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 <[email protected]> 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 > [email protected] > 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
