I have T1volume+org.BRIK - should I use those with mri_convert?
Thanks again,
Jesse
On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] < saadz@mail.nih.gov> wrote:
mri_convert usually work with BRIK files.
Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format which FreeSurfer can read fine.
cheers, ziad
On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote:
These are not the standard .BRIK files? Ziad (ccd) will know.
Bruce
On Tue, 24 Nov 2009, Jesse Bledsoe wrote:
Hello,
So far I have had no problems running recon-all with .mnc files but could use some guidance converting/reconstructing brains processed with AFNI (MRDC).
There are 120 MRDC files in the T1 directory.
I believe I need to run mri_convert on these MRDC files but am unsure of what the correct command would be?
Thanks in advance,
Jesse
Yes, though you may need to be careful about the orientation. I'm not sure if BRIKs have orientation info, but I'm sure that mri_convert does not read it. If you can go back to the dicoms, that is best.
doug
Jesse Bledsoe wrote:
I have T1volume+org.BRIK - should I use those with mri_convert?
Thanks again,
Jesse
On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] <saadz@mail.nih.gov mailto:saadz@mail.nih.gov> wrote:
mri_convert usually work with BRIK files. Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format which FreeSurfer can read fine. cheers, ziad On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote: > These are not the standard .BRIK files? Ziad (ccd) will know. > > Bruce > > > On Tue, 24 Nov 2009, Jesse Bledsoe wrote: > >> Hello, >> >> So far I have had no problems running recon-all with .mnc files but >> could >> use some guidance converting/reconstructing brains processed with >> AFNI >> (MRDC). >> >> There are 120 MRDC files in the T1 directory. >> >> I believe I need to run mri_convert on these MRDC files but am >> unsure of >> what the correct command would be? >> >> Thanks in advance, >> >> Jesse >>-- Jesse Bledsoe, M.A. Clinical Psychology Assistant Director, Center for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.
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I have all of the dicoms - what is the best way to run mri_convert on all of the dicoms in the t1 directory?
Thank you,
Jesse
On Sun, Nov 29, 2009 at 5:29 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Yes, though you may need to be careful about the orientation. I'm not sure if BRIKs have orientation info, but I'm sure that mri_convert does not read it. If you can go back to the dicoms, that is best.
doug
Jesse Bledsoe wrote:
I have T1volume+org.BRIK - should I use those with mri_convert?
Thanks again,
Jesse
On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] < saadz@mail.nih.gov mailto:saadz@mail.nih.gov> wrote:
mri_convert usually work with BRIK files.
Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format which FreeSurfer can read fine.
cheers, ziad
On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote:
These are not the standard .BRIK files? Ziad (ccd) will know.
Bruce
On Tue, 24 Nov 2009, Jesse Bledsoe wrote:
Hello,
So far I have had no problems running recon-all with .mnc files but could use some guidance converting/reconstructing brains processed with AFNI (MRDC).
There are 120 MRDC files in the T1 directory.
I believe I need to run mri_convert on these MRDC files but am unsure of what the correct command would be?
Thanks in advance,
Jesse
-- Jesse Bledsoe, M.A. Clinical Psychology Assistant Director, Center for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Just run
mri_convert dicom-from-series.dcm 001.mgz
where "dicom-from-series.dcm" is a single file from the T1 series (it will find the rest).
doug
On Sun, 29 Nov 2009, Jesse Bledsoe wrote:
I have all of the dicoms - what is the best way to run mri_convert on all of the dicoms in the t1 directory?
Thank you,
Jesse
On Sun, Nov 29, 2009 at 5:29 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Yes, though you may need to be careful about the orientation. I'm not sure if BRIKs have orientation info, but I'm sure that mri_convert does not read it. If you can go back to the dicoms, that is best.
doug
Jesse Bledsoe wrote:
I have T1volume+org.BRIK - should I use those with mri_convert?
Thanks again,
Jesse
On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] < saadz@mail.nih.gov mailto:saadz@mail.nih.gov> wrote:
mri_convert usually work with BRIK files.
Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format which FreeSurfer can read fine.
cheers, ziad
On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote:
These are not the standard .BRIK files? Ziad (ccd) will know.
Bruce
On Tue, 24 Nov 2009, Jesse Bledsoe wrote:
Hello,
So far I have had no problems running recon-all with .mnc files but could use some guidance converting/reconstructing brains processed with AFNI (MRDC).
There are 120 MRDC files in the T1 directory.
I believe I need to run mri_convert on these MRDC files but am unsure of what the correct command would be?
Thanks in advance,
Jesse
-- Jesse Bledsoe, M.A. Clinical Psychology Assistant Director, Center for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It looks like this worked, thank you very much for all of your time.
Jesse
On Sun, Nov 29, 2009 at 8:08 PM, Doug Greve greve@nmr.mgh.harvard.eduwrote:
Just run
mri_convert dicom-from-series.dcm 001.mgz
where "dicom-from-series.dcm" is a single file from the T1 series (it will find the rest).
doug
On Sun, 29 Nov 2009, Jesse Bledsoe wrote:
I have all of the dicoms - what is the best way to run mri_convert on all
of the dicoms in the t1 directory?
Thank you,
Jesse
On Sun, Nov 29, 2009 at 5:29 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Yes, though you may need to be careful about the orientation. I'm not sure if BRIKs have orientation info, but I'm sure that mri_convert does not read it. If you can go back to the dicoms, that is best.
doug
Jesse Bledsoe wrote:
I have T1volume+org.BRIK - should I use those with mri_convert?
Thanks again,
Jesse
On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] < saadz@mail.nih.gov mailto:saadz@mail.nih.gov> wrote:
mri_convert usually work with BRIK files.
Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format which FreeSurfer can read fine.
cheers, ziad
On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote:
These are not the standard .BRIK files? Ziad (ccd) will know.
Bruce
On Tue, 24 Nov 2009, Jesse Bledsoe wrote:
Hello,
So far I have had no problems running recon-all with .mnc files but could use some guidance converting/reconstructing brains processed with AFNI (MRDC).
There are 120 MRDC files in the T1 directory.
I believe I need to run mri_convert on these MRDC files but am unsure of what the correct command would be?
Thanks in advance,
Jesse
-- Jesse Bledsoe, M.A. Clinical Psychology Assistant Director, Center for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Douglas N Greve
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Jesse Bledsoe