Hi Michael, That's right, no _tfce_ in the file names in the Example 9. Fixed, thanks.
All the best, Anderson On 21 September 2016 at 00:54, Timothy Coalson <tsc...@mst.edu> wrote: > The switch in command was my suggestion, as -from-template means it will > always match the brainordinates of the template file, while the previous > command did not specify the ROI files that are required in order to make > -cifti-create-dense-scalar match the input brainordinate space (and in rare > cases, -cifti-create-dense-scalar can't reproduce the input brainordinate > space, because it puts the structures in a predetermined order every time). > > Tim > > > On Tue, Sep 20, 2016 at 6:47 PM, Michael F.W. Dreyfuss < > mid2...@med.cornell.edu> wrote: > >> Hi, I noticed the examples page has been updated. I wanted to ask why you >> switched from using wb_command >> >> -cifti-create-dense-scalar to wb_command -cifti-create-dense-from-templ >> ate? >> >> >> Also, I think example 9 the naming of the files is off, probably copy and >> pasted from example 10. Given the palm command above it, it should probably >> be: results_dpv_tstat_m1_c1.gii instead of results_tfce_tstat_mfwep_m1_c1.gii >> ,and the same for the other inputs. Maybe I am wrong, but I think that >> naming would have resulted from a call of palm with TFCE. >> >> >> Thanks, >> >> Michael >> >> ------------------------------ >> *From:* andersonwink...@gmail.com <andersonwink...@gmail.com> on behalf >> of Anderson M. Winkler <wink...@fmrib.ox.ac.uk> >> *Sent:* Friday, September 16, 2016 11:35:44 AM >> *To:* Michael F.W. Dreyfuss >> *Cc:* hcp-users@humanconnectome.org >> >> *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data >> >> Hi Michael, >> >> No, I have no idea of what is going on. What was the command line used? >> >> All the best, >> >> Anderson >> >> On 16 September 2016 at 16:32, Michael F.W. Dreyfuss < >> mid2...@med.cornell.edu> wrote: >> >>> Hello, >>> >>> >>> When I follow the steps of example 10, I end up with essentially a blank >>> cifti file. When I load it it is totally transparent, and the wb_command >>> -file-information gives the below information. The individual .gii files >>> will not load on wb_view as well. This occurs whether I use local >>> midthickness files for the -s option or the HCP 900 subject average as >>> recommended. Would you perhaps have any idea what may be going on? >>> >>> >>> Thanks as usual, >>> >>> Michael >>> >>> >>> Name: FoodGo_results_merged_tfce_tst >>> at_fwep.dscalar.nii >>> >>> Type: Connectivity - Dense Scalar >>> >>> Structure: CortexLeft CortexRight >>> >>> Data Size: 387.42 Kilobytes >>> >>> Maps to Surface: true >>> >>> Maps to Volume: true >>> >>> Maps with LabelTable: false >>> >>> Maps with Palette: true >>> >>> All Map Palettes Equal: true >>> >>> Map Interval Units: NIFTI_UNITS_UNKNOWN >>> >>> Number of Maps: 1 >>> >>> Number of Rows: 96854 >>> >>> Number of Columns: 1 >>> >>> Volume Dim[0]: 91 >>> >>> Volume Dim[1]: 109 >>> >>> Volume Dim[2]: 91 >>> >>> Palette Type: Map (Unique for each map) >>> >>> CIFTI Dim[0]: 1 >>> >>> CIFTI Dim[1]: 96854 >>> >>> ALONG_ROW map type: SCALARS >>> >>> ALONG_COLUMN map type: BRAIN_MODELS >>> >>> Has Volume Data: true >>> >>> Volume Dims: 91,109,91 >>> >>> Volume Space: -2,0,0,90;0,2,0,-126;0,0,2,-72 >>> >>> CortexLeft: 32492 out of 32492 vertices >>> >>> CortexRight: 32492 out of 32492 vertices >>> >>> AccumbensLeft: 135 voxels >>> >>> AccumbensRight: 140 voxels >>> >>> AmygdalaLeft: 315 voxels >>> >>> AmygdalaRight: 332 voxels >>> >>> BrainStem: 3472 voxels >>> >>> CaudateLeft: 728 voxels >>> >>> CaudateRight: 755 voxels >>> >>> CerebellumLeft: 8709 voxels >>> >>> CerebellumRight: 9144 voxels >>> >>> DiencephalonVentralLeft: 706 voxels >>> >>> DiencephalonVentralRight: 712 voxels >>> >>> HippocampusLeft: 764 voxels >>> >>> HippocampusRight: 795 voxels >>> >>> PallidumLeft: 297 voxels >>> >>> PallidumRight: 260 voxels >>> >>> PutamenLeft: 1060 voxels >>> >>> PutamenRight: 1010 voxels >>> >>> ThalamusLeft: 1288 voxels >>> >>> ThalamusRight: 1248 voxels >>> >>> >>> Map Minimum Maximum Mean Sample Dev % Positive % Negative >>> Inf/NaN Map Name >>> >>> 1 0.000 0.000 0.000 0.000 0.000 0.000 >>> 0 #1 >>> >>> >>> >>> ------------------------------ >>> *From:* andersonwink...@gmail.com <andersonwink...@gmail.com> on behalf >>> of Anderson M. Winkler <wink...@fmrib.ox.ac.uk> >>> *Sent:* Friday, September 16, 2016 4:19:06 AM >>> *To:* Michael F.W. Dreyfuss >>> >>> *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data >>> >>> Hi Michael, >>> >>> The "-s" option can take 1 or 2 arguments. The first is mandatory and it >>> is a surface file (.surf.gii for instance). If only this argument is given, >>> PALM will use this file and do two things with it: it will use it for the >>> adjacency information and it will also use this file to calculate the >>> area-per-vertex, which is necessary to compute the cluster extent >>> statistic, and also to calculate the area of the support region of TFCE. >>> This means that if only one argument is given, in order to have a >>> reasonable approximation, this file should look like a brain (e.g., >>> midthickness or white, but not sphere). >>> >>> If a second argument is given, this second argument should be a scalar >>> file with the area per vertex for the same vertices of the surface file. >>> Ideally this file should be an average of the areas of the same subjects in >>> your sample, but if in your lab you are having difficulties in calculating >>> it, use the midthickness_va.shape.gii that Tim suggested. It is based on a >>> different set subjects, but should already be better than using the area of >>> the surface, even if that looks like a brain already. If the area file is >>> supplied (i.e., the 2nd argument then), then the surface file (1st >>> argument) can have any shape, even a sphere then. >>> >>> The option -s should be used for each -i. If you enter left and right >>> separately as inputs, then there should be two -s options, one for left and >>> another for right, in the same order. >>> >>> About compiling: please give it a try for your platform -- maybe you can >>> skip that step with the conversion then. >>> >>> Hope this helps. >>> >>> All the best, >>> >>> Anderson >>> >>> >>> On 15 September 2016 at 21:57, Michael F.W. Dreyfuss < >>> mid2...@med.cornell.edu> wrote: >>> >>>> Ah ok, so it sounds like the best and most data-specific thing to do >>>> would be to use each subjects midthickness file as separate inputs to -s. >>>> I'm referring to the file that is produced from the preprocessing stream in >>>> MNINonLinear/fsaverage_LR32k/${Subject}.L.midthick >>>> ness.32k_fs_LR.surf.gii >>>> >>>> Is that correct? >>>> >>>> >>>> Thanks again, >>>> >>>> Michael >>>> ------------------------------ >>>> *From:* Timothy Coalson <tsc...@mst.edu> >>>> *Sent:* Thursday, September 15, 2016 4:46:12 PM >>>> >>>> *To:* Michael F.W. Dreyfuss >>>> *Cc:* Anderson M. Winkler; hcp-users@humanconnectome.org; Dierker, >>>> Donna >>>> *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data >>>> >>>> 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 < >>>> mid2...@med.cornell.edu> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_Pipelines_tree_master_global_templates_standard-5Fmesh-5Fatlases_resample-5Ffsaverage&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=XBMPF2RHrxNWP8kAzlc8VR5C9A5jl6wCaLfoCs3cJ6w&s=44LdqlN7nRABsWwWMwVK8JKXAOcyWg8mdM9QX1micco&e=>. >>>>> Use preferably the *midthickness*." Where "here" is a link to : >>>>> >>>>> >>>>> https://github.com/Washington-University/Pipelines/tree/mast >>>>> er/global/templates/standard_mesh_atlases/resample_fsaverage >>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_Pipelines_tree_master_global_templates_standard-5Fmesh-5Fatlases_resample-5Ffsaverage&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=XBMPF2RHrxNWP8kAzlc8VR5C9A5jl6wCaLfoCs3cJ6w&s=44LdqlN7nRABsWwWMwVK8JKXAOcyWg8mdM9QX1micco&e=> >>>>> >>>>> 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 <tsc...@mst.edu> >>>>> *Sent:* Thursday, September 15, 2016 4:05:19 PM >>>>> *To:* Michael F.W. Dreyfuss >>>>> *Cc:* Anderson M. Winkler; hcp-users@humanconnectome.org; 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.ph >>>>> p?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 < >>>>> mid2...@med.cornell.edu> 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_fsave >>>>>> rage/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:* andersonwink...@gmail.com <andersonwink...@gmail.com> on >>>>>> behalf of Anderson M. Winkler <wink...@fmrib.ox.ac.uk> >>>>>> *Sent:* Thursday, September 15, 2016 5:39:12 AM >>>>>> *To:* Michael F.W. Dreyfuss >>>>>> *Cc:* Dierker, Donna; hcp-users@humanconnectome.org >>>>>> >>>>>> *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 < >>>>>> wink...@fmrib.ox.ac.uk> 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 < >>>>>>> mid2...@med.cornell.edu> 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 <do...@wustl.edu> >>>>>>>> *Sent:* Wednesday, September 14, 2016 11:09:04 PM >>>>>>>> *To:* Michael F.W. Dreyfuss >>>>>>>> *Cc:* hcp-users@humanconnectome.org >>>>>>>> *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 < >>>>>>>> mid2...@med.cornell.edu> 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 >>>>>>>> >>>>>>>> > HCP-Users@humanconnectome.org >>>>>>>> >>>>>>>> > 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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