsl swapdim <input> -z -x -y <output>
> robustfov -i input -r output -i -r
>
> Of course, the output files are different concerning some characteristics,
> but they should not differ in the segmentation produced, should they?
>
> In the files attached to my last mail, you can see just by looking at the
> pictures that there are some variations in the form of the brain, which
> souldnt be there, or am I mistaken?
>
> Thanks very much in advance
> Susanne
>
>
> Today's Topics:
>
> 1. Re: recon-all issue (Bruce Fischl)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 13 Jan 2016 10:59:04 -0500 (EST)
> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all issue
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <alpine.lrh.2.20.1601131057350.21...@gate.nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Susanne
>
> can you include prior correspondance so we have some context for your emails.
> Certainly 2 vs. 1 and 3 will give different results since you have changed
> the input file. I would think think 1 and 3 would be the same, but we need
> to know how you did the conversion. Look at the 001.mgz in the subjects'
> mri/orig dir in the cases of 1 and 3 and see if they are the same (or use
> mri_diff)
>
> cheers
> Bruce
>
> On Wed, 13 Jan 2016, Schell, Susanne wrote:
>
>>
>> Dear Bruce,
>>
>> ?
>>
>> thanks for answering. The recon-all command lines we use is:
>>
>> ?
>>
>> recon-all ?s subjectID ?i /data/subjectID.nii.gz
>>
>> recon-all ?s subjectID -all
>>
>> ?
>>
>> The files we used are
>>
>> 1)????? DICOM files
>>
>> 2)????? nii.gz files, but standard oriented and cut
>>
>> 3)????? nii.gz files
>>
>> ?
>>
>> When we look at the output pictures, they look different (see attached
>> files)
>>
>> ?
>>
>> Greetings,
>>
>> Susanne
>>
>> ?
>>
>> ?
>>
>> ?
>>
>> ______________________________________
>>
>> Susanne Schell, Dipl.-Psych.
>>
>> ?
>>
>> Sektion St?rungen der Pers?nlichkeitsentwicklung
>>
>> Klinik f?r Kinder- und Jugendpsychiatrie
>>
>> Universit?tsklinikum Heidelberg
>>
>> ?
>>
>> Tel: (+49) ? (0)6221-56 35135
>>
>> e-mail: susanne.sch...@med.uni-heidelberg.de
>>
>> ?
>>
>>
>>
>
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