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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