Eshita, You need a visualization spec with surfaces suitable for display, e.g.:
http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases:Conte69_Atlas Unfortunately, sumsdb seems to be having connection issues right now. (I think that building was having network issues today.) If that is still the case tomorrow, I can find the dataset on disk and make it available for you. Donna On Nov 25, 2013, at 3:12 PM, Eshita Shah <eshs...@ucla.edu> wrote: > Hi Donna, > > Thanks. It seems that TFCE is working properly. However, for the paint files, > what file do I overlay it on? I have the average fiducial coordinate file, > but I'm not able to see any fiducial surface when I open it. > > Let me know, > Eshita > > > On Sat, Nov 23, 2013 at 10:20 AM, Donna Dierker <donna.dier...@sbcglobal.net> > wrote: > 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 > > >> > > > >> > --- 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: 757492.48204...@smtp119.sbc.mail.ne1.yahoo.com > > >> > 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] (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; > > >> > 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 > > >> > > <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 > > > _______________________________________________ > 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
