It is possible the TFCE test found no significant vertices, while the cluster
method did.
The TFCE generated report *does* list significant clusters near the top. (Note
that the TFCE test only establishes the enhanced threshold a vertex must meet
to be significant. it doesn't assign clusters as significant the way the
cluster method does, but if any vertices do meet the significance threshold and
they form clusters, then caret_stats writes a paint/label file and includes a
list of them with areas near the top of the report.)
It could look like this:
Column Thresh Num-Nodes Area Area-Corrected COG-X COG-Y
COG-Z P-Value
3 0.975 1997 1286.165283 2093.538574 51.174 -26.128
-1.203
3 0.975 906 740.481445 937.846191 54.076 -30.397
17.204
3 0.975 346 373.274231 513.194214 39.922 10.387
10.669
3 0.975 796 432.754486 459.654327 31.071 8.880
-12.815
3 0.975 317 145.114990 428.371918 40.161 -50.331
42.466
3 0.975 13 8.440027 19.833586 50.474 -57.879
33.487
If you just see the column heads, then TFCE results were negative.
On Nov 22, 2013, at 4:18 PM, Eshita Shah <eshs...@ucla.edu> wrote:
> I am also wondering how I should interpret the results that are generated by
> the TFCE script. I know the ANOVA test on caret_command generated some text
> files noting nodes of significance, but from what I'm seeing, the TFCE script
> does not do so. How would I use the metric file to see the significant
> differences that were found?
>
> Thank you,
> Eshita
>
>
> On Fri, Nov 22, 2013 at 1:42 PM, Eshita Shah <eshs...@ucla.edu> wrote:
> Should I be using the Depth or the Smoothed Depth column? Are there
> significant differences between them?
>
> Also, I haven't been able to properly load any of the paint files onto the
> fiducial for viewing in caret. I'm wondering how to do that, especially if I
> want to highlight the areas that are found significantly different between
> the two groups after statistical analysis.
>
> Thank you,
> Eshita
>
>
> On Thu, Nov 21, 2013 at 4:33 PM, Donna Dierker <donna.dier...@sbcglobal.net>
> wrote:
> I would use the Conte69 for TFCE/cluster area computation purposes. Think of
> it as a neutral, unbiased atlas surface.
>
> The topology files only define neighbor relationships, so on a standard mesh,
> the same topo will work with a variety of configurations that are on that
> mesh. The ones I gave you should be fine.
>
> One thing I don't recall talking about is generating composite files of the
> depth metric/shape files. (Metric and shape are identical in data format.
> Metric was intended more for overlay/functional, while surface_shape is
> intended more for anatomical measures like depth, curvature, thickness, etc.
> But the metric menu has more features than the surface_shape menu, so I
> sometimes purposely use metric. For this purpose, either is fine.)
>
> The ANOVA test wants composite files for each treatment/group (maybe what you
> meant by factor level. So at some point you need to generate composite files
> to concatenate your subjects into one composite per group.
>
> http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2009_10/SCRIPTS/gen_composite_filcav.sh
> login pub
> password download
>
> In that example, Depth was the second of multiple columns per subject. I
> don't recall what it is for the fs_LR stream. But if you run caret_command
> -metric-information on one of your surface_shape files, you'll find out which
> column has Depth.
>
>
> On Nov 21, 2013, at 4:58 PM, Eshita Shah <eshs...@ucla.edu> wrote:
>
> > Hi Donna,
> >
> > Thank you for the files. I seem to be understanding so far what the sample
> > script is doing but I do have a few questions. For the data file input into
> > ANOVA using caret_stats, I notice it's in a different format than in
> > caret_command ANOVA. I just want to clarify that each data file is still a
> > metric file that contains all of the subjects for one factor level.
> > Secondly, I realize I am using the fs_LR average open topo files you
> > provided earlier, but for the average fiducial coordinate file, should I be
> > also using the Conte69 average? I know you pointed out that my data is less
> > comparable to the fs_LR standard mesh data, so I am curious as to whether I
> > should just generate my own average fiducial file and use that instead.
> >
> > Let me know if I'm heading the right way.
> >
> > Thanks for all your help,
> > Eshita
> >
> >
> >
> > On Tue, Nov 19, 2013 at 2:35 PM, Donna Dierker <do...@brainvis.wustl.edu>
> > wrote:
> > Here are the caret_stats and jre zip files:
> >
> > http://brainvis.wustl.edu/pub/donna/SCRIPTS/caret6.zip
> > http://brainvis.wustl.edu/pub/donna/SCRIPTS/linux_java.zip
> > login pub
> > password download
> >
> > A sample script that calls TFCE is here:
> >
> > http://brainmap.wustl.edu/pub/donna/SCRIPTS/SHAPE/depth_anova.LH.CHILD.sh
> >
> > I am sure you will have more questions. You can try searching caret-users
> > for TFCE, but if you get stuck, I'll be here in the morning.
> >
> >
> >
> > On 11/19/2013 02:56 PM, Eshita Shah wrote:
> >> Hi Donna,
> >>
> >> I would definitely be interested in using the TFCE method. Where can I
> >> download caret_stats and the JRE?
> >>
> >> Thank you,
> >> Eshita
> >>
> >>
> >> On Tue, Nov 19, 2013 at 11:40 AM, Donna Dierker <do...@brainvis.wustl.edu>
> >> wrote:
> >> Hi Eshita,
> >>
> >> You don't need to create an average topo of your subjects, because your
> >> data is on the 164k fs_LR standard mesh, so the open topology files in the
> >> link I provided below is all you will need to define the neighbor
> >> relationships between the vertices.
> >>
> >> You do need to make a decision or two, though: The caret_command
> >> -metric-anova-one-way feature is a valid test, but it requires a
> >> cluster-forming threshold (e.g., whatever f-stat corresponds to p=.01 or
> >> p=.025/hem). It can make a big difference which cluster-forming threshold
> >> you use, as is described here:
> >>
> >> http://www.jneurosci.org/content/suppl/2010/02/12/30.6.2268.DC1/Supplemental_Material.pdf
> >> page 6 and supplementary material figure 7
> >>
> >> Instead, we now use Threshold-Free Cluster Enhancement (TFCE), which
> >> essentially integrates over the whole range f-stats:
> >>
> >> http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation:Statistics:TFCE_Implementation
> >>
> >> Smith SM, Nichols TE., "Threshold-free cluster enhancement: addressing
> >> problems of smoothing, threshold dependence and localisation in cluster
> >> inference." Neuroimage. 2009 Jan 1;44(1):83-98. PMID: 18501637
> >> http://www.ncbi.nlm.nih.gov/pubmed/18501637
> >>
> >> Using TFCE requires downloading caret_stats and the java runtime engine
> >> (JRE) that has been shown to work well with it. (Some JREs hang or get
> >> bogged down.)
> >>
> >> These features aren't documented in tutorials, but at least two others
> >> have managed to get it to work.
> >>
> >> If you're fine with the caret_command feature, you should be good to go.
> >>
> >> Donna
> >>
> >>
> >> On Nov 19, 2013, at 12:26 PM, Eshita Shah <eshs...@ucla.edu> wrote:
> >>
> >> > Hi Donna,
> >> >
> >> > The above script was helpful, thanks. My main concern now is to run the
> >> > ANOVA test (using caret_command -metric-anova-one-way). You stated
> >> > earlier that I don't need to worry about the open topo file, but to
> >> > input into ANOVA should I be creating an average topo file of all my
> >> > subjects?
> >> >
> >> > Please let me know. Thank you for your patience and help.
> >> >
> >> > Eshita
> >> >
> >> >
> >> > On Fri, Nov 15, 2013 at 3:50 PM, Donna Dierker
> >> > <donna.dier...@sbcglobal.net> wrote:
> >> > Scroll down eshita
> >> >
> >> > From: mailer-dae...@yahoo.com <mailer-dae...@yahoo.com>;
> >> > To: <donna.dier...@sbcglobal.net>;
> >> > Subject: Failure Notice
> >> > Sent: Fri, Nov 15, 2013 10:41:08 PM
> >> >
> >> > Sorry, we were unable to deliver your message to the following address.
> >> >
> >> > <caret-users@brainvis.wustl.edu>:
> >> > No MX or A records for brainvis.wustl.edu
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> >> > X-Rocket-Received: from [128.252.37.103] (donna.dierker@128.252.37.103
> >> > with )
> >> > by smtp119.sbc.mail.ne1.yahoo.com with SMTP; 15 Nov 2013
> >> > 21:15:12 +0000 UTC
> >> > Message-ID: <52868ee3.3030...@sbcglobal.net>
> >> > Date: Fri, 15 Nov 2013 15:15:15 -0600
> >> > From: Donna Dierker <donna.dier...@sbcglobal.net>
> >> > User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101
> >> > Thunderbird/24.1.0
> >> > MIME-Version: 1.0
> >> > To: "Caret, SureFit, and SuMS software users"
> >> > <caret-users@brainvis.wustl.edu>
> >> > Subject: Re: [caret-users] Different Node Numbers
> >> > References:
> >> > <caewtdbixrykoqdg4n5xqdfawhre0wdlmhmbswuu7irxznp+...@mail.gmail.com>
> >> > <CALvPP=_6XMYhcAPSn3ebOOJ2rmo-Y55+wk3zX99-=a8gnpw...@mail.gmail.com>
> >> > <CAEwtdbjAp4TrY=WUMbSZsdBD-HgdOxbc=gvdznnpjirn7+a...@mail.gmail.com>
> >> > <caewtdbgykdtjqo6_vugadnay3q5jkbwbvhsbtcsr-gaa5hu...@mail.gmail.com>
> >> > <caewtdbj-hqvrsskd1lxdhhs_-duith2oro__g4+qzirgw-d...@mail.gmail.com>
> >> > In-Reply-To:
> >> > <caewtdbj-hqvrsskd1lxdhhs_-duith2oro__g4+qzirgw-d...@mail.gmail.com>
> >> > Content-Type: multipart/alternative;
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> >> >
> >> > This is a multi-part message in MIME format.
> >> > --------------060202070608050109090303
> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >> > Content-Transfer-Encoding: 7bit
> >> >
> >> > What you're doing seems reasonable. If this is all you're trying to do,
> >> > you don't need to worry about the medial wall borders, because the open
> >> > topo file will exclude the medial wall vertices.
> >> >
> >> > The preborder.sh script only works with the PALS 74k mesh. This one
> >> > might be more helpful:
> >> >
> >> > http://brainvis.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/gen_depth.sh
> >> > login pub
> >> > password download
> >> >
> >> > Replace the subject directories named like SAIS* with your own list.
> >> >
> >> >
> >> > On 11/15/2013 02:28 PM, Eshita Shah wrote:
> >> > > Hi Donna,
> >> > >
> >> > > Thank you, that clears up a lot. Just to clarify, my main purpose is
> >> > > to use Caret to generate sulcal depth maps for each subject and run
> >> > > statistical analysis (such as ANOVA) to compare the results of two
> >> > > groups. I have completed importing all my data to the fs_LR standard
> >> > > mesh, and now I have to generate sulcal depth maps and run analyses.
> >> > > To do this, I am planning on running the "generate depth" function
> >> > > from PALS-B12/preborder.sh. Will this generate the appropriate input
> >> > > parameters for running the one-way ANOVA test through caret_command?
> >> > >
> >> > > Here is a list of what's needed:
> >> > >
> >> > > METRIC STATISTICS ONE-WAY ANOVA
> >> > > caret_command -metric-statistics-anova-one-way
> >> > > <fiducial-coord-file>
> >> > > <open-topo-file>
> >> > > <distortion-metric-shape-file>
> >> > > <distortion-column-number>
> >> > > <output-file-names-prefix>
> >> > > ...
> >> > > <metric-file-names>
> >> > >
> >> > > After the import of the data into fs_LR mesh, I have multiple coord
> >> > > files, shape files, and closed topo files. I do not have specific
> >> > > paint or border files. So I am not exactly sure how to exclude the
> >> > > paint files that label the medial wall from my analysis, like you
> >> > > stated previously. I found a command in postborder.sh that converts
> >> > > the closed topo file into an open topo file using the roi file that's
> >> > > generated for the medial wall. Any guidance on doing that would be
> >> > > appreciated.
> >> > >
> >> > > Please let me know if I'm going on the right track to generate the
> >> > > sulcal depth maps and run my analyses.
> >> > >
> >> > > Thank you,
> >> > > Eshita
> >> > >
> >> > >
> >> > > On Nov 15, 2013, at 10:07 AM, Donna Dierker <do...@brainvis.wustl.edu
> >> > > <mailto:do...@brainvis.wustl.edu>> wrote:
> >> > >
> >> > > >Hi Eshita,
> >> > > >
> >> > > >topi = topology, and I hate auto-correct
> >> > > >You mean the surface_shape/metric files -- not the topology, right?
> >> > > >
> >> > > >When all your data is on a standard mesh, as Caret requires to do
> >> > > >group
> >> > > >analysis (except for summary stats that are not vertex-wise, e.g.,
> >> > > >gyrification
> >> > > >index), then typically the stats tests use a single mean midthickness
> >> > > >and open
> >> > > >topology for computing the areas that are used for the TFCE/cluster
> >> > > >distributions.
> >> > > >
> >> > > >You typically don't need to generate an open topo file for each
> >> > > >subject on the
> >> > > >standard mesh. You have a single paint/label file that labels the
> >> > > >medial wall
> >> > > >vertices, so you can exclude them from your analysis. Or in this
> >> > > >case, you
> >> > > >have an open topology file that will accomplish the same thing. If
> >> > > >they're all
> >> > > >on standard mesh, then your standard open topi file should look
> >> > > >reasonable with
> >> > > >all your standard mesh midthickness surfaces.
> >> > > >
> >> > > >An example of a time when you would need an open topi is when you
> >> > > >want the
> >> > > >gyrification index computed on the native mesh. Then you can use a
> >> > > >strategy
> >> > > >like thePALS_B12.LR/postborder.sh <http://PALS_B12.LR/postborder.sh>
> >> > > >(http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2011_10/PALS_B12.LR/postborder.sh
> >> > > > ; login pub, password download) uses in the freesurfer to PALS
> >> > > > pipeline, which
> >> > > >essentially writes a border around the standard mesh medial wall;
> >> > > >"unprojects"
> >> > > >the border on the standard mesh midthickness; and then projects it on
> >> > > >the
> >> > > >native mid thickness. When you do that, you need to project to/from
> >> > > >the
> >> > > >spherical or ellipsoid, so that your medial wall border points don't
> >> > > >get hosed.
> >> > > >
> >> > > >You can use your own study-specific mean midthickness, but then you
> >> > > >should
> >> > > >compute your own mean distortion metric to go with it. Besides being
> >> > > >a bit of
> >> > > >a hassle, it strikes me that your results are slightly less
> >> > > >comparable to
> >> > > >others computed on the fs_LR standard mesh that used the more
> >> > > >standard Conte69
> >> > > >mean mid thickness/distortion. I don't use study-specific files for
> >> > > >this
> >> > > >purpose, unless the populations are so different (e.g., baby vs
> >> > > >adult) that you
> >> > > >can't use the adult.
> >> > > >
> >> > > >Visualization is another story. I almost always show the
> >> > > >study-specific mean
> >> > > >midthickness for each group in morphometry studies.
> >> > > >
> >> > > >Donna
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > On Thu, Nov 14, 2013 at 1:38 PM, Eshita Shah <eshs...@ucla.edu
> >> > > <mailto:eshs...@ucla.edu>> wrote:
> >> > >
> >> > > Hi Donna,
> >> > >
> >> > >
> >> > >
> >> > > Thank you for your help. From what I understand, the topology files
> >> > > from each subject have to be compiled (using caret_command
> >> > > -metric-composite) into one, and that file is then entered into the
> >> > > ANOVA test. My question however, is regarding the generation of the
> >> > > open topo files for each subject. I have used freesurfer_to_fs_LR
> >> > > pipeline, and I'm wondering if the topo files generated (there is only
> >> > > one for each subject) are indeed the open topo file, because looking
> >> > > at the script for freesurfer_to_fs_LR it looks like it is the closed
> >> > > topo file. Any advice on how to obtain an open topo file?
> >> > >
> >> > >
> >> > > Also, to clarify, the first parameter in the ANOVA test is a
> >> > > fiducial coord file. I have used caret_command -surface-average to
> >> > > generate an average fiducial file for each hemisphere. Is this correct?
> >> > >
> >> > >
> >> > > Please let me know.
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > Thanks,
> >> > >
> >> > > Eshita
> >> > >
> >> > > On Wed, Nov 13, 2013 at 10:50 PM. Donna Dierker wrote:
> >> > >
> >> > > >Hi Eshita,
> >> > >
> >> > > >
> >> > > >I always use the open topology for this purpose (i.e., excludes
> >> > > only medial
> >> > > >wall vertices). The files here will be helpful:
> >> > >
> >>
> >> > > >login pub
> >> > > >password download
> >> > > >
> >> > > >You can get them all in this zip file:
> >> > > >
> >> > >
> >> > > >http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/TFCE_164k.zip
> >> > > >
> >> > > >Just to explain what is going on, the areas in the TFCE/cluster
> >> > > computations
> >> > > >are computed on the Conte69 mean mid thickness, with the open topo
> >> > > file
> >> > > >(excluding medial wall). The distortion maps pump up the areal
> >> > > value where
> >> > > >substantial smoothing occurs as a result of averaging individuals'
> >> > > coordinate
> >> > > >files (e.g., high 3D variability). The intent is to make the
> >> > > areas more like
> >> > > >an individual's area would be in that region. For folks not
> >> > > attuned to what
> >> > > >you are doing, this is during group analysis.
> >> > >
> >> > > >
> >> > > >Cheers,
> >> > > >
> >> > > >Donna
> >> > >
> >> > > >
> >> > > >On Tue, Nov 12, 2013 at 1:18 PM, Eshita Shah <eshs...@ucla.edu
> >> > > <mailto:eshs...@ucla.edu>> wrote:
> >> > >
> >> > > Hello,
> >> > >
> >> > > Thanks for your input. I successfully was able to use
> >> > > freesurfer_to_fs_LR Pipeline to import my FreeSurfer files
> >> > > into caret, however when I try running ANOVA, it asks for
> >> > > certain files that have not been generated by the pipeline.
> >> > > Specifically, how do I generate the
> >> > > "distortion-metric-shape-file" that is being asked for?
> >> > > Lastly, is the .topo file that is generated via the pipeline
> >> > > the open topo file or closed? Previously I was able generate
> >> > > the closed topo file, so I'm not sure if the
> >> > > freesurfer_to_fs_LR pipeline does the same. The parameter
> >> > > required for the ANOVA analysis is the open topo file.
> >> > >
> >> > > Thank you,
> >> > > Eshita Shah
> >> > >
> >> > >
> >> > > On Thu, Nov 7, 2013 at 4:12 PM, Rouhollah Abdollahi
> >> > > <roohy...@gmail.com <mailto:roohy...@gmail.com>> wrote:
> >> > >
> >> > > Hi
> >> > > Actually the code import the original data from freesurfer
> >> > > to caret then automatically you will have different node
> >> > > number for different subjects and hemispheres. To have the
> >> > > same mesh you can use Freesurfer_to_fs_LR Pipeline which
> >> > > is available in the caret website. It imports all the data
> >> > > to the same mesh which here is fs_LR mesh.
> >> > > Hope it helps
> >> > > Best
> >> > > Rouhi
> >> > >
> >> > > On Nov 8, 2013 12:06 AM, "Eshita Shah" <eshs...@ucla.edu
> >> > > <mailto:eshs...@ucla.edu>> wrote:
> >> > >
> >> > > Hello,
> >> > >
> >> > > I have just recently started using Caret, and I am
> >> > > running the freesurfer2caret.sh script in order to
> >> > > import my FreeSurfer files into Caret as well as
> >> > > generate sulcal depth for all subjects. I tried doing
> >> > > a One-Way ANOVA test, but I've realized that the
> >> > > number of nodes in the metric/surface_shape files for
> >> > > the two subjects are different. How is it possible
> >> > > that the same script is creating files with different
> >> > > node numbers? Also, within each subject, sometimes the
> >> > > node numbers for the left and right hemisphere are
> >> > > different as well. How can I resolve this issue so I
> >> > > can successfully run ANOVA on my subjects?
> >> > >
> >> > > Any help would be appreciated.
> >> > >
> >> > > Thank you,
> >> > > Eshita Shah
> >> > >
> >> > > _______________________________________________
> >> > > caret-users mailing list
> >> > > caret-users@brainvis.wustl.edu
> >> > > <mailto:caret-users@brainvis.wustl.edu>
> >> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > caret-users mailing list
> >> > > caret-users@brainvis.wustl.edu
> >> > > <mailto:caret-users@brainvis.wustl.edu>
> >> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > --
> >> > > Eshita Shah
> >> > > University of California, Los Angeles | 2014
> >> > > B.S. Neuroscience
> >> > > eshs...@ucla.edu <mailto:eshs...@ucla.edu>
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > caret-users mailing list
> >> > > caret-users@brainvis.wustl.edu
> >> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >> >
> >> >
> >> > --------------060202070608050109090303
> >> > Content-Type: text/html; charset=ISO-8859-1
> >> > Content-Transfer-Encoding: 7bit
> >> >
> >> > <html>
> >> > <head>
> >> > <meta content="text/html; charset=ISO-8859-1"
> >> > http-equiv="Content-Type">
> >> > </head>
> >> > <body bgcolor="#FFFFFF" text="#000000">
> >> > What you're doing seems reasonable. If this is all you're
> >> > trying to
> >> > do, you don't need to worry about the medial wall borders, because
> >> > the open topo file will exclude the medial wall vertices.<br>
> >> > <br>
> >> > The preborder.sh script only works with the PALS 74k mesh.
> >> > This one
> >> > might be more helpful:<br>
> >> > <br>
> >> > <a class="moz-txt-link-freetext"
> >> > href="http://brainvis.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/gen_depth.sh";>http://brainvis.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/gen_depth.sh</a><br>
> >> > login pub<br>
> >> > password download<br>
> >> > <br>
> >> > Replace the subject directories named like SAIS* with your own
> >> > list.<br>
> >> > <br>
> >> > <br>
> >> > <div class="moz-cite-prefix">On 11/15/2013 02:28 PM, Eshita Shah
> >> > wrote:<br>
> >> > </div>
> >> > <blockquote
> >> > cite="mid:caewtdbj-hqvrsskd1lxdhhs_-duith2oro__g4+qzirgw-d...@mail.gmail.com"
> >> > type="cite">
> >> > <div dir="ltr">Hi Donna,
> >> > <div><br>
> >> > </div>
> >> > <div>Thank you, that clears up a lot. Just to clarify, my main
> >> > purpose is to use Caret to generate sulcal depth maps for each
> >> > subject and run statistical analysis (such as ANOVA) to
> >> > compare the results of two groups. I have completed importing
> >> > all my data to the fs_LR standard mesh, and now I have to
> >> > generate sulcal depth maps and run analyses. To do this, I am
> >> > planning on running the "generate depth" function from
> >> > PALS-B12/preborder.sh. Will this generate the appropriate
> >> > input parameters for running the one-way ANOVA test through
> >> > caret_command? </div>
> >> > <div><br>
> >> > </div>
> >> > <div>Here is a list of what's needed: </div>
> >> > <div><br>
> >> > </div>
> >> > <div>
> >> > <div> METRIC STATISTICS ONE-WAY ANOVA</div>
> >> > <div> caret_command
> >> > -metric-statistics-anova-one-way</div>
> >> > <div>
> >> > <fiducial-coord-file></div>
> >> > <div>
> >> > <open-topo-file></div>
> >> > <div>
> >> > <distortion-metric-shape-file></div>
> >> > <div>
> >> > <distortion-column-number></div>
> >> > <div>
> >> > <output-file-names-prefix></div>
> >> > <div> ... </div>
> >> > <div>
> >> > <metric-file-names></div>
> >> > </div>
> >> > <div><br>
> >> > </div>
> >> > <div>After the import of the data into fs_LR mesh, I have
> >> > multiple coord files, shape files, and closed topo files. I do
> >> > not have specific paint or border files. So I am not exactly
> >> > sure how to exclude the paint files that label the medial wall
> >> > from my analysis, like you stated previously. I found a
> >> > command in postborder.sh that converts the closed topo file
> >> > into an open topo file using the roi file that's generated for
> >> > the medial wall. Any guidance on doing that would be
> >> > appreciated. </div>
> >> > <div><br>
> >> > </div>
> >> > <div>Please let me know if I'm going on the right track to
> >> > generate the sulcal depth maps and run my analyses. </div>
> >> > <div><br>
> >> > </div>
> >> > <div>Thank you, </div>
> >> > <div>Eshita</div>
> >> > <div><br>
> >> > </div>
> >> > <div><br>
> >> > </div>
> >> > <div>
> >> > <pre style="font-family:courier,'courier
> >> > new',monospace;font-size:14px;white-space:pre-wrap;word-wrap:break-word;margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);line-height:19px">On
> >> > Nov 15, 2013, at 10:07 AM, Donna Dierker <<a moz-do-not-send="true"
> >> > href="mailto:do...@brainvis.wustl.edu";>do...@brainvis.wustl.edu</a>>
> >> > wrote:</pre>
> >> > </div>
> >> > <div><br>
> >> > </div>
> >> > <div>
> >> > <pre style="font-family:courier,'courier
> >> > new',monospace;font-size:14px;white-space:pre-wrap;word-wrap:break-word;margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);line-height:19px">>Hi
> >> > Eshita,
> >> > >
> >> > >topi = topology, and I hate auto-correct</pre>
> >> > <pre style="font-family:courier,'courier
> >> > new',monospace;font-size:14px;white-space:pre-wrap;word-wrap:break-word;margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);line-height:19px">>You
> >> > mean the surface_shape/metric files -- not the topology, right?
> >> > >
> >> > >When all your data is on a standard mesh, as Caret requires to do
> >> > group
> >> > >analysis (except for summary stats that are not vertex-wise, e.g.,
> >> > gyrification
> >> > >index), then typically the stats tests use a single mean
> >> > midthickness and open
> >> > >topology for computing the areas that are used for the TFCE/cluster
> >> > >distributions.
> >> > >
> >> > >You typically don't need to generate an open topo file for each
> >> > subject on the
> >> > >standard mesh. You have a single paint/label file that labels the
> >> > medial wall
> >> > >vertices, so you can exclude them from your analysis. Or in this
> >> > case, you
> >> > >have an open topology file that will accomplish the same thing. If
> >> > they're all
> >> > >on standard mesh, then your standard open topi file should look
> >> > reasonable with
> >> > >all your standard mesh midthickness surfaces.
> >> > >
> >> > >An example of a time when you would need an open topi is when you
> >> > want the
> >> > >gyrification index computed on the native mesh. Then you can use a
> >> > strategy
> >> > >like the <a moz-do-not-send="true"
> >> > href="http://PALS_B12.LR/postborder.sh";>PALS_B12.LR/postborder.sh</a>
> >> > >(<a moz-do-not-send="true" rel="nofollow"
> >> > href="http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2011_10/PALS_B12.LR/postborder.sh";
> >> >
> >> > style="color:rgb(160,30,30)">http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2011_10/PALS_B12.LR/postborder.sh</a>
> >> > > ; login pub, password download) uses in the freesurfer to PALS
> >> > pipeline, which
> >> > >essentially writes a border around the standard mesh medial wall;
> >> > "unprojects"
> >> > >the border on the standard mesh midthickness; and then projects it
> >> > on the
> >> > >native mid thickness. When you do that, you need to project to/from
> >> > the
> >> > >spherical or ellipsoid, so that your medial wall border points don't
> >> > get hosed.
> >> > >
> >> > >You can use your own study-specific mean midthickness, but then you
> >> > should
> >> > >compute your own mean distortion metric to go with it. Besides
> >> > being a bit of
> >> > >a hassle, it strikes me that your results are slightly less
> >> > comparable to
> >> > >others computed on the fs_LR standard mesh that used the more
> >> > standard Conte69
> >> > >mean mid thickness/distortion. I don't use study-specific files for
> >> > this
> >> > >purpose, unless the populations are so different (e.g., baby vs
> >> > adult) that you
> >> > >can't use the adult.
> >> > >
> >> > >Visualization is another story. I almost always show the
> >> > study-specific mean
> >> > >midthickness for each group in morphometry studies.
> >> > >
> >> > >Donna</pre>
> >> > </div>
> >> > <div><br>
> >> > </div>
> >> > <div><br>
> >> > </div>
> >> > </div>
> >> > <div class="gmail_extra"><br>
> >> > <br>
> >> > <div class="gmail_quote">On Thu, Nov 14, 2013 at 1:38 PM, Eshita
> >> > Shah <span dir="ltr"><<a moz-do-not-send="true"
> >> > href="mailto:eshs...@ucla.edu";
> >> > target="_blank">eshs...@ucla.edu</a>></span>
> >> > wrote:<br>
> >> > <blockquote class="gmail_quote" style="margin:0 0 0
> >> > .8ex;border-left:1px #ccc solid;padding-left:1ex">
> >> > <div dir="ltr">
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">Hi Donna, </font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">
> >> >
> >> > </font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">Thank you for your help. From what
> >> > I understand, the topology files from each subject have to be compiled
> >> > (using caret_command -metric-composite) into one, and that file is then
> >> > entered into the ANOVA test. My question however, is regarding the
> >> > generation of the open topo files for each subject. I have used
> >> > freesurfer_to_fs_LR pipeline, and I'm wondering if the topo files
> >> > generated (there is only one for each subject) are indeed the open topo
> >> > file, because looking at the script for freesurfer_to_fs_LR it looks
> >> > like it is the closed topo file. Any advice on how to obtain an open
> >> > topo file?</font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">
> >> > </font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">Also, to clarify, the first
> >> > parameter in the ANOVA test is a fiducial coord file. I have used
> >> > caret_command -surface-average to generate an average fiducial file for
> >> > each hemisphere. Is this correct?</font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">
> >> > </font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">Please let me know. </font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">
> >> >
> >> >
> >> > </font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">Thanks,</font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;margin-top:0px;word-wrap:break-word"><font
> >> > face="arial, helvetica, sans-serif">Eshita </font></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;font-family:courier,'courier
> >> > new',monospace;margin-top:0px;word-wrap:break-word">
> >> > </pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;font-family:courier,'courier
> >> > new',monospace;margin-top:0px;word-wrap:break-word"><pre
> >> > style="font-family:courier,'courier
> >> > new',monospace;white-space:pre-wrap;word-wrap:break-word;margin-top:0px;margin-bottom:0px"><span
> >> >
> >> > style="color:rgb(34,34,34);font-family:arial;font-size:small;line-height:normal;white-space:normal">On
> >> > Wed, Nov 13, 2013 at 10:50 PM. Donna Dierker
> >> > wrote: </span></pre></pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;font-family:courier,'courier
> >> > new',monospace;margin-top:0px;word-wrap:break-word">>Hi Eshita,
> >> > </pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;font-family:courier,'courier
> >> > new',monospace;margin-top:0px;word-wrap:break-word">>
> >> > >I always use the open topology for this purpose (i.e., excludes only
> >> > medial
> >> > >wall vertices). The files here will be helpful:</pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;font-family:courier,'courier
> >> > new',monospace;margin-top:0px;word-wrap:break-word">><a
> >> > moz-do-not-send="true" rel="nofollow"
> >> > href="http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/TFCE_164k/";
> >> > style="color:rgb(160,30,30)"
> >> > target="_blank">http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/TFCE_164k/</a>
> >> > >login pub
> >> > >password download
> >> > >
> >> > >You can get them all in this zip file:
> >> > >
> >> > ><a moz-do-not-send="true" rel="nofollow"
> >> > href="http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/TFCE_164k.zip";
> >> > style="color:rgb(160,30,30)"
> >> > target="_blank">http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/TFCE_164k.zip</a>
> >> > >
> >> > >Just to explain what is going on, the areas in the TFCE/cluster
> >> > computations
> >> > >are computed on the Conte69 mean mid thickness, with the open topo
> >> > file
> >> > >(excluding medial wall). The distortion maps pump up the areal
> >> > value where
> >> > >substantial smoothing occurs as a result of averaging individuals'
> >> > coordinate
> >> > >files (e.g., high 3D variability). The intent is to make the areas
> >> > more like
> >> > >an individual's area would be in that region. For folks not attuned
> >> > to what
> >> > >you are doing, this is during group analysis.</pre>
> >> > <pre
> >> > style="line-height:19px;font-size:14px;white-space:pre-wrap;margin-bottom:0px;font-family:courier,'courier
> >> > new',monospace;margin-top:0px;word-wrap:break-word">>
> >> > >Cheers,
> >> > >
> >> > >Donna
> >> > </pre>
> >> > <div>
> >> > <div class="h5">
> >> > <div>></div>
> >> > <div class="gmail_extra">
> >> > <div class="gmail_quote">>On Tue, Nov 12, 2013 at
> >> > 1:18 PM, Eshita Shah <span dir="ltr"><<a
> >> > moz-do-not-send="true"
> >> > href="mailto:eshs...@ucla.edu";
> >> > target="_blank">eshs...@ucla.edu</a>></span>
> >> > wrote:<br>
> >> > <blockquote class="gmail_quote" style="margin:0px
> >> > 0px 0px
> >> > 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
> >> > <div dir="ltr">Hello,
> >> > <div><br>
> >> > </div>
> >> > <div>Thanks for your input. I successfully was
> >> > able to use freesurfer_to_fs_LR Pipeline to
> >> > import my FreeSurfer files into caret,
> >> > however when I try running ANOVA, it asks
> >> > for certain files that have not been
> >> > generated by the pipeline. Specifically, how
> >> > do I generate the
> >> > "distortion-metric-shape-file" that is being
> >> > asked for? Lastly, is the .topo file that is
> >> > generated via the pipeline the open topo
> >> > file or closed? Previously I was able
> >> > generate the closed topo file, so I'm not
> >> > sure if the freesurfer_to_fs_LR pipeline
> >> > does the same. The parameter required for
> >> > the ANOVA analysis is the open topo
> >> > file. </div>
> >> > <div><br>
> >> > </div>
> >> > <div>Thank you, </div>
> >> > <span><font color="#888888">
> >> > <div>Eshita Shah </div>
> >> > </font></span>
> >> > <div>
> >> > <div>
> >> > <div>
> >> > <div class="gmail_extra"><br>
> >> > <br>
> >> > <div class="gmail_quote">On Thu, Nov
> >> > 7, 2013 at 4:12 PM, Rouhollah
> >> > Abdollahi <span dir="ltr"><<a
> >> > moz-do-not-send="true"
> >> > href="mailto:roohy...@gmail.com";
> >> >
> >> > target="_blank">roohy...@gmail.com</a>></span>
> >> > wrote:<br>
> >> > <blockquote class="gmail_quote"
> >> > style="margin:0px 0px 0px
> >> > 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
> >> > <p dir="ltr">Hi<br>
> >> > Actually the code import the
> >> > original data from freesurfer to
> >> > caret then automatically you
> >> > will have different node number
> >> > for different subjects and
> >> > hemispheres. To have the same
> >> > mesh you can use
> >> > Freesurfer_to_fs_LR Pipeline
> >> >
> >> > [remainder of message body omitted; too large]
> >> >
> >> > _______________________________________________
> >> > caret-users mailing list
> >> > caret-users@brainvis.wustl.edu
> >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >> >
> >> > _______________________________________________
> >> > caret-users mailing list
> >> > caret-users@brainvis.wustl.edu
> >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>
> >>
> >> _______________________________________________
> >> caret-users mailing list
> >> caret-users@brainvis.wustl.edu
> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >>
> >>
> >>
> >> _______________________________________________
> >> caret-users mailing list
> >>
> >> caret-users@brainvis.wustl.edu
> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >
> >
> > _______________________________________________
> > caret-users mailing list
> > caret-users@brainvis.wustl.edu
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >
> > _______________________________________________
> > caret-users mailing list
> > caret-users@brainvis.wustl.edu
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
> _______________________________________________
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
>
> _______________________________________________
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
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