Hello Experts,
I did the procedure to create a template from scratch by following the steps explaining in this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
The objective was to create a template to use it in the command recon-all qcache target my template.
So, after creating mytemp2.tif I did mris_register for the subjects used for the template (80 subjects) and then I used make_average_subject --subjects <80 subjects> --out mytemplate. Finally I ran recon-all -qcache target mytemplate in order to visualize my analyzes in QDEC. This procedure seems correct to you because when I just visually compared your template (fsaverage) with mine it looks like very different, as if mine was more smoothed (cf ppt file) ? What do you think ?
Best regards.
Sophie Maingault
Hi Sophie I think fsaverage was made from 40 subjects so your 80 subject average will naturally be smoother Cheers Bruce
On Oct 11, 2013, at 11:35 AM, Sophie Maingault sophie.maingault@etud.u-bordeaux2.fr wrote:
Hello Experts,
I did the procedure to create a template from scratch by following the steps explaining in this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
The objective was to create a template to use it in the command recon-all –qcache –target my template.
So, after creating mytemp2.tif I did mris_register for the subjects used for the template (80 subjects) and then I used make_average_subject --subjects <80 subjects> --out mytemplate. Finally I ran recon-all -qcache –target mytemplate in order to visualize my analyzes in QDEC. This procedure seems correct to you because when I just visually compared your template (fsaverage) with mine it looks like very different, as if mine was more smoothed (cf ppt file) ? What do you think ?
Best regards.
Sophie Maingault
<fsaverage VS my template.pptx> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
At the beginning I thought the same thing but a colleague built an another specific template with n = 40 like fsaverage. The results seems to be equivalent. Actually it is weird because when you look at the shape of the inflated fsaverage, it is smoother than mine but when you look at the curvature profile, gyri and sulci seem to be smoother in my template than in fsaverage. Do you have an explanation ? Maybe the treatment of our subjects is less precise than the one used for images required to build fsaverage ?
De : Bruce Fischl fischl@nmr.mgh.harvard.edu Date : vendredi 18 octobre 2013 04:01 À : Sophie Maingault sophie.maingault@etud.u-bordeaux2.fr Cc : "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Comparison between fsaverage and a template created from scratch
Hi Sophie I think fsaverage was made from 40 subjects so your 80 subject average will naturally be smoother Cheers Bruce
On Oct 11, 2013, at 11:35 AM, Sophie Maingault sophie.maingault@etud.u-bordeaux2.fr wrote:
Hello Experts,
I did the procedure to create a template from scratch by following the steps explaining in this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
The objective was to create a template to use it in the command recon-all qcache target my template.
So, after creating mytemp2.tif I did mris_register for the subjects used for the template (80 subjects) and then I used make_average_subject --subjects <80 subjects> --out mytemplate. Finally I ran recon-all -qcache target mytemplate in order to visualize my analyzes in QDEC. This procedure seems correct to you because when I just visually compared your template (fsaverage) with mine it looks like very different, as if mine was more smoothed (cf ppt file) ? What do you think ?
Best regards.
Sophie Maingault
<fsaverage VS my template.pptx> _______________________________________________ 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.
Do you mean that the inflated surface has more curves in it than the fsaverage one? What version are you using? I think that newer versions of make_average_surface (run by make_average_subject) run the inflation out further. Try this
cd $SUBJECTS_DIR/averagesubject/surf mris_inflate -dist .01 -f .001 -no-save-sulc -n 15 ./${hemi}.smoothwm ./${hemi}.inflated
On 10/18/2013 03:41 AM, Sophie Maingault wrote:
At the beginning I thought the same thing but a colleague built an another specific template with n = 40 like fsaverage. The results seems to be equivalent. Actually it is weird because when you look at the shape of the inflated fsaverage, it is smoother than mine but when you look at the curvature profile, gyri and sulci seem to be smoother in my template than in fsaverage. Do you have an explanation ? Maybe the treatment of our subjects is less precise than the one used for images required to build fsaverage ?
De : Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Date : vendredi 18 octobre 2013 04:01 À : Sophie Maingault <sophie.maingault@etud.u-bordeaux2.fr mailto:sophie.maingault@etud.u-bordeaux2.fr> Cc : "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Objet : Re: [Freesurfer] Comparison between fsaverage and a template created from scratch
Hi Sophie I think fsaverage was made from 40 subjects so your 80 subject average will naturally be smoother Cheers Bruce
On Oct 11, 2013, at 11:35 AM, Sophie Maingault <sophie.maingault@etud.u-bordeaux2.fr mailto:sophie.maingault@etud.u-bordeaux2.fr> wrote:
Hello Experts,
I did the procedure to create a template from scratch by following the steps explaining in this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
The objective was to create a template to use it in the command recon-all –qcache –target my template.
So, after creating mytemp2.tif I did mris_register for the subjects used for the template (80 subjects) and then I used make_average_subject --subjects <80 subjects> --out mytemplate. Finally I ran recon-all -qcache –target mytemplate in order to visualize my analyzes in QDEC. This procedure seems correct to you because when I just visually compared your template (fsaverage) with mine it looks like very different, as if mine was more smoothed (cf ppt file) ? What do you think ?
Best regards.
Sophie Maingault
<fsaverage VS my template.pptx> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Yes that what I mean and the command mris_inflate fixed this problem, thanks a lot ! However the curvature profile between fsaverage and my template seems to be very different (attached file), do you know why ?
Sophie
Le 18/10/13 16:19, « Douglas N Greve » greve@nmr.mgh.harvard.edu a écrit :
Do you mean that the inflated surface has more curves in it than the fsaverage one? What version are you using? I think that newer versions of make_average_surface (run by make_average_subject) run the inflation out further. Try this
cd $SUBJECTS_DIR/averagesubject/surf mris_inflate -dist .01 -f .001 -no-save-sulc -n 15 ./${hemi}.smoothwm ./${hemi}.inflated
On 10/18/2013 03:41 AM, Sophie Maingault wrote:
At the beginning I thought the same thing but a colleague built an another specific template with n = 40 like fsaverage. The results seems to be equivalent. Actually it is weird because when you look at the shape of the inflated fsaverage, it is smoother than mine but when you look at the curvature profile, gyri and sulci seem to be smoother in my template than in fsaverage. Do you have an explanation ? Maybe the treatment of our subjects is less precise than the one used for images required to build fsaverage ?
De : Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Date : vendredi 18 octobre 2013 04:01 À : Sophie Maingault <sophie.maingault@etud.u-bordeaux2.fr mailto:sophie.maingault@etud.u-bordeaux2.fr> Cc : "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Objet : Re: [Freesurfer] Comparison between fsaverage and a template created from scratch
Hi Sophie I think fsaverage was made from 40 subjects so your 80 subject average will naturally be smoother Cheers Bruce
On Oct 11, 2013, at 11:35 AM, Sophie Maingault <sophie.maingault@etud.u-bordeaux2.fr mailto:sophie.maingault@etud.u-bordeaux2.fr> wrote:
Hello Experts,
I did the procedure to create a template from scratch by following the steps explaining in this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
The objective was to create a template to use it in the command recon-all qcache target my template.
So, after creating mytemp2.tif I did mris_register for the subjects used for the template (80 subjects) and then I used make_average_subject --subjects <80 subjects> --out mytemplate. Finally I ran recon-all -qcache target mytemplate in order to visualize my analyzes in QDEC. This procedure seems correct to you because when I just visually compared your template (fsaverage) with mine it looks like very different, as if mine was more smoothed (cf ppt file) ? What do you think ?
Best regards.
Sophie Maingault
<fsaverage VS my template.pptx> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- 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
I think it is just what bruce said: with 80 subjects instead of 40 you will have a lot more smearing.
On 10/18/2013 11:27 AM, Sophie Maingault wrote:
Yes that what I mean and the command mris_inflate fixed this problem, thanks a lot ! However the curvature profile between fsaverage and my template seems to be very different (attached file), do you know why ?
Sophie
Le 18/10/13 16:19, « Douglas N Greve » greve@nmr.mgh.harvard.edu a écrit :
Do you mean that the inflated surface has more curves in it than the fsaverage one? What version are you using? I think that newer versions of make_average_surface (run by make_average_subject) run the inflation out further. Try this
cd $SUBJECTS_DIR/averagesubject/surf mris_inflate -dist .01 -f .001 -no-save-sulc -n 15 ./${hemi}.smoothwm ./${hemi}.inflated
On 10/18/2013 03:41 AM, Sophie Maingault wrote:
At the beginning I thought the same thing but a colleague built an another specific template with n = 40 like fsaverage. The results seems to be equivalent. Actually it is weird because when you look at the shape of the inflated fsaverage, it is smoother than mine but when you look at the curvature profile, gyri and sulci seem to be smoother in my template than in fsaverage. Do you have an explanation ? Maybe the treatment of our subjects is less precise than the one used for images required to build fsaverage ?
De : Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Date : vendredi 18 octobre 2013 04:01 À : Sophie Maingault <sophie.maingault@etud.u-bordeaux2.fr mailto:sophie.maingault@etud.u-bordeaux2.fr> Cc : "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Objet : Re: [Freesurfer] Comparison between fsaverage and a template created from scratch
Hi Sophie I think fsaverage was made from 40 subjects so your 80 subject average will naturally be smoother Cheers Bruce
On Oct 11, 2013, at 11:35 AM, Sophie Maingault <sophie.maingault@etud.u-bordeaux2.fr mailto:sophie.maingault@etud.u-bordeaux2.fr> wrote:
Hello Experts,
I did the procedure to create a template from scratch by following the steps explaining in this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
The objective was to create a template to use it in the command recon-all qcache target my template.
So, after creating mytemp2.tif I did mris_register for the subjects used for the template (80 subjects) and then I used make_average_subject --subjects <80 subjects> --out mytemplate. Finally I ran recon-all -qcache target mytemplate in order to visualize my analyzes in QDEC. This procedure seems correct to you because when I just visually compared your template (fsaverage) with mine it looks like very different, as if mine was more smoothed (cf ppt file) ? What do you think ?
Best regards.
Sophie Maingault
<fsaverage VS my template.pptx> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Sophie Maingault