Hi everyone,
I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images.
I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate HippoCampus -1 Otherwise - 0
Here are sample files link https://drive.google.com/drive/folders/0B6rH1c6LupG_b3I4WUJ1RWZCbnM?usp=sharing
Kindly help me!
Dilip Puri http://dilippuri.github.io IIIT Vadodara http://www.iiitvadodara.ac.in
Use
mri_binarize --i aseg.mgz --match 17 --binval -1 --o your.lefthippo.nii.gz
On 4/6/17 6:00 AM, Dilip Puri wrote:
Hi everyone,
I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images.
I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate HippoCampus -1 Otherwise - 0
Here are sample files link https://drive.google.com/drive/folders/0B6rH1c6LupG_b3I4WUJ1RWZCbnM?usp=sharing
Kindly help me!
Dilip Puri http://dilippuri.github.io IIIT Vadodara http://www.iiitvadodara.ac.in
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Dilip
yes, freesurfer will do this for you, although the labels will be 17 for left hippocampus and 53 for right.
cheers Bruce On Thu, 6 Apr 2017, Dilip Puri wrote:
Hi everyone,
I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images.
I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate HippoCampus -1 Otherwise - 0
Here are sample files link
Kindly help me!
Dilip Puri IIIT Vadodara
Hi everyone,
when I used following command:
mri_binarize --i myfile.img --match 17 --binval -1 --o your.lefthippo.nii.gz
then I got output your.lefthippo.nii.gz file when I read this file using FREEVIEW then it completly different from original mask.
Thanks
Dilip
On Thu, Apr 6, 2017 at 11:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dilip
yes, freesurfer will do this for you, although the labels will be 17 for left hippocampus and 53 for right.
cheers Bruce On Thu, 6 Apr 2017, Dilip Puri wrote:
Hi everyone,
I am working on Hippocampus segmentation using Neural Networks for that
I need labeled images of Hippocampus corresponding to original images.
I am using OASIS Dataset for this. I want to generate labeled images
using FREESURFER. Is there any way to label each 3D co-ordinate
HippoCampus -1 Otherwise - 0
Here are sample files link
Kindly help me!
Dilip Puri IIIT Vadodara
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.
what is your freeview command? Are you trying to view it on a surface?
On 04/07/2017 12:53 AM, Dilip Puri wrote:
Hi everyone,
when I used following command:
mri_binarize --i myfile.img --match 17 --binval -1 --o your.lefthippo.nii.gz
then I got output your.lefthippo.nii.gz file when I read this file using FREEVIEW then it completly different from original mask.
Thanks
Dilip
On Thu, Apr 6, 2017 at 11:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Dilip yes, freesurfer will do this for you, although the labels will be 17 for left hippocampus and 53 for right. cheers Bruce On Thu, 6 Apr 2017, Dilip Puri wrote: > Hi everyone, > > I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images. > > I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate > HippoCampus -1 > Otherwise - 0 > > Here are sample files link > > Kindly help me! > > > Dilip Puri > IIIT Vadodara > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 used command
freeview -v .
then from title bar I uploaded your.lefthippo.nii file.
On Fri, Apr 7, 2017 at 9:40 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
what is your freeview command? Are you trying to view it on a surface?
On 04/07/2017 12:53 AM, Dilip Puri wrote:
Hi everyone,
when I used following command:
mri_binarize --i myfile.img --match 17 --binval -1 --o your.lefthippo.nii.gz
then I got output your.lefthippo.nii.gz file when I read this file using FREEVIEW then it completly different from original mask.
Thanks
Dilip
On Thu, Apr 6, 2017 at 11:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Dilip yes, freesurfer will do this for you, although the labels will be 17 for left hippocampus and 53 for right. cheers Bruce On Thu, 6 Apr 2017, Dilip Puri wrote: > Hi everyone, > > I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images. > > I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3Dco-ordinate
> HippoCampus -1 > Otherwise - 0 > > Here are sample files link > > Kindly help me! > > > Dilip Puri > IIIT Vadodara > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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
that freeview command is incorrect. it would need to be something like freeview -v file.nii.gz
On 04/07/2017 12:31 PM, Dilip Puri wrote:
I used command
freeview -v .
then from title bar I uploaded your.lefthippo.nii file.
On Fri, Apr 7, 2017 at 9:40 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what is your freeview command? Are you trying to view it on a surface? On 04/07/2017 12:53 AM, Dilip Puri wrote: > Hi everyone, > > when I used following command: > > mri_binarize --i myfile.img --match 17 --binval -1 --o > your.lefthippo.nii.gz > > then I got output your.lefthippo.nii.gz file when I read this file > using FREEVIEW then it completly different from original mask. > > > > Thanks > > Dilip > > > On Thu, Apr 6, 2017 at 11:08 PM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Dilip > > yes, freesurfer will do this for you, although the labels will be > 17 for > left hippocampus and 53 for right. > > cheers > Bruce > On Thu, 6 Apr 2017, Dilip Puri wrote: > > > Hi everyone, > > > > I am working on Hippocampus segmentation using Neural Networks > for that I need labeled images of Hippocampus corresponding to > original images. > > > > I am using OASIS Dataset for this. I want to generate labeled > images using FREESURFER. Is there any way to label each 3D co-ordinate > > HippoCampus -1 > > Otherwise - 0 > > > > Here are sample files link > > > > Kindly help me! > > > > > > Dilip Puri > > IIIT Vadodara > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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