If you use -per-session, all of them should be processed. Why do you think they are not? Also, just saying something is not working is not very informative. Send command lines and terminal output of the error. thanks! doug
On 05/06/2013 05:46 AM, Jörg Pfannmöller wrote: > Sorry, I have to cancel my last contribution. Another Problem crossed my way. > If I have more than one run, only the first one is preprocessed if i use > -per-session. What can I do about it? > If I use -per-run all runs are preprocessed, but selxavg3-sess tells me that > it can not determine the file format of the fmc files. Actually those files > are called fmcpr, if I use -per-run. How can do I have to proceed if there is > more than one run? > > > > > > On Mon, 6 May 2013 10:54:54 +0200 > Jörg Pfannmöller <pfannmo...@uni-greifswald.de> wrote: > >> 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 > -- 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: 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
