Hi, all Bruce has suggested that we can directly give recon-all dcm file as input. However, I have done recon-all with mgz file as input. Is that input file OK? For example, sub1 has 128 dcm files, 001~128, I just ran a syntax: mri_convert 001 sub1.mgz then the computer read 128 dcm files and convert them into sub1.mgz, then I ran recon-all with "sub1.mgz" as input file The version I used was freesurfer-Linux-centos4-stable-pub-v4.5.0 Besides, I have checked the aseg.stats and lh/rh.aparc.stats generated from different input files(dcm or mgz) in one subject, and find that they are completely the same. It must be a very stupid question, however, I need some confirmation. Too much Thanks! Jin
2010/5/4 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > if the directions are labeled properly then you aer probably ok. In general > you are better off just giving recon-all the dicom files as input and not > doing any conversions beforehand. > > cheers > Bruce > > On Tue, 4 May 2010, chenchunhuichina wrote: > > Hello FreeSurfer users, >> >> I may be asking a stupid question but it really troubled me a while. >> >> I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it >> displayed in RAS coordinates, but template of FSL are in LAS coordinates. >> Should I filp L-R before doing any further analysis? >> Besides, my structrual imagews were scanned in sagittal view, and after >> dcm2niigui transforation, it's in PIL coordinates in fslview. Should I >> reorient the image to LAS coordinates too? >> But the letters L R I S A P are labled correctly (at least A-P and I－S are >> correct), which means FSL can read in orientation information correctly. So >> I am confused whether I should reorient my data or not. >> I then processed strucutre images with Freesurfer, and the results from >> reoriented and not-reoriented images are different, so which one is correct? >> >> Any help is appreciated, >> Thanks! >> -- >> >> Chunhui Chen >> >> >> 2010-05-04 >> >> >> >> Chunhui Chen >> _________________ >> >> Institute of Cognitive Neuroscience and Learning >> Beijing Normal University >> Beijing, China 100875 >> > > _______________________________________________ > 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. > >
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