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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, February 06, 2014 12:47 PM To: freesurfer@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 04, 2014 3:01 PM To: freesurfer@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, February 04, 2014 11:21 AM To: freesurfer@nmr.mgh.harvard.edu 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 dicomfilethis 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
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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/
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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/
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Douglas Greve