p.s or maybe on the 001.mgz in the mri/orig subdir as well On Thu, 28 Jan 2016, Parzer, Peter wrote:
> mri_convert > ________________________________________ > Von: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von dgw > <dgwake...@gmail.com> > Gesendet: Donnerstag, 28. Januar 2016 15:55 > An: Freesurfer support list > Betreff: Re: [Freesurfer] Segmentation depends on image file format > > What software did you use to generate the NIFTI files? Many of the > converters do different things to the axes of the data, and this does > affect results. > > hth > d > > On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter > <peter.par...@med.uni-heidelberg.de> wrote: >> Hi, >> >> we have brain images stored as DICOM and as NIFTI files. For some time we >> used to import the NIFTI files to freesurfer for segmentation. I was curious >> if it makes a difference if we would import the DICOM files directly, and >> was surprised that it actually did. Here are the commands we used: >> >> # Import DICOM files >> recon-all -s 3003PC_dcm -i >> ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm >> >> # Convert DICOM to NIFTI and import NIFTI file >> mri_convert ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm >> 3003PC.nii.gz >> recon-all -s 3003PC_nii -i 3003PC.nii.gz >> >> # Segmentation of DICOM file import >> recon-all -s 3003PC_dcm -all >> >> # Segmentation of NIFTI file import >> recon-all -s 3003PC_nii -all >> >> Here are the first 3 volumes from aseg.stats for 3003PC_dcm (DICOM import) >> >> 1 4 5612 5611.8 Left-Lateral-Ventricle 27.6355 >> 12.8465 8.0000 93.0000 85.0000 >> 2 5 452 452.2 Left-Inf-Lat-Vent 42.1100 >> 14.9377 7.0000 86.0000 79.0000 >> 3 7 13765 13765.1 Left-Cerebellum-White-Matter 87.7808 >> 6.6008 36.0000 109.0000 73.0000 >> >> and here the the first 3 volumes for 3003PC_nii (NIFTI import) >> >> 1 4 5582 5582.2 Left-Lateral-Ventricle 27.4507 >> 12.7212 8.0000 93.0000 85.0000 >> 2 5 421 421.1 Left-Inf-Lat-Vent 40.8032 >> 14.6554 7.0000 83.0000 76.0000 >> 3 7 13899 13898.6 Left-Cerebellum-White-Matter 87.6707 >> 6.7539 36.0000 109.0000 73.0000 >> >> The differences are small but I think there should be no differences at all. >> Has someone an explanation for this differences and which file format is >> better? >> >> Greetings >> Peter >> >> P. S.: Our system: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on >> Ubuntu 14.04 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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. >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
