Thanks for your help. It works fine if one uses preproc-sess -per-run -fwhm 5 -fsd bold -s sess01 ... .
On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > You'll have to run preproc like: > preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 > In this case, you are just specifiying -per-session and not specifying > -mni305 or -surface > > When you run mkanalysis-sess, specify -native instead of -mni305 or > -surface, like: > mkanalysis-sess -native -fwhm 5 ... > > doug > > > > On 10/19/2012 03:59 AM, Jörg Pfannmöller wrote: > > Hi Doug, > > > > the preprocessing is fine the quaility factor for the registration between > > functional and anatomical is ~0.3. Have I to use feat to do the volume > > analysis? > > > > Cheers pfannmoe > > > > On Thu, 18 Oct 2012 11:50:38 -0400 > > Douglas N Greve<gr...@nmr.mgh.harvard.edu> wrote: > > > >> It is too hard to tell what is going on here from just this image. I > >> would not immediately conclude that it is a vessel. Does the activation > >> otherwise look ok? What about other contrasts? Is the registration > >> accurate? When trying to debug these things, it often makes sense to > >> analyze the data in the volume. > >> doug > >> > >> On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote: > >>> It is attached to this mail. > >>> > >>> > >>> > >>> On Tue, 16 Oct 2012 16:16:54 -0400 > >>> Douglas N Greve<gr...@nmr.mgh.harvard.edu> wrote: > >>> > >>>> can you send a pic? > >>>> > >>>> > >>>> On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: > >>>>> Hi Doug, > >>>>> > >>>>> the analysis is done on the cortex surface. The following commands are > >>>>> used for the analysis of the functional activation in the right > >>>>> hemisphere cortex: > >>>>> > >>>>> preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh > >>>>> -mni305 -fwhm 0 -per-run -nosmooth > >>>>> > >>>>> plot-twf-sess -s sessionID -fsd bold -mc > >>>>> > >>>>> tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum > >>>>> > >>>>> mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related > >>>>> -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 > >>>>> -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force > >>>>> > >>>>> mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 > >>>>> > >>>>> selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc > >>>>> > >>>>> tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl > >>>>> ./label_01.tcl. > >>>>> > >>>>> Left hemisphere and sub-cortical analysis are also carried out. Results > >>>>> are depicted on the flatted cortex surface in the primary somatosensory > >>>>> cortex. > >>>>> This label is a combination of the freesurfer areas BA1, BA2, BA3a and > >>>>> BA3b. The activation is masked to this label. An example of the line > >>>>> like pattern > >>>>> is uploaded on your ftp server using my email (pfannmoelj ... > >>>>> uni-greifswald.de, the at sign is replaced by dots) as the password. > >>>>> There is a snaking > >>>>> line in the middle of the image which is a candidate for a vessel. In > >>>>> other images the straight line like patterns or line like patterns with > >>>>> gaps are > >>>>> found. Is there a way to analyze the data in a volume based stream > >>>>> without differentiation between cortex and sub-cortical brain in which > >>>>> the distance > >>>>> of the line like pattern relative to the gray substance is visible? > >>>>> This could be used in order to classify between true activation and > >>>>> vessel activation. > >>>>> We have epi data with spatial resolution of 2x2x4mm^3 (used to generate > >>>>> attached image) and 1.5x1.5x2mm^3 which both show line like patterns. > >>>>> Structural > >>>>> data are taken using the single echo freesurfer protocol for the flash > >>>>> sequence, recommended for cortex. I hope those information are of help. > >>>>> > >>>>> Sincerely yours > >>>>> > >>>>> pfannmoe > >>>>> > >>>>> > >>>>> On Mon, 15 Oct 2012 17:52:04 -0400 > >>>>> Douglas N Greve<gr...@nmr.mgh.harvard.edu> wrote: > >>>>> > >>>>>> Hi Jorg, can you tell us a little more? A picture would be good. Also, > >>>>>> describe how you have done your analysis (eg, on the surface or in the > >>>>>> volume, how much smoothing). > >>>>>> doug > >>>>>> > >>>>>> On 10/15/2012 11:01 AM, wrote: > >>>>>>> Dear Freesurfers, > >>>>>>> > >>>>>>> I computed the functional activation in a sensory task using > >>>>>>> freesurfer's fsfast stream. In the cortex surface line like activated > >>>>>>> regions are present. Their extension is much larger than the > >>>>>>> extension of the expected regions. Therefore, I suppose that those > >>>>>>> regions are due to vessels. Is there a possibility in freesurfer to > >>>>>>> remove them. Ideally there would be something like a volume based > >>>>>>> mode which does not sxclude the cortex. In this mode the vessels > >>>>>>> couls be identified and removed. Any help is highly apprexiated. > >>>>>>> > >>>>>>> Respectfully yours > >>>>>>> > >>>>>>> pfannmoe > >>>>>>> _______________________________________________ > >>>>>>> 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 > >>>>>> gr...@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. > >>>>>> > >>>>> _______________________________________________ > >>>>> 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 > >>>> gr...@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 > >>> > >>> > >>> _______________________________________________ > >>> 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 > >> gr...@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 > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 -- <pfannmo...@uni-greifswald.de> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
