Dear Koen, thank you very much for your help!! by summing the intensities and dividing by 255 I get the same volumes estimated by freesurfer. Thank you again and greets,
Lorenzo Pasquini
--- Ven 7/12/12, Koen Van Leemput koen@nmr.mgh.harvard.edu ha scritto:
Da: Koen Van Leemput koen@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] hippocampal segmentation converting mgz to nii A: "lorenzo pasquini" lollopasquini@yahoo.it Cc: "Freesurfer Mailinglist" freesurfer@nmr.mgh.harvard.edu Data: Venerdì 7 dicembre 2012, 11:47
Hi Lorenzo, The correct way to calculate the expected (not an integer value) number of voxels belonging to a subfield is by summing ( intensity / 255 ) across all voxels. Not sure where things go wrong: the integer values you report are a bit suspicious, or perhaps some rescaling of image intensities is done during the conversion. You should also be able to convert from .mgz to .nii using the command "kvlConvert"
Cheers, Koen
On Wed, Nov 28, 2012 at 8:21 AM, lorenzo pasquini lollopasquini@yahoo.it wrote:
Dear freesurfer users,
I have used freesurfer to segment hippocampal subfields. Then I used freeview to convert the derived .mgz files in .nii files for further analysis. I estimated the hippocampal subfields volumes with the command:
kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ data/ GEMS/ compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz
I have calculated the number of voxels in the converted .nii files using SPM and realized that they do not fit the estimated volumes through freesurfer
Example
for CA2-2 estimated voxel number though freesurfer: 6851 voxels found in .nii file: 15812
Did somebody had similar problems? Do you have any suggestion? Are there any incompatibilities between SPM and freesurfer? I did not find any apparent error in my counting script. Thank you very much and regards,
Lorenzo Pasquini
Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen)
Neuroimaging Lab, Neuroradiology
Klinikum r. d. Isar (Technische Universität)
81675 München
Tel.: 0049 (0) 89 4140-7666
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