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 fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all issue To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1601131057350.21689@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.schell@med.uni-heidelberg.de
?
------------------------------
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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:
- Re: recon-all issue (Bruce Fischl)
Message: 1 Date: Wed, 13 Jan 2016 10:59:04 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all issue To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1601131057350.21689@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.schell@med.uni-heidelberg.de
?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 143, Issue 19
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Schell, Susanne