I'm not sure what is going on with that dicom file (we usually have dicoms from MRI machines). I ran this command
mri_convert CT000000.dcm ct.mgh -iks 5 -it dicom -iid 1 0 0 -ijd 0 0.1153970063 -0.9933194518 -ikd 0 -.9933 .1154 and it starts to look ok. The problem appears to be that the slice thickness is wrong. It is set to 5mm in the cmd above (-iks 5). This is the value that is in the dicom. Sorry, don't know what else to tell you since it looks like the dicom itself si wrong doug On 02/04/2014 03:29 PM, Borzello, Mia wrote: > Okay, I separated and moved everything into its own folder. I just ran > spmregister and then tkregister and the CT is really skewed. I'm wondering if > I accidentally fussed with something or if there is another way I can fix > this. Can someone look at the data? I chose the CT with the most slices, and > the second highest scan has 35 slices. > > Thanks so much, > m > ________________________________________ > From: [email protected] > [[email protected]] on behalf of Douglas N Greve > [[email protected]] > Sent: Tuesday, February 04, 2014 3:01 PM > To: [email protected] > Subject: Re: [Freesurfer] dicom loading difficulty > > I would put the new ones into a different folder > doug > > On 02/04/2014 02:35 PM, Borzello, Mia wrote: >> Hmm this didn't seem to work. I converted all 78 files. Is it okay to leave >> both versions of the dicoms (the ones with the .dcm extension and the >> original in the same folder)? >> >> Thanks, >> m >> ________________________________________ >> From: [email protected] >> [[email protected]] on behalf of Douglas N Greve >> [[email protected]] >> Sent: Tuesday, February 04, 2014 11:21 AM >> To: [email protected] >> Subject: Re: [Freesurfer] dicom loading difficulty >> >> FS does not natively uncompress jpeg compressed dicoms, however, you can >> get and use the dcmdjpeg to do the decompression like this >> >> dcmdjpeg +te dicomfile dicomfile >> >> this will overwrite the dicom file, so make a backup. You will have to >> run this for all of your dicoms >> >> doug >> >> >> On 02/04/2014 10:31 AM, Borzello, Mia wrote: >>> Hi Freesurfers, >>> >>> I'm trying to convert CT dicoms to the MGZ format, but am getting an >>> error saying "the pixel data cannot be loaded as it is JPEG >>> compressed." I originally got dicoms without the extension .dcm, but >>> then resaved them with the extension. Using either version didn't >>> work. If you can shed some light on this, that would be great! >>> >>> Thanks, >>> m >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> 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 >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [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.
