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 greve@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 Grevegreve@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
pfannmoeOn Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegreve@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
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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