Hello,
I am attempting to run preproc-sess on my functional data, and am following the tutorial found here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc
I downloaded the tutorial data, and find that when I view fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does not look like a brain). I would expect this file to look like the fsaverage brain, is that not correct?
Andrew
yes, you would expect that. what does it look like? how are you visualizing it?
On 09/20/2012 06:18 PM, Andrew Bock wrote:
Hello,
I am attempting to run preproc-sess on my functional data, and am following the tutorial found here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc
I downloaded the tutorial data, and find that when I view fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does not look like a brain). I would expect this file to look like the fsaverage brain, is that not correct?
Andrew
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It looks like a very patchy, warped version of the brain. I find that this is true for all subjects (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). I used both freeview and fslview to visualize the images.
On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
yes, you would expect that. what does it look like? how are you visualizing it?
On 09/20/2012 06:18 PM, Andrew Bock wrote:
Hello,
I am attempting to run preproc-sess on my functional data, and am following the tutorial found here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc
I downloaded the tutorial data, and find that when I view fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does not look like a brain). I would expect this file to look like the fsaverage brain, is that not correct?
Andrew
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 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.
Can you upload it to our file drop at www.nmr.mgh.harvard.edu/facility/filedrop/
On 09/24/2012 02:58 PM, Andrew Bock wrote:
It looks like a very patchy, warped version of the brain. I find that this is true for all subjects (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). I used both freeview and fslview to visualize the images.
On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
yes, you would expect that. what does it look like? how are you visualizing it? On 09/20/2012 06:18 PM, Andrew Bock wrote: > Hello, > > I am attempting to run preproc-sess on my functional data, and am > following the tutorial found here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc > > I downloaded the tutorial data, and find that when I view > fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does not look > like a brain). I would expect this file to look like the fsaverage > brain, is that not correct? > > Andrew > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ 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.
Actually, before you do that, can you check two things 1. Does the raw data (eg, f.nii) look ok? 2. Does the talairach transform for this subject look ok? doug
On 09/24/2012 04:02 PM, Douglas N Greve wrote:
Can you upload it to our file drop at www.nmr.mgh.harvard.edu/facility/filedrop/
On 09/24/2012 02:58 PM, Andrew Bock wrote:
It looks like a very patchy, warped version of the brain. I find that this is true for all subjects (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). I used both freeview and fslview to visualize the images.
On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
yes, you would expect that. what does it look like? how are you visualizing it? On 09/20/2012 06:18 PM, Andrew Bock wrote: > Hello, > > I am attempting to run preproc-sess on my functional data, and am > following the tutorial found here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc > > I downloaded the tutorial data, and find that when I view > fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does not look > like a brain). I would expect this file to look like the fsaverage > brain, is that not correct? > > Andrew > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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<mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358<tel:617-724-2358> Fax: 617-726-7422<tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ 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.
Hi Doug,
I uploaded two example files, as far as I can tell the raw f.nii and talairach transform look okay. I obtained these files from the tutorial data set, so I'm assuming they were processed properly.
Andrew
On Mon, Sep 24, 2012 at 1:03 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Actually, before you do that, can you check two things
- Does the raw data (eg, f.nii) look ok?
- Does the talairach transform for this subject look ok?
doug
On 09/24/2012 04:02 PM, Douglas N Greve wrote:
Can you upload it to our file drop at
www.nmr.mgh.harvard.edu/facility/filedrop/
On 09/24/2012 02:58 PM, Andrew Bock wrote:
It looks like a very patchy, warped version of the brain. I find that this is true for all subjects (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). I used both freeview and fslview to visualize the images.
On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
yes, you would expect that. what does it look like? how are you visualizing it? On 09/20/2012 06:18 PM, Andrew Bock wrote: > Hello, > > I am attempting to run preproc-sess on my functional data, andam
> following the tutorial found here: >http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc
> > I downloaded the tutorial data, and find that when I view > fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does not look > like a brain). I would expect this file to look like thefsaverage
> brain, is that not correct? > > Andrew > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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<mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358<tel:617-724-2358> Fax: 617-726-7422<tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ 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.-- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Oh, I see now. There is not a problem here. The volume data has the cortical structure masked out (since those are analyzed in the cortical stream). doug
On 09/24/2012 04:22 PM, Andrew Bock wrote:
Hi Doug,
I uploaded two example files, as far as I can tell the raw f.nii and talairach transform look okay. I obtained these files from the tutorial data set, so I'm assuming they were processed properly.
Andrew
On Mon, Sep 24, 2012 at 1:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Actually, before you do that, can you check two things 1. Does the raw data (eg, f.nii) look ok? 2. Does the talairach transform for this subject look ok? doug On 09/24/2012 04:02 PM, Douglas N Greve wrote: > Can you upload it to our file drop at www.nmr.mgh.harvard.edu/facility/filedrop/ <http://www.nmr.mgh.harvard.edu/facility/filedrop/> > > > > On 09/24/2012 02:58 PM, Andrew Bock wrote: >> It looks like a very patchy, warped version of the brain. I find that >> this is true for all subjects >> (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). >> I used both freeview and fslview to visualize the images. >> >> On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> yes, you would expect that. what does it look like? how are you >> visualizing it? >> >> On 09/20/2012 06:18 PM, Andrew Bock wrote: >> > Hello, >> > >> > I am attempting to run preproc-sess on my functional data, and am >> > following the tutorial found here: >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc >> > >> > I downloaded the tutorial data, and find that when I view >> > fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does >> not look >> > like a brain). I would expect this file to look like the fsaverage >> > brain, is that not correct? >> > >> > Andrew >> > >> > >> > >> > >> > >> > >> > _______________________________________________ >> > 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 >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358><tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422><tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> _______________________________________________ >> 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 >> >> >> 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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
ps, here are slides that explain the masking (along with a bunch of other stuff) http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
On 09/24/2012 04:22 PM, Andrew Bock wrote:
Hi Doug,
I uploaded two example files, as far as I can tell the raw f.nii and talairach transform look okay. I obtained these files from the tutorial data set, so I'm assuming they were processed properly.
Andrew
On Mon, Sep 24, 2012 at 1:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Actually, before you do that, can you check two things 1. Does the raw data (eg, f.nii) look ok? 2. Does the talairach transform for this subject look ok? doug On 09/24/2012 04:02 PM, Douglas N Greve wrote: > Can you upload it to our file drop at www.nmr.mgh.harvard.edu/facility/filedrop/ <http://www.nmr.mgh.harvard.edu/facility/filedrop/> > > > > On 09/24/2012 02:58 PM, Andrew Bock wrote: >> It looks like a very patchy, warped version of the brain. I find that >> this is true for all subjects >> (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). >> I used both freeview and fslview to visualize the images. >> >> On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> yes, you would expect that. what does it look like? how are you >> visualizing it? >> >> On 09/20/2012 06:18 PM, Andrew Bock wrote: >> > Hello, >> > >> > I am attempting to run preproc-sess on my functional data, and am >> > following the tutorial found here: >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc >> > >> > I downloaded the tutorial data, and find that when I view >> > fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does >> not look >> > like a brain). I would expect this file to look like the fsaverage >> > brain, is that not correct? >> > >> > Andrew >> > >> > >> > >> > >> > >> > >> > _______________________________________________ >> > 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 >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358><tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422><tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> _______________________________________________ >> 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 >> >> >> 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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Andrew Bock -
Douglas N Greve