Freesurfer,
I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences?
Thank you, Crystal
QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in a volume, you can use mri_surf2vol doug
On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
Freesurfer,
I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences?
Thank you, Crystal
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Which options should I use when running mri_surf2vol?
Crystal
On 2/1/13 1:08 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in a volume, you can use mri_surf2vol doug
On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
Freesurfer,
I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences?
Thank you, Crystal
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
You can run it with --help to get more info, let me know if you have questions after that On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
Which options should I use when running mri_surf2vol?
Crystal
On 2/1/13 1:08 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in a volume, you can use mri_surf2vol doug
On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
Freesurfer,
I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences?
Thank you, Crystal
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
So I ran mri_surf2vol --help and I am still a little confused on what to run. Where do I actually give the sig.mgh file? All the options seem to ask for an individual subjects file.
Thanks, Crystal
On 2/1/13 5:57 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can run it with --help to get more info, let me know if you have questions after that On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
Which options should I use when running mri_surf2vol?
Crystal
On 2/1/13 1:08 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in a volume, you can use mri_surf2vol doug
On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
Freesurfer,
I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences?
Thank you, Crystal
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
I never received a reply, so I am reposting my message below. Any help would be greatly appreciated.
Thanks in advance, Crystal
On 2/4/13 10:35 AM, "Franklin, Crystal G" FRANKLINC@uthscsa.edu wrote:
So I ran mri_surf2vol --help and I am still a little confused on what to run. Where do I actually give the sig.mgh file? All the options seem to ask for an individual subjects file.
Thanks, Crystal
On 2/1/13 5:57 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can run it with --help to get more info, let me know if you have questions after that On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
Which options should I use when running mri_surf2vol?
Crystal
On 2/1/13 1:08 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in a volume, you can use mri_surf2vol doug
On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
Freesurfer,
I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences?
Thank you, Crystal
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
something like
mri_surf2vol --surfval sig.mgh --hemi lh --identity fsaverage --o sig.lh.vol.nii.gz
doug
On 02/06/2013 09:50 AM, Franklin, Crystal G wrote:
I never received a reply, so I am reposting my message below. Any help would be greatly appreciated.
Thanks in advance, Crystal
On 2/4/13 10:35 AM, "Franklin, Crystal G" FRANKLINC@uthscsa.edu wrote:
So I ran mri_surf2vol --help and I am still a little confused on what to run. Where do I actually give the sig.mgh file? All the options seem to ask for an individual subjects file.
Thanks, Crystal
On 2/1/13 5:57 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can run it with --help to get more info, let me know if you have questions after that On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
Which options should I use when running mri_surf2vol?
Crystal
On 2/1/13 1:08 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in a volume, you can use mri_surf2vol doug
On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
Freesurfer,
I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences?
Thank you, Crystal
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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
-- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Franklin, Crystal G