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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> >> 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 <[email protected]> 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 >> > <[email protected]> wrote: >> > Scroll down eshita >> > >> > From: [email protected] <[email protected]>; >> > To: <[email protected]>; >> > Subject: Failure Notice >> > Sent: Fri, Nov 15, 2013 10:41:08 PM >> > >> > Sorry, we were unable to deliver your message to the following address. >> > >> > <[email protected]>: >> > No MX or A records for brainvis.wustl.edu >> > >> > --- Below this line is a copy of the message. >> > >> > Received: from [216.39.60.175] by nm11.access.bullet.mail.gq1.yahoo.com >> > with NNFMP; 15 Nov 2013 21:15:13 -0000 >> > Received: from [98.138.104.99] by tm11.access.bullet.mail.gq1.yahoo.com >> > with NNFMP; 15 Nov 2013 21:15:12 -0000 >> > Received: from [127.0.0.1] by smtp119.sbc.mail.ne1.yahoo.com with NNFMP; >> > 15 Nov 2013 21:15:12 -0000 >> > DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=sbcglobal.net; >> > s=s1024; t=1384550112; bh=NtxBzru9khKDAsba5SAlV4YrRgVkHeW8b9YGv0bMztA=; >> > h=X-Yahoo-Newman-Id:X-Yahoo-Newman-Property:X-YMail-OSG:X-Yahoo-SMTP:X-Rocket-Received:Message-ID:Date:From:User-Agent:MIME-Version:To:Subject:References:In-Reply-To:Content-Type; >> > >> > b=WV5yG6d6wYHiVVhb2EQHyNRXQWxW1LesfyqTNaXOXmqqqOvPIFG2YS//Ij/FdfTPJj/2vVds/n4M6IksP/0A0F9p1DFQ0f99NlI5Kdnig45dD3sfU7lcXCOg4yTSnjFCUOwFbOKNDdhbE5qw7rGSY2mkoTbXduJwrvIHu6fC/LQ= >> > X-Yahoo-Newman-Id: [email protected] >> > X-Yahoo-Newman-Property: ymail-3 >> > X-YMail-OSG: gXcHylQVM1l09L.PSsdYMzRKwLwkv.NYwqaMp.6BrpjiXNE >> > ho6UQJJXjmXuAKMCqpRBD2pMHNRD6C6IljqIBAI6R6Qm8xhM3bVHels3.Fm5 >> > w8b7Ond.bbI2YmxgKPd57rAIo6ok.Q.vhp4ZhM8s_TaTPWlswXpD2yAlcLHq >> > 1J3g4GvdFzgSgJ_YzgaHMEiNZaUTqjMiAsBZ30klPBT.yrdrNl9W_9TShNiA >> > bCG4r9u36LVWGZHlQVxynSOJXA8ldy_K2eYACxDrpigxbeyqkL30yLrOmtQv >> > rdfyk.fCTiiBI6TOCO_yOj.NPnYttzBTJEhvKwTNrhoIs3t6QxOjFKZI.zOl >> > js7LRoCYbirS1mueqpF25Kz_lMdVsB3O6ofotbtALNwdi18tELGjU33pq6Hy >> > .tmvnVoOH1Wy9dd9Gm1O.j2DtcMH1OWMIHROL8lAhs8hGhffYi3T7YY33LIh >> > ujuoDMqy1hr5D4XI96NYpViITdei1lS_V51d_uov235Mw5xaWhCVuLwNwG7Q >> > N_saCzXaf8DGq1fTdNgz2LfRRAdnh6yuEkB57kTF4BjRG2YSYgnHiPnfABCY >> > 45DWmSS4cDvTRob2HbfUDsx5nwS0t6N4joyIUQ3I2_gz2502fqOnNC0h4mDj >> > cZAi9sdtFy2QMAaFYDLUg62LXsFSlpCxY0gvSmu3MlUoZLuw9wFN0IDHOKBl >> > YK9SPRb7erKBkS2zi1POQoQOpB2iyoWJsF7_XnF6H.LEnzp0BfxjMvCm0.o9 >> > pdWNfeuoKF3UbR5wwnXXz2LY7okbApoTG7UK_gUrsqG_aLea.qRDsFi5INWP >> > uOFJfU1pSVKYeCpn7IpEVN7BaeeVww6BI0Iwanc3H0wJtHwMm8HgCUIb4gzL >> > S8Bls2IYSlA0OYGW_ >> > X-Yahoo-SMTP: q5QnzDOswBAGQX7OHacFHTX9.UGNm04EhVsFT8nwx8VksFe0qzkFUA-- >> > X-Rocket-Received: from [128.252.37.103] ([email protected] >> > with ) >> > by smtp119.sbc.mail.ne1.yahoo.com with SMTP; 15 Nov 2013 21:15:12 >> > +0000 UTC >> > Message-ID: <[email protected]> >> > Date: Fri, 15 Nov 2013 15:15:15 -0600 >> > From: Donna Dierker <[email protected]> >> > 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" >> > <[email protected]> >> > 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; >> > boundary="------------060202070608050109090303" >> > >> > 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 <[email protected] >> > > <mailto:[email protected]>> 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 <[email protected] >> > > <mailto:[email protected]>> 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 <[email protected] >> > > <mailto:[email protected]>> 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 >> > > <[email protected] <mailto:[email protected]>> 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" <[email protected] >> > > <mailto:[email protected]>> 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 >> > > [email protected] >> > > <mailto:[email protected]> >> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > >> > > >> > > _______________________________________________ >> > > caret-users mailing list >> > > [email protected] >> > > <mailto:[email protected]> >> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > >> > > >> > > >> > > >> > > >> > > -- >> > > Eshita Shah >> > > University of California, Los Angeles | 2014 >> > > B.S. Neuroscience >> > > [email protected] <mailto:[email protected]> >> > > >> > > >> > > >> > > >> > > _______________________________________________ >> > > caret-users mailing list >> > > [email protected] >> > > 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:[email protected]";>[email protected]</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:[email protected]"; >> > target="_blank">[email protected]</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:[email protected]"; >> > target="_blank">[email protected]</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:[email protected]"; >> > >> > target="_blank">[email protected]</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 >> > [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 >> >> >> >> _______________________________________________ >> 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
