Re: [Freesurfer] (no subject)

-- On Tue, 25 May 2010, [GB2312] Àîèª wrote: > 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 fischl@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. >> >> >