Hi experts-I have to document for some non-Freesurfer users what is in all the Freesurfer 3.05 subdirectories from an analysis. We have come up with a lot of it from the Wiki pages and tutorials, but there are some things that still aren't clear (what exactly is the bem directory for? What exactly is the mri_nu_correct.mni.log file? Etc.). Is it laid out clearly somewhere? I've seen the pages about which files are created by what process, etc. and it seems like it should say somewhere what these directories and files really are, I'm just missing it.
Thanks,
Jess
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Jessica Turner, Ph.D.
Project Manager, FBIRN (www.nbirn.net)
Department of Psychiatry and Human Behavior
University of California, Irvine
Phone: (949) 824-3331
Fax: (949) 824-3324
Hi Jess,
the bem dir is where the boundary element models needed for EEG/MEG inverse solutions are stored if you generate them. The mri_nu_correct.mni.log file is the log file created by the MNI N3 nonuniformity correction software. Most of the other relevant files should be documented on the wiki.
cheers, Bruce On Fri, 30 Nov 2007, Turner, Jessica wrote:
Hi experts-I have to document for some non-Freesurfer users what is in all the Freesurfer 3.05 subdirectories from an analysis. We have come up with a lot of it from the Wiki pages and tutorials, but there are some things that still aren't clear (what exactly is the bem directory for? What exactly is the mri_nu_correct.mni.log file? Etc.). Is it laid out clearly somewhere? I've seen the pages about which files are created by what process, etc. and it seems like it should say somewhere what these directories and files really are, I'm just missing it.
Thanks,
Jess
Jessica Turner, Ph.D.
Project Manager, FBIRN (www.nbirn.net)
Department of Psychiatry and Human Behavior
University of California, Irvine
Phone: (949) 824-3331
Fax: (949) 824-3324
Hallo, does somebody know, if there exist a similar program as DicomSorter for Linux, that organize that images and put it in the right folders? I run both, Windows and Linux on diferent parititions and its always a time spending thing to load into windows just for DicomSorter...I tried to install DicomSorter within the Wine Emulator, but it doesn´t work. I tested the other windowsprograms and they are running normally. Thanks for any help, suggestion. Cheers, Thomas
Try using unpacksdcmdir and specify dicom as the output format. It will also do conversions to various formats too.
doug
Thomas Doering wrote:
Hallo, does somebody know, if there exist a similar program as DicomSorter for Linux, that organize that images and put it in the right folders? I run both, Windows and Linux on diferent parititions and its always a time spending thing to load into windows just for DicomSorter...I tried to install DicomSorter within the Wine Emulator, but it doesn´t work. I tested the other windowsprograms and they are running normally. Thanks for any help, suggestion. Cheers, Thomas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, it has been a while that last message. Well, i tried recently to use unpacksdcmdir, but without sucess. I used unpacksdcmdir -src /Desktop/08976652 -targ /Desktop/Sorted -generic, knowing that something is missing to specify dicom as you indicated in your last mail. Please, could you give me a hint? Thanks a lot, Thomas ----- Original Message ----- From: "Doug Greve" greve@nmr.mgh.harvard.edu To: "Thomas Doering" mri@cdpi.com.br Cc: freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 03, 2007 2:46 PM Subject: Re: [Freesurfer] DicomSorter
Try using unpacksdcmdir and specify dicom as the output format. It will also do conversions to various formats too.
doug
Thomas Doering wrote:
Hallo, does somebody know, if there exist a similar program as DicomSorter for Linux, that organize that images and put it in the right folders? I run both, Windows and Linux on diferent parititions and its always a time spending thing to load into windows just for DicomSorter...I tried to install DicomSorter within the Wine Emulator, but it doesn´t work. I tested the other windowsprograms and they are running normally. Thanks for any help, suggestion. Cheers, Thomas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
MRI CDPI -
Thomas Doering
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Turner, Jessica