Hi Donna, Thanks for the explanation.
So you are saying that Caret cannot create these permuted f-maps, since the statistical model needs to be applied to create the f-map, but also to create the permuted f-maps. I would have to create them myself using the statistical model, right? How are the permuted f-maps created? What permutation is used? Thanks again, Casper -----Oorspronkelijk bericht----- Van: [email protected] [mailto:[email protected]] Namens Donna Dierker Verzonden: maandag 16 november 2009 17:00 Aan: Caret, SureFit, and SuMS software users Onderwerp: Re: [caret-users] multiple comparison correction on SUMA data On 11/16/2009 05:27 AM, Oers, C.A.M. van wrote: > Hi, > > Although I saw a post by Donna Dierker regarding the subject, I am > afraid I still have a question. > > I have created SUMA files using a mixed model analysis. The resulting > files have an individual statistical threshold (and coefficient). I > would like to use Caret to do a multiple comparison correction with a > cluster size threshold. I'm not sure how straightforward this will be, due to the randomization component. The caret_command utility has these features: caret_command -metric-statistics-anova-one-way caret_command -metric-statistics-anova-two-way caret_command -metric-statistics-coordinate-difference caret_command -metric-statistics-interhemispheric-clusters caret_command -metric-statistics-kruskal-wallis caret_command -metric-statistics-levene-map caret_command -metric-statistics-normalization caret_command -metric-statistics-one-sample-t-test caret_command -metric-statistics-paired-t-test caret_command -metric-statistics-shuffled-cross-correlation-map caret_command -metric-statistics-shuffled-t-map caret_command -metric-statistics-subtract-group-average caret_command -metric-statistics-t-map caret_command -metric-statistics-two-sample-t-test caret_command -metric-statistics-z-map Enter the command for the help for that feature, or enter "caret_command -help-ful > caret_command.txt" to get a text file with all the help. Let's choose the case of a two-sample-t-test. In this case, your caret_command line will look like so: DISTCOL=1 ITERATIONS=2500 THRESHNEG=-2.68 THRESHPOS=2.68 P_VALUE=0.05 VAR_SMOOTH_ITERATIONS=0 VAR_SMOOTH_STRENGTH=0.0 DO_TMAP_DOF=true DO_TMAP_PVALUE=true THREADS=4 FIDUCIAL=Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL.clean.align.73730.coord OPENTOPO=Human.sphere_6.LEFT_HEM_OPEN.73730.topo DISTMETRIC=Human.PALS_B12.B1-12_LEFT_DISTORTION-vs-AVG-FIDUCIAL_ONLY.737 30.metric COMPOSITE_IN_A=Composite.DEPTH.LEFT.KIDS.73730.surface_shape COMPOSITE_IN_B=Composite.DEPTH.LEFT.ADULTS.73730.surface_shape OUT_PREFIX=KIDS29vADULTS23_Depth.LEFT COMMAND="caret_command -metric-statistics-two-sample-t-test NO_TRANSFORM UNPOOLED" COMMAND="$COMMAND $COMPOSITE_IN_A $COMPOSITE_IN_B" COMMAND="$COMMAND $FIDUCIAL $OPENTOPO $DISTMETRIC $DISTCOL $OUT_PREFIX" COMMAND="$COMMAND $ITERATIONS $THRESHNEG $THRESHPOS $P_VALUE" COMMAND="$COMMAND $VAR_SMOOTH_ITERATIONS $VAR_SMOOTH_STRENGTH" COMMAND="$COMMAND $DO_TMAP_DOF $DO_TMAP_PVALUE $THREADS" $COMMAND These sample scripts (e.g., tstt.sh and gen_composites.sh) are here: http://brainmap.wustl.edu/pub/donna/WUSTL/BURTON/SCRIPTS/SBM/ login pub password download But note that this takes two composite shape files (imagine your 1D files concatenated together in one file, with one 1D column per subject, with the node number preceding all os them). I don't think generating composites is hard (see below about adding header). Rather, the tricky bit here is that you already have your stat -- not raw scores/activations. The example above uses sulcal depth scores, but this could be any measure. But if it is already a stat, then it's less clear to me how to randomize it. With the two-sample t-test, a t-map is generated using the two groups' composites. Then, the composites are combined and group memberships randomized to create permuted t-maps. The max size of each permuted map is stored to create a distribution, and the size of the 95th percentile is used as the significance cut-off. If you've got stats already, how are we randomizing? If you can create your own permuted t- or f-maps, as well as your own real t- or f-map, then there is a newer caret_stats feature that can take these real and permuted maps and do either cluster operations or TFCE on them. But in your case, it isn't clear to me where/how the randomizing comes in. > > How can I convert a 1D surface file into a metric or surface_shape file? This part is easy: 1. Add a node number in column 1, using matlab or some other tool. 2. Slap on a header as shown in http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file _formats.html#metricFile: metric-version 2 tag-number-of-nodes 71723 tag-number-of-columns 2 tag-title untitled tag-column-name 0 Depth tag-column-name 1 Smoothed Depth tag-column-color-mapping 0 -1.000000 1.000000 tag-BEGIN-DATA 0 1.803019 -0.045549 1 1.704132 -0.007309 2 1.523951 0.026103 ... 71722 .822899 0.112485 If you can generate metric/surface_shape files from all your 1D files, then it's not hard to generate a composite using something like the gen_composites.sh script mentioned above). > Which way to perform the correction? > > I appreciate the help, > Casper > ---------------------------------------------------------------------- > -- > > /De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de > afzender direct te informeren door het bericht te retourneren. Het > Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Midden-Nederland onder nr. 30244197. / > > / Denk s.v.p aan het milieu voor u deze e-mail afdrukt. / > > ---------------------------------------------------------------------- > -- > > /This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the sender > immediately by return e-mail. University Medical Center Utrecht is a > legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. / > > / Please consider the environment before printing this e-mail. / > > ---------------------------------------------------------------------- > -- > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
