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_
> tstat_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=
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>>
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>>>>>
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>>>>
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>>
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