As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s <subjID> for the second and third steps of the workflow.
jon
In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running?
On Mon, 8 Jul 2013, Jonathan Holt wrote:
As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s <subjID> for the second and third steps of the workflow.
jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Allison I'm running the following
recon-all -all -s <subjID> -i path/to/nifti
attatched is the error recon log
I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and these mgz's are generated before the recon-all process exits with errors.
On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:
In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running?
On Mon, 8 Jul 2013, Jonathan Holt wrote:
As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s <subjID> for the second and third steps of the workflow.
jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I see now. If the orientation information is incorrect, this will continue to be a problem. It sounds like you have access to the dicoms? If so, it's better to wait and use those. Allison
On Mon, 8 Jul 2013, Jonathan Holt wrote:
Allison I'm running the following
recon-all -all -s <subjID> -i path/to/nifti
attatched is the error recon log
I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and these mgz's are generated before the recon-all process exits with errors.
On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:
In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running?
On Mon, 8 Jul 2013, Jonathan Holt wrote:
As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s <subjID> for the second and third steps of the workflow.
jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I potentially have access to dicoms. My PI was confused as we're using GE 2D dcm images with 126 images per timepoint, he wasn't sure how to have them organized for a test run.
On Jul 8, 2013, at 2:20 PM, Allison Stevens Player wrote:
I see now. If the orientation information is incorrect, this will continue to be a problem. It sounds like you have access to the dicoms? If so, it's better to wait and use those. Allison
On Mon, 8 Jul 2013, Jonathan Holt wrote:
Allison I'm running the following
recon-all -all -s <subjID> -i path/to/nifti
attatched is the error recon log
I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and these mgz's are generated before the recon-all process exits with errors.
On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:
In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running?
On Mon, 8 Jul 2013, Jonathan Holt wrote:
As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s <subjID> for the second and third steps of the workflow.
jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Jon,
I am also confused about this whole discussion. It seems from what you said earlier that at some point you have been able to run freesurfer on your images. You did not use the -i flag back then, but somehow managed to get from the original dicom (via nifti, via some mri_convert command) to some image that free surfer was able to use.
Just do the same thing here and then once that is done, run the base and long stream on top of it.
Best, Martin
On Jul 8, 2013, at 2:45 PM, Jonathan Holt whatsdac@umich.edu wrote:
I potentially have access to dicoms. My PI was confused as we're using GE 2D dcm images with 126 images per timepoint, he wasn't sure how to have them organized for a test run.
On Jul 8, 2013, at 2:20 PM, Allison Stevens Player wrote:
I see now. If the orientation information is incorrect, this will continue to be a problem. It sounds like you have access to the dicoms? If so, it's better to wait and use those. Allison
On Mon, 8 Jul 2013, Jonathan Holt wrote:
Allison I'm running the following
recon-all -all -s <subjID> -i path/to/nifti
attatched is the error recon log
I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and these mgz's are generated before the recon-all process exits with errors.
On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote:
In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running?
On Mon, 8 Jul 2013, Jonathan Holt wrote:
As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s <subjID> for the second and third steps of the workflow.
jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
freesurfer@nmr.mgh.harvard.edu
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Allison Stevens Player -
Jonathan Holt -
Martin Reuter