Hi Jennifer, We had the same problem with importing scans into Freesurfer that had been converted from PAR/REC to NIFTI using nipy. The problem only affected a subset of the data. When visualising the data with Fiji the brain appeared highly skewed. Upon closer inspection of the header data of the NIFTI file we discovered that there was an extra byte somewhere between the description fields and the magic number sequence, causing the magic number to be misinterpreted by Freesurfer. The extra byte was somewhere in the transformation matrix that is located between the description field and the magic number, but it's impossible to fix unless you know what the content of the transformation matrix is supposed to be. However, when using dcm2nii, part of mricron (from what I understand a newer version of mricro), to convert our PAR/REC files to NIFTI the problem disappeared.
Maybe you could try dcm2nii and see if that helps your case as well? It's available from here: http://www.mccauslandcenter.sc.edu/mricro/mricron/install.html If you are on Linux or Mac OS X you could try to run the command `head -c350 <path-to-nifti-file> | hexdump -Cv`, where <path-to-nifti-file> is the path to your NIFTI file. This command will print the first 350 bytes of the NIFTI file that contains the header (plus two extra bytes) in hexadecimal and ASCII format. I don't have an example available at the moment, but the header should end in 'ni1..' or 'n+1..' in the rightmost column. If you get 'ni1.' or 'n+1.' (only one dot at the end), you probably have the same problem as we experienced. We don't know the origin of this extra byte, but most likely it is a bug in the conversion software that is affecting only some of the scans. Regards, Jalmar > On 09 Jun 2015, at 22:21, Kriegel, Jennifer Lynn Sarai > <jlk130...@utdallas.edu> wrote: > > mricro > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, June 09, 2015 3:16 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] bad magic number > > how was it created? > > On 06/09/2015 04:03 PM, Kriegel, Jennifer Lynn Sarai wrote: >> MRIcro opens it, and so does SPM 8. >> >> >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Tuesday, June 09, 2015 3:02 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] bad magic number >> >> Hi Jennifer >> >> can MRIcro read it? Usually that means it is corrupted Bruce >> >> >> On Tue, 9 Jun 2015, Kriegel, Jennifer Lynn Sarai >> wrote: >> >>> Hi, >>> >>> >>> >>> I’m getting a bad magic number error using mri_convert. I’m trying to >>> convert a .nii file to a .mgz file. I’ve searched all over and all I >>> can find is that you can use python in another program to delete this >>> number, and it is related to the file extension. I’ve tried using the >>> .nifti1 extension, as well as .nii, as I have a .img file in the >>> folder as well, but then it doesn’t recognize the file extension. The >>> files were converted using mricro from hdr/img MPRAGE files to correct >>> orientation into the .nii files. >>> >>> >>> >>> I also tried using the original .hdr file to convert, and it spits >>> out an orientation error. >>> >>> >>> >>> Any help would be appreciated. >>> >>> >>> >>> >>> >>> - Jennifer Lynn Sarai Kriegel >>> >>> MS in Psychological Sciences, Cognition and Neuroscience Emphasis >>> >>> Functional Neuroimaging of Memory Lab, Center for Vital Longevity >>> >>> The University of Texas at Dallas >>> >>> jlk130...@utdallas.edu >>> >>> ------------------------------------------------------------ >>> >>> I am looking for a lot of men who have an infinite capacity to not >>> know what can't be done. >>> >>> - Henry Ford >>> >>> >>> >>> The important thing is not to stop questioning. Curiosity has its own >>> reason for existing. >>> >>> - Albert Einstein >>> >>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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
