trying to make sense of this: 1. ran the initial recon-all to convert analyze to .mgz 2. then mri_convert on the DICOMs overwriting 001.mgz.
Now running the full autorecon-all to see what it looks like, but is seems that mri_convert added spatial cosine information to the 001.mgz. this was the output: ------------------------------ reading from 090725kc9b/e8845s5i1... Starting DICOMRead2() dcmfile = 090725kc9b/e8845s5i1 dcmdir = 090725kc9b Ref Series No = 5 Found 103 files, checking for dicoms Found 100 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1.4 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 100 ndcmfiles = 100 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=8.96, TE=1.79, TI=400.00, flip angle=15.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to FS090725kc9b/mri/orig/001.mgz... On 4 May 2010 10:48, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > usually you create an mri/orig/001.mgz, but you can also just point > recon-all directly at the dicoms I think > > On Tue, 4 May 2010, Antoine Leflon wrote: > > So I have to write : mri_convert -it dicom -i (first image) -o (name >> of the file) ? >> I did it outputing orig.mgz as usually before getting the error . >> >> Antoine >> >> >> ________________________________________________________________________________ >> Bruce Fischl <fis...@nmr.mgh.harvard.edu> a écrit : >> >> mri_convert can be used to change the format, assuming it is standard >>> dicom. >>> >>> cheers >>> Bruce >>> >>> On Tue, 4 May 2010, Antoine Leflon wrote: >>> >>> My files are dicoms and have no extension in the end of their name >>>> (IM_0465 for example) . Is it possible to change the format ? >>>> >>>> thanks , >>>> >>>> Antoine >>>> >>>> >>>> >>>> ________________________________________________________________________________ >>>> >>>> Talairach is about orientation. What is the format of your file? If it >>>> is .hdr and.img, it will fail. >>>> >>>> >>>> On 4 May 2010 11:43, Antoine Leflon >>>> <antoine1.lef...@etudiant.univ-lille1.fr> wrote: >>>> >>>> Hi all , >>>> >>>> I've used data from another Doctor , freesurfer told me the FOV was >>>> 330 so I put the flag -cw256 in the command recon-all but the >>>> Talairach just failed ... >>>> I got this error message . Can someone explain please ? >>>> >>>> ________________________________________________________________________________ >>>> >>>> #...@# Talairach Failure Detection Tue May 4 12:31:55 IST 2010 >>>> /home/cami/freesurfer/subjects/a1/mri >>>> >>>> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >>>> >>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) >>>> Linux pride 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC >>>> 2009 i686 GNU/Linux >>>> >>>> recon-all exited with ERRORS at Tue May 4 12:31:55 IST 2010 >>>> >>>> ________________________________________________________________________________ >>>> >>>> thanks , >>>> >>>> Antoine >>>> >>>> _______________________________________________ >>>> 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 >> >> >> > _______________________________________________ > 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. > > -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************
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