TFCE doesn't use distances along the surface, so using spherical surfaces and the average vertex area files should give the correct answer (it is best to provide average vertex area files when using any group data). I don't know if PALM does anything that uses surface distances (such as smoothing), but for operations that do (like wb_command -cifti-smoothing), spherical surfaces are not recommended, instead use either individual surfaces (matching the data the subject is for), or a group average midthickness surface and average vertex areas.
As in my previous email (though it was a bit hidden), the group average midthickness surfaces should be on connectomedb - open dataset on the HCP 900 (soon to be more) dataset, then scroll down to "group average". The PALM example talking about TFCE is very new, and needs some revision to be correct. Tim On Thu, Sep 15, 2016 at 3:21 PM, Michael F.W. Dreyfuss < [email protected]> wrote: > OK thank you for your answer and for clarifying. I am still a bit confused > about how to proceed with what to use for the surface file for the -s > option with palm for TFCE on the .gii data. > > > I was wondering because on example 10 for palm it says "Various common > meshes at different resolutions used in the HCP pipelines are available > here > <https://github.com/Washington-University/Pipelines/tree/master/global/templates/standard_mesh_atlases/resample_fsaverage>. > Use preferably the *midthickness*." Where "here" is a link to : > > > https://github.com/Washington-University/Pipelines/tree/ > master/global/templates/standard_mesh_atlases/resample_fsaverage > > So I was hoping that the 32k midthickness files would be usable fore the > -s option of palm there for processing surface data, but I guess not? Are > there files recommended for this? > > > Thank you, > > Michael > ------------------------------ > *From:* Timothy Coalson <[email protected]> > *Sent:* Thursday, September 15, 2016 4:05:19 PM > *To:* Michael F.W. Dreyfuss > *Cc:* Anderson M. Winkler; [email protected]; Dierker, Donna > > *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data > > That .shape.gii file is not a surface file, you need .surf.gii files to > use that command. The standard_mesh_atlases folder does not contain any > anatomical surfaces (it only has spheres). > > See wb_command -gifti-help for an explanation of the types of gifti file: > > http://www.humanconnectome.org/software/workbench-command. > php?function=-gifti-help > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.humanconnectome.org_software_workbench-2Dcommand.php-3Ffunction-3D-2Dgifti-2Dhelp&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=gm0rcNwkH04qTmxXiPGQwA3Er4v-XqQRWQCJbV5Zi88&s=KMqdCUnTb-qhBGGQ9cCd5Wznv0uOWbk0cJlvRZfefIA&e=> > > The "midthickness_va" .shape.gii files in the resample_fsaverage folder > are the vertex areas of the S900 group of subjects, averaged across > subjects, so that documentation needs to be changed (the group average > midthickness *surfaces* are not here, try connectomedb, "open dataset" on > the main HCP project, then scroll down to "group average data"). This > folder wasn't intended for the purposes of processing data, it exists for > resampling between atlases. > > Side note, I believe octave can handle the default base64_gzip gifti > encoding if you compile the zip implementation that comes with the gifti > toolbox (via "make PLATFORM=octave" in @gifti/private). > > Tim > > > On Thu, Sep 15, 2016 at 11:25 AM, Michael F.W. Dreyfuss < > [email protected]> wrote: > >> Thank you very much! This is very helpful. >> >> >> Two small problems remain before running palm on surface data: >> >> 1) I cannot download the left and right 32k midthickness meshes from the >> site linked to in the examples page: >> >> >> ie. https://github.com/Washington-University/Pipelines/blob/ >> master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR.L. >> midthickness_va_avg.32k_fs_LR.shape.gii >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_Pipelines_blob_master_global_templates_standard-5Fmesh-5Fatlases_resample-5Ffsaverage_fs-5FLR.L.midthickness-5Fva-5Favg.32k-5Ffs-5FLR.shape.gii&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=gm0rcNwkH04qTmxXiPGQwA3Er4v-XqQRWQCJbV5Zi88&s=NUlsEyPgTeUCbp3Q4cGCZkukzDdOyBKh31CaQEmr4ew&e=> >> >> >> 2) I get errors when I try to get average areas for the -s option. When I >> use *-surface-vertex-areas* on an individual subjects for example I get >> the following: >> >> >> *command:* >> >> wb_command -surface-vertex-areas data_L.func.gii >> >> >> *error:* >> >> ERROR: Number of data arrays MUST be two in a SurfaceFile. >> >> I am again not sure what this error means and I have not found any >> information about it or how to resolve it. All the other steps are super >> well explained and demonstrated, but then the three steps using >> wb_command on how to find average areas of gii files are quickly passed >> over. Is there any explanation on how that might work? >> >> >> Thank you! >> >> Michael >> >> ------------------------------ >> *From:* [email protected] <[email protected]> on behalf >> of Anderson M. Winkler <[email protected]> >> *Sent:* Thursday, September 15, 2016 5:39:12 AM >> *To:* Michael F.W. Dreyfuss >> *Cc:* Dierker, Donna; [email protected] >> >> *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data >> >> Hi Michael, >> >> Please see an example in this page: https://fsl.fmrib.ox.ac.uk/fsl >> /fslwiki/PALM/Examples >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__fsl.fmrib.ox.ac.uk_fsl_fslwiki_PALM_Examples&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=sPzxLm_SMMk5275scURO0sERCdJS6N76AckPIzYZyXE&s=1VAqCh8ViCwPk9iSx03nPlQ4XvNFdEQYQ-SGgB3Ywk0&e=> >> >> The Example 9 is for simple statistics on brainordinates (no spatial >> statistics) and Example 10 is for TFCE and cluster-level inference. >> >> Thanks to Tim Coalson for the help with the wb_command options. >> >> Hope this helps! >> >> All the best, >> >> Anderson >> >> >> On 15 September 2016 at 07:21, Anderson M. Winkler < >> [email protected]> wrote: >> >>> Hi Michael, >>> >>> TFCE needs to be run separately for the surface-based and for the >>> volume-based parts of the CIFTI file. This means that the input file has to >>> be separated using wb_command, then PALM be executed, then the results need >>> to be corrected via Bonferroni or Šidák. I will add hopefully today still a >>> section in the documentation with the steps and update here. >>> >>> Also, although it's unrelated to this error, Donna is right: the >>> extension for the -t option wasn't supplied correctly. >>> >>> All the best, >>> >>> Anderson >>> >>> >>> On 15 September 2016 at 06:22, Michael F.W. Dreyfuss < >>> [email protected]> wrote: >>> >>>> Thank you, >>>> >>>> >>>> The $ContrastName is the argument of the -o option, so it is just the >>>> name designated for the output. There are no csv files unless you mean the >>>> .mat and .con files which are the arguments of -d and -t respectively for >>>> the design files and contrast files. Since it is a group average, it >>>> actually runs without the contrast file as well. >>>> >>>> >>>> Again, this whole command runs fine and gives reasonable output with >>>> the -fdr flag instead of -T, but I would like to be able to run TFCE here. >>>> Has the -T option been used with palm on cifti data successfully? Maybe it >>>> is not meant is only for use on volumetric data? >>>> >>>> >>>> Thanks a lot, >>>> >>>> Michael >>>> ------------------------------ >>>> *From:* Dierker, Donna <[email protected]> >>>> *Sent:* Wednesday, September 14, 2016 11:09:04 PM >>>> *To:* Michael F.W. Dreyfuss >>>> *Cc:* [email protected] >>>> *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data >>>> >>>> Michael, if $ContrastName is a csv file, make sure its extension is >>>> csv. I’ve gotten errors like that before when I named it .con. >>>> >>>> >>>> >>>> >>>> >>>> > On Sep 14, 2016, at 11:29 AM, Michael F.W. Dreyfuss < >>>> [email protected]> wrote: >>>> >>>> > >>>> >>>> > Hello, I am trying to run palm on cifti data with TFCE to find mean >>>> activation across a group. When I use the -T flag, the program crashed with >>>> the error: >>>> >>>> > >>>> >>>> > Command: >>>> >>>> > palm -i ${ContrastName}.dtseries.nii -transposedata -d >>>> $LevelThreeFEATDir/design.mat -o $ContrastName -t >>>> /tmp/CtxFGNG/CtxFGNG_Level3_Analysis/desion -T -ise >>>> >>>> > >>>> >>>> > Error: >>>> >>>> > 0.01% [Design 1/1, Contrast 1/1, Shuffling 1/10000, Modality 1/1] >>>> >>>> > Saving file: FoodNogo_dat_tstat >>>> >>>> > Index exceeds matrix dimensions. >>>> >>>> > >>>> >>>> > Error in palm_tfce (line 77) >>>> >>>> > elseif plm.Yisvtx(y) || plm.Yisfac(y), >>>> >>>> > >>>> >>>> > Error in palm_core (line 1680) >>>> >>>> > Gtfce{y}{m}{c} = >>>> tfcefunc(G{y}{m}{c},y,opts,plm); >>>> >>>> > >>>> >>>> > Error in palm (line 81) >>>> >>>> > palm_core(varargin{:}); >>>> >>>> > >>>> >>>> > >>>> >>>> > Alternatively, if I use the same command, but replace -T with -fdr, >>>> the program runs smoothly, so I do not think the problem is with my design >>>> files or data unless they need to be generated in a special way for TFCE >>>> using palm. Are there any recommendation or previous examples of how I can >>>> use TFCE on cifti data using palm? >>>> >>>> > >>>> >>>> > Any help on this is very appreciated. >>>> >>>> > >>>> >>>> > Thank you, >>>> >>>> > Michael >>>> >>>> > _______________________________________________ >>>> >>>> > HCP-Users mailing list >>>> >>>> > [email protected] >>>> >>>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hu >>>> manconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb >>>> 62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf9 >>>> 9IoNsmxWf1JolkKMmL6bXnYFSwg&m=r90wcW3hZmEtN5Op3za0BAuX5uqah- >>>> NHkwg8a_Q7XII&s=3G_GSd6Y2Hl4j0R9IXFYn7JG7IJ5qEetuM339dG1HHg&e= >>>> >>>> >>>> >>>> >>>> >>>> ________________________________ >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. 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