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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The label ctx_lh_G_parietal_sup is in the aparc.a2009s and not the aparc, so try aparc.a2009s+aseg.mgz doug

On 08/12/2013 12:29 PM, lorenzo pasquini wrote:

Dear Freesurfer users,

I used freesurfer to extract the cortical thickness of several regions, which are saved in the aparc.a2009s.stats text file.

To create a mask of this regions for further analyzes I used the command line:

mri_binarize --i aparc+aseg.mgz --min number --max number -- o testname.mask.nii as numbers I used for example 11126.5 and 11127.5 (ctx_lh_G_parietal_sup) derived from the aparc.a2009.s FreesurferColorLUT table

Unfortunately, the created mask is empty and freesurfer "tells" me that there are no voxels in the created nii image. Did anybody experience the same problem? Am I using the wrong binarization command line? Should I download an extra toolbox? How can I solve this problem? Thank you very much and kind regards,

Lorenzo Pasquini

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