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-
> template?
>
>
> 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
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>>>>>>> NHkwg8a_Q7XII&s=3G_GSd6Y2Hl4j0R9IXFYn7JG7IJ5qEetuM339dG1HHg&e=
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>
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