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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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