I just noticed that the data I am currently working with are from a data set in which the freesurfer protocol for the anatomical sequence has not been used. Instead an in-house protocol is applied.
On Wed, 17 Oct 2012 18:31:05 +0200 Jörg Pfannmöller <pfannmo...@uni-greifswald.de> 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 > > > -- > Jörg Pfannmöller <pfannmo...@uni-greifswald.de> -- Jörg Pfannmöller <pfannmo...@uni-greifswald.de> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
