Hi Lena,
you definitely want to avoid analyze format, as it will remove the direction cosine information you need for example to tell left from right (it's probably why you have a flip).
We don't have much experience with dicom. Have you tried using -it dicom in mri_convert to be explicit about the format?
cheers, Bruce
On Thu, 30 Jul 2009, Lena Palaniyappan wrote:
Dear group
Many thanks for all your help and encouragement. I avoided analyze format as suggested - Converted extensionless dicom files to nifti1 mode using MRICONVERT ( http://lcni.uoregon.edu/~jolinda/MRIConvert/) and then used mri_convert to obtain .mgz files. It worked :) !!
The MRICONVERT program does not mind the absence of .dcm extensions from Philips scanner.
Cheers Lena
On 30/07/2009 13:36, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Lena,
you definitely want to avoid analyze format, as it will remove the direction cosine information you need for example to tell left from right (it's probably why you have a flip).
We don't have much experience with dicom. Have you tried using -it dicom in mri_convert to be explicit about the format?
cheers, Bruce
On Thu, 30 Jul 2009, Lena Palaniyappan wrote:
glad it worked out
Bruce On Fri, 31 Jul 2009, Lena Palaniyappan wrote:
Dear group
Many thanks for all your help and encouragement. I avoided analyze format as suggested - Converted extensionless dicom files to nifti1 mode using MRICONVERT ( http://lcni.uoregon.edu/~jolinda/MRIConvert/) and then used mri_convert to obtain .mgz files. It worked :) !!
The MRICONVERT program does not mind the absence of .dcm extensions from Philips scanner.
Cheers Lena
On 30/07/2009 13:36, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Lena,
you definitely want to avoid analyze format, as it will remove the direction cosine information you need for example to tell left from right (it's probably why you have a flip).
We don't have much experience with dicom. Have you tried using -it dicom in mri_convert to be explicit about the format?
cheers, Bruce
On Thu, 30 Jul 2009, Lena Palaniyappan wrote:
1. What's your cmd line and what does it say when it fails? See surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for more useful info you can send.
2. Without the mat file, the geometry on them could be horribly wrong. I would suggest loading it into tkmedit to make sure that it is oriented properly.
doyug
Lena Palaniyappan wrote:
--
Hello group
I am new to freesurfer. I have two problems. Please accept my apologies if these queries are bit naïve! Any help will be much appreciated. I am trying to autorecon1 a single image obtained from Philips 3T as dicom output. I use MacOS – X11 terminal.
- I am not able to use mri_convert to change these images to .mgz or niftii format. Is this because these files lack .dcm extension? For some reason all these files don’t have .dcm extension though my radiology colleagues repeatedl assure me that they are dicoms!
- I obtained some T1 MPRAGEs in img hdr format (no mat files came with them) and I am trying to recon1 this subject. There is a problem with talairach transforms (z –8) that needs manual correction. But when I try to open the brainmask.mgz on tkmedit for visual inspection I get the following msg
Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.
Nevertheless when I proceed to open the tkregister2 for manual correction, ( without —surf orig), I see the moveable image 180* flipped compared to the target image in sagittal view. Could this be due to some error in conversion of dcms? Or is this due to acquisition differences? Please help.
Many thanks in advance Lena
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