Freesurfer February 2006

freesurfer@nmr.mgh.harvard.edu

40 participants
52 discussions

editing pre-existing annotations
by Eric Feczko 09 Nov '06

09 Nov '06

Hey, Is there a way to add structures/labels to a pre-existing annotation file? I sampled an annotated atlas onto a subjects surface. But when I load the annotation and try to create a new label, I can't export the edited annotation without eliminating the new label. I tried to create a new color lookup table with the new structure included, and I can load the table in tksurfer just fine. However, when I also try to import the pre-existing annotation(in order to edit it), the color table existing in the annotation overrides the color lookup table I load. If it try to load the table after importing the annotation, the new structure/label does not show up in the label window. If anyone can help me with this issue, that would be great, thanks! -Eric

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Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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retinotopy and FsFast
by Jane Aspell 17 May '06

17 May '06

Hi Thanks for all your previous help with freesurfer. I am trying to use FsFast to do retinotopy analysis and have been following the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I come undone at the stage of running the actual analysis, where the command should be: >sfa-sess -s avdk -a rtopy what does 'avdk' refer to? when i run it i get: ERROR: could not find session avdk when i try it with the arguments: >sfa-sess -analysis rtopy -sf sessid which is similar to the arguments needed for 'selxavg-sess' i get a similar error of not been able to find my (particular subject's) session. i believe i have set up the all the directory structures etc correctly for the sessions format as previous steps worked fine. any ideas what's going wrong? thanks Jane Aspell

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Re: [Freesurfer] Re: mk-fieldsign problems
by Jane Aspell 03 May '06

03 May '06

Hi I would be really grateful if someone could help me with the problems I am having with mk-fieldsign. Even after installing a new version of freesurfer and making various changes to libraries etc. when i run: "paint-sess -sf sessid -a rtopy -hemi rh" i get the error below: tksurfer: run tcl script: mk-fieldsign.tcl couldn't read file "mk-fieldsign.tcl": no such file or directory even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which works fine). i am running Red Hat Linux release 9 (Shrike) and installed from freesurfer-Linux-rh9-v2.2.tar.gz any idea what to do? thanks again for your help! Jane In message <1134599450.17318.34.camel(a)minerva.nmr.mgh.harvard.edu> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> writes: > Jane, > > Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does > not use these libraries any more (I think the older -20040218 release > did, however). > > Do you have the environment variable ITCL_LIBRARY defined in your > startup .cshrc file? You can test if it is set by typing (in csh or > tcsh): > > env|grep ITCL > > If it is set (which it might be, from your older freesurfer > installation), then it should be deleted or commented-out from > your .cshrc (or possibly it was placed in your > $FREESURFER_HOME/SetUpFreeSurfer.csh file). > > You can also just type this: > > unsetenv ITCL_LIBRARY > > and then try tkmedit. > > If this is not the problem, can you tell me which OS you are running? > Type: > > cat /etc/redhat-release > > and > > uname -a > > A last ditch effort is to install the itcl libs, from this site: > > http://rpmfind.net/linux/rpm2html/search.php?query=itcl > > But this should not be necessary, as tkmedit that you have does not use > this library (I am truly puzzled why 'ldd' shows that it needs these > libs). > > Thanks, > > Nick > > > On Mon, 2005-12-12 at 11:40 +0000, Jane Aspell wrote: > > hi nick > > > > when i type >ldd `which tkmedit` i get the ouput pasted below this email. > > libitk3.2.so and libitcl3.2.so are not found - could be the problem? > > > > uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh > > (and typing 'unsetenv TCLLIBPATH') had no effect. > > > > an earlier version of freesurfer(freesurfer-20040218) didn't give me any of > > these problems and tkmedit etc worked fine. > > > > also, does ANYONE know how to interpret the colour coding (for fovea/vertical > > meridian etc) produced by the FsFast retinotopy analysis?! > > > > thanks again! > > > > jane > > > > > > >ldd `which tkmedit` > > libtix8.1.8.3.so => > > /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000) > > libtk8.4.so => /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so > > (0x40051000) > > libtcl8.4.so => > > /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000) > > libglut.so.3 => /usr/lib/libglut.so.3 (0x401ba000) > > libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401ef000) > > libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401f8000) > > libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x40210000) > > libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000) > > libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000) > > libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x402ab000) > > libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x402ef000) > > libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x403ce000) > > libtiff.so.3 => /usr/lib/libtiff.so.3 (0x403ed000) > > libcrypt.so.1 => /lib/libcrypt.so.1 (0x4042e000) > > libz.so.1 => /usr/lib/libz.so.1 (0x4045b000) > > libm.so.6 => /lib/tls/libm.so.6 (0x40469000) > > libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4048b000) > > libc.so.6 => /lib/tls/libc.so.6 (0x42000000) > > libitk3.2.so => not found > > libitcl3.2.so => not found > > libdl.so.2 => /lib/libdl.so.2 (0x4049a000) > > libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x4049e000) > > libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x404f0000) > > libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x404ff000) > > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x405b2000) > > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) > > > > > > > > In message <1133802940.21136.14.camel(a)minerva.nmr.mgh.harvard.edu> Nick > > Schmansky <nicks(a)nmr.mgh.harvard.edu> writes: > > > Jane, > > > > > > This is an unusual error, since tkmedit and tksurfer do not use the ITK > > > library. To figure out how libitk3.2.so is being referenced, can you > > > send me the output of this command: > > > > > > ldd `which tkmedit` > > > > > > I suspect there is some conflict between the FSL setup and Freesurfer, > > > as FSL does use ITK, and Freesurfer does not, but performs the FSL setup > > > (as a convenience to MGH-NMR users). Along this line, one option is to > > > edit the file FreeSurferEnv.csh (found in your $FREESURFER_HOME) and > > > comment-out this line: > > > > > > source ${FSL_DIR}/etc/fslconf/fsl.csh > > > > > > like this: > > > > > > # source ${FSL_DIR}/etc/fslconf/fsl.csh > > > > > > Another option is to type this after sourcing the freesurfer setup file: > > > > > > unsetenv TCLLIBPATH > > > > > > This last option is just a guess at a fix though. > > > > > > Nick > > > > > > > > > On Mon, 2005-12-05 at 15:37 +0000, Jane Aspell wrote: > > > > hi > > > > > > > > i installed a newer version of freesurfer (using download > > > > freesurfer-Linux-rh9-v2.2.tar.gz) but when i try and run tkmedit or tksurfer i > > > > get the error: > > > > > > > > "error while loading shared libraries: libitk3.2.so: cannot open shared object > > > > file: No such file or directory" > > > > > > > > this is my output when i source SetUpFreeSurfer.csh: > > > > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > FREESURFER_HOME /home/jaspell/freesurfer > > > > FSFAST_HOME /home/jaspell/freesurfer/fsfast > > > > SUBJECTS_DIR /home/jaspell/freesurfer/subjects > > > > FUNCTIONALS_DIR /home/jaspell/freesurfer/sessions > > > > MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin > > > > MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib > > > > TCLLIBPATH /home/jaspell/freesurfer/lib/tcltktixblt/lib > > > > FSL_DIR /usr/local/fsl > > > > > > > > and these are the contents of /home/jaspell/freesurfer/lib/tcltktixblt/lib: > > > > > > > > blt2.4/ libBLTlite24.a libtclstub8.4.a libtk8.4.so* > > > > tix8.1/ > > > > libBLT24.a* libBLTlite.2.4.dylib* libtix8.1.8.3.so libtk.so.0* > > > > tixConfig.sh > > > > libBLT.2.4.dylib* libBLTlite.a libtix8.1.8.4.so libtkstub8.4.a > > > > tk8.4/ > > > > libBLT.2.dylib* libtcl8.4.so* libtixsam8.1.8.4.so tcl8.4/ > > > > tkConfig.sh > > > > libBLT.a* libtcl.so.0* libtix.so.0 tclConfig.sh > > > > > > > > > > > > any idea how to fix it? > > > > > > > > i don't suppose there's a way of updating an old version of freesurfer without > > > > reinstalling the entire (new version) package? > > > > > > > > thanks! > > > > > > > > jane > > > > > > > > > > > > > > > > > > > > In message <Pine.LNX.4.62.0512021326490.5676(a)icebox.nmr.mgh.harvard.edu> Doug > > > > Greve <greve(a)nmr.mgh.harvard.edu> writes: > > > > > > > > > > That's a pretty old version. Can you download and install a new version? > > > > > > > > > > I actually don't know that much about the interpretation of the color > > > > > wheel. Maybe Nouchine or Sari can help with this. > > > > > > > > > > doug > > > > > > > > > > > > > > > On Fri, 2 Dec 2005, Jane Aspell wrote: > > > > > > > > > > > hi again > > > > > > > > > > > > i'm still really stuck with my retinotopy analysis as i'm not sure if my > > > > > > version of paint-sess $Id: paint-sess,v 1.2 2003/08/06 00:53:50 greve Exp $ > > > > > > FAST Version 20031218) has a bug in it (it doesn't make the field sign > > map). i > > > > > > originally downloaded freesurfer-20040218-Linux.tar.gz (for RedHat 9). > > > > > > > > > > > > also, can someone also confrim the colour coding is: red=upper field/fovea, > > > > > > blue=horizontal meridian/parafovea, green=lower visual field/periphery? > > > > > > > > > > > > i can't work out what the overlay threshold settings should be in > > tksurfer to > > > > > > correctly display the colours to code the retinotopy, is there some > > rationale > > > > > > for choosing them? > > > > > > > > > > > > thanks a lot for your help! > > > > > > > > > > > > Jane > > > > > > > > > > > > > > > > > > In message > > <Pine.LNX.4.62.0511280225500.19611(a)icebox.nmr.mgh.harvard.edu> Doug > > > > > > Greve <greve(a)nmr.mgh.harvard.edu> writes: > > > > > >> > > > > > >> What version of freesurfer (and paint-sess) are you using? This was a > > > > > >> problem in some versions about 6 mo ago, but I thought I fixed them > > > > > >> all. > > > > > >> > > > > > >> doug > > > > > >> > > > > > >> > > > > > >> > > > > > >> On Thu, 24 Nov 2005, Jane Aspell wrote: > > > > > >> > > > > > >>> hi again > > > > > >>> I have been proceeding with the retinotopy analysis using FsFast, > > > > > > following the > > > > > >>> instructions at: > > > > > >>> > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > > > > > >>> and i believe i have successfully overlaid the results on my surfaces and > > > > > > now > > > > > >>> have two questions: > > > > > >>> > > > > > >>> i wasn't able to create the fieldsign with 'paint-sess' because it > > > > > > couldn't find > > > > > >>> tksurfer.new. when i run 'surf-sess' i use the flag -old which forces it > > > > > > to use > > > > > >>> tksurfer.old but this doesn't work in the former case. how can i make > > > > > >>> 'paint-sess' use tksurfer.old and thus create the fieldsign? > > > > > >>> > > > > > >>> there are no instructions on how to relate the colours seen when viewing > > > > > > eccen > > > > > >>> and polar to the location of the ring and wedge. is there a map somewhere > > > > > > that > > > > > >>> can be loaded that tells me what order the colours run from fovea to > > > > > > periphery > > > > > >>> and from vertical to horizontal meridian etc.? > > > > > >>> > > > > > >>> thanks again for your help! > > > > > >>> > > > > > >>> jane > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >> > > > > > >> -- > > > > > >> Douglas N. Greve, Ph.D. > > > > > >> MGH-NMR Center > > > > > >> greve(a)nmr.mgh.harvard.edu > > > > > >> Phone Number: 617-724-2358 > > > > > >> Fax: 617-726-7422 > > > > > >> > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > >

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Short Course in fMRI
by Doug Greve 10 Apr '06

10 Apr '06

Mark Vangel and I are offering a short course in the statistical signal processing of fMRI. October 31 (Mon) & November 1 (Tue), 2005 7th Floor Auditorium Building 149 Charlestown Navy Yard Free, but limited to 40 attendees. Register at: http://www.nmr.mgh.harvard.edu/martinos/training/shortCoursefMRIStats.php doug

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FS-FAST registration across sessions
by Jane Aspell 08 Mar '06

08 Mar '06

Hi My question was asked last year by Tommi Raij (see email pasted below) but I couldn't find a reply to it in the archives. I am analysing retinotopy data that was collected over several sessions but I cannot see how to register scans from multiple sessions together, and to the subject's anatomical scan. Although Fs-Fast appears to combine the data from multiple sessions during the retinotopy analysis it only seems to be possible to use one registration file (register.dat) when overlaying the results onto the anatomical. I would have thought that registering scans from multiple sessions together would be a feature that many people would require. Is there anyway to do it? Tommi gives some possible methods in his email below. When I do try and overlay my data onto a surface I see 'gaps' in the blue/yellow colouring of the fieldsign map overlaid onto the cortical surface. I wonder if this could be due to the inaccuracy of the registration given that I only used the register.dat from the registration of the first session. hope that makes sense! i'd be grateful for any help with this! Jane -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ------------------------------------------- [Freesurfer] FS-FAST Registration Question: registration across sessions within subjects Tommi Raij Thu, 20 Oct 2005 15:43:46 -0700 Hi Doug/All, This is a question about registering several functional scans from the same subject in the same space. The functional scans are from different sessions, so even if the slice recording parameters are identical, the head will inavoidably be in different locations and with different rotation. The data have already been collected, so we cannot use any on-line corrections. Four different techniques come to mind that could be used to achieve this, but I would expect that the accuracy of the methods varies a lot. Optimally IMHO one should register the different functional runs with respect to each other directly, simply because the EPI images are very similar with respect to each other (or at least their T1 contrast is). The high-resolution structural image is very different compared to the EPI images so functional-to-structural registration is expected to be much more inaccurate. Here are the four different techniques (please tell me if you can think of more): 1. One possibility would be to use mc-sess for all runs from the same subject (place all the runs from the different sessions in a single "bold" directory and just run mc-sess). Possible problem: If I have understood correctly, mc- sess only corrects for motion within slices. Therefore the different head rotations would make this technique very inaccurate. Or does there exist an updated version of mc-sess that could handle even large displacements and rotations? 2. A second possibility would be to use one of the automatic functional-to- structural registration programs and register each functional run to the same hires structural image. However, based on the discussion above, there are expected to be inaccuracies in the functional-to- structural registration that could be large enough to make comparisons across the functional sessions meaningless (i.e., the differences would mainly be driven by inaccuracies in the registration). 3. A third possibility would be to use the same technique as for registration across subjects, i.e., resampling the different runs from the same subject into a spherical space calculated from this specific subject. Again this is just as variety of registration from functional to structural, and would be expected to provide suboptimal results. 4. A fourth possibility would be to find a method for registering all the functional images in a single space with respect to each other, e.g. by picking one of the functional sessions as the target space and resampling all other functional sessions from this subject into this space (without using the hires structurals at all). I guess this would be kind of motion correction but capable of handling rotations. If such a tool exists, it might be more accurate than any of the methods above, simply because the functional images are more similar compared to each other than compared to the subject's hires structural image. Any ideas/suggestions which method would give the most accurate result? And what kind of tools currently exist? Thanks, Tommi --- Tommi Raij MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Re: Re: [Freesurfer] activation levels of each voxel
by Joongnam Yang 28 Feb '06

28 Feb '06

Thanks for the answer, > If you want to create statistical maps in surface space, then use > mris_preproc to assemble the data. Then use one of the FSL tools to > do stats or use mri_glmfit Where could I get mris_preproc and mri_glmfit? Google displays nothing on those two functions.....^_^ > You cannot do corrections for mult comparisons > on the surface with the fSL tools. I wanted to know if it's possible to pinpoint a data point corresponding to a particular voxel. If I can do that, I want to do statisitcal test of my own. You mean it's not possible? I mean, 'is it not possible to match each voxel with each data point in the data file?' Nam.

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cannot locate talairach.xfm
by Darren Weber 28 Feb '06

28 Feb '06

I have some path problems when using tksurfer, eg dnlweber:/data/freesurfer/subjects> tksurfer -ucsf_cj rh inflated surfer: current subjects dir: /home/dweber/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/freesurfer/subjects can't find talairach file '/home/dweber/freesurfer/subjects/ucsf_cj/mri/T1/COR-.info/../transforms/talairach.xfm' surfer: Reading header info from /home/dweber/freesurfer/subjects/ucsf_cj/mri/T1/COR-.info INFO: NOT fixing vertex area surfer: vertices=154539, faces=309074 can't find talairach file '/home/dweber/freesurfer/subjects/ucsf_cj/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: single buffered window surfer: using interface /home/dweber/freesurfer/home/lib/tcl/tksurfer.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkm_common.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkm_wrappers.tcl Reading /home/dweber/freesurfer/home/lib/tcl/fsgdfPlot.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl The .xfm file exists, ie dnlweber:/data/freesurfer/subjects> ls ucsf_cj/mri/transforms/ talairach.xfm So the question is, how can I work around this failure to find the talairach.xfm file? Do I need to edit the tksurfer.tcl script? It seems to have a strange way of using relative paths (..) to find the talairach.xfm file. In case it makes any difference, this is my set up: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/dweber/freesurfer/home FSFAST_HOME /home/dweber/freesurfer/home/fsfast SUBJECTS_DIR /home/dweber/freesurfer/subjects FUNCTIONALS_DIR /home/dweber/freesurfer/sessions MINC_BIN_DIR /home/dweber/freesurfer/home/mni/bin MINC_LIB_DIR /home/dweber/freesurfer/home/mni/lib PERL5LIB /home/dweber/freesurfer/home/mni/lib/perl5/5.8.0 GSL_DIR /home/dweber/freesurfer/home/lib/gsl QTDIR /home/dweber/freesurfer/home/lib/qt TCLLIBPATH /home/dweber/freesurfer/home/lib/tcltktixblt/lib FSL_DIR /usr/local/fsl where the /home/dweber/freesurfer contains symlinks (please don't ask me why), eg: dnlweber:/data/freesurfer/subjects> ls -l /home/dweber/freesurfer/ total 0 lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 functionals -> /data/freesurfer/sessions lrwxrwxrwx 1 dweber dnl 21 2006-02-24 20:26 home -> /usr/local/freesurfer lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 sessions -> /data/freesurfer/sessions lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 subjects -> /data/freesurfer/subjects -- Darren L. Weber, Ph.D. Visiting Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." --Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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activation levels of each voxel
by Joongnam Yang 28 Feb '06

28 Feb '06

Hi all, When I overlay functional data (e.g. from FSL) onto a Freesurfer-produced inflated brain, I see the activations shown in colors. I want to pick a voxel in Talairach coordinates in those activations and see how the particular voxel's activation level changes throughout different data sets of the same brain. So, my question is how can I get the activation level of a particular voxel consistently throughout different data sets, so that I can do some sort of statistical tests? Thanks in advance. Nam.

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Question: FS-FAST mc-sess -perrun
by raij＠nmr.mgh.harvard.edu 28 Feb '06

28 Feb '06

Hi Doug, The issue is motion correction in FS-FAST. The environment is nmr-dev-env. mc-sess flag -perrun is documented like this: "MC each run separately (targ=mid)". 1. Does "targ=mid" implicate that the target, within each run, is the image half way through the run? 2. Does this equal to using the mc-sess -rlf runlistfile flag, and changing the contents of the runlistfile to match each of the run numbers, one at a time? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

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Freesurfer February 2006