If you know the acquisition parameters, you can enter them by hand into the mri_convert cmd line. You could also specify a 9DOF registration to have the registration program attempt to estimate the scale. doug
ps. Please post all responses to the list and not to us personally. On 2/7/14 9:59 AM, Borzello, Mia wrote: > Hey Doug, > > Thanks a lot for looking through files- I really appreciate it. In this case, > these dicoms files can't be use then right? I'm used to using dicoms with > slice thickness of between 1 -1.5 mm. This is for an old patient of ours, so > I'm not certain that they were running particular type of scans that we > request now. > > Thanks again, > m > ________________________________________ > From: [email protected] > [[email protected]] on behalf of Douglas N Greve > [[email protected]] > Sent: Thursday, February 06, 2014 12:47 PM > To: [email protected] > Subject: Re: [Freesurfer] dicom loading difficulty > > 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 > > _______________________________________________ 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.
