Hi Michael,

This is a bug, sorry. When these lines were written it wasn't assumed that
a CIFTI file would be used to supply the areas, hence some options are
missing. Please try editing that line 1509 from palm_takeargs.m from where
it reads:

*plm.srfarea{s} = palm_miscread(opts.sa <http://opts.sa>{s});*


to:

*plm.srfarea{s} = palm_miscread(opts.sa
<http://opts.sa>{s},opts.useniiclass,opts.o);*


Thanks.

All the best,

Anderson



On 17 September 2016 at 06:59, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:

> Thanks for explaining, and thanks for updating example 10. When I follow
> those commands to get an average vertex area, unfortunately, the palm
> command ultimately fails with the error:
>
> Error using palm_miscread (line 157)
>
> Not enough input arguments.
>
>
> Error in palm_takeargs (line 1509)
>
>             plm.srfarea{s} = palm_miscread(opts.sa{s});
>
>
> Error in palm_core (line 33)
>
> [opts,plm] = palm_takeargs(varargin{:});
>
>
> Error in palm (line 81)
>
> palm_core(varargin{:});
>
>
> Any thought why this may be? Should I attach the file to verify that it is
> the correct output for this?
>
> It runs smoothly if I just use one input, such as
> S900.L.midthickness_MSMAll.32k_fs_LR.surf.gii from the HCP data. Is that
> the file you would suggest using (for the left hemisphere)? I'd prefer to
> use a local index of vertex area if I can as that seems more appropriate.
> Do you think that is important?
>
> As for the previous errors, I had left out the -ise flag, so I'm not sure
> what the program was putting out (I guess nothing).
>
> Thank you again for all your help,
> Michael
> ------------------------------
> *From:* andersonwink...@gmail.com <andersonwink...@gmail.com> on behalf
> of Anderson M. Winkler <wink...@fmrib.ox.ac.uk>
> *Sent:* Friday, September 16, 2016 11:33:51 AM
> *To:* Michael F.W. Dreyfuss
> *Cc:* hcp-users@humanconnectome.org
>
> *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data
>
> Hi Michael,
>
> This isn't correct I'm afraid. Even if PALM run to completion, with these
> inputs it is shuffling the timeseries data within-subject, but because of
> serial correlations, this violates the most important assumption of
> permutation tests: the one of exchangeability.
>
> The analysis needs to use with -i input file(s) that include all subjects.
> The reason why PALM allows multiple inputs is that one can test multiple
> different imaging modalities, such as cortical area and BOLD FMRI, and/or
> different variants of the same modality, such as different ICA maps, or
> different diffusion tensor metrics, or different morphological metrics, or
> different FMRI tasks. The -i isn't meant to be used one per subject.
>
> The -s should be one per input, and should be the group mesh to which all
> subjects were resampled, as opposed to one per subject.
>
> All the best,
>
> Anderson
>
> PS: I the last email I accidentally clicked "reply to" instead of "reply
> to all", only to more than an hour later realise it hadn't been sent to the
> HCP list. Ideally we should keep conversations as this in the list as it
> can be helpful to others in the future. Hope you won't mind that I'm cc'ing
> the list now.
>
>
> On 16 September 2016 at 13:07, Michael F.W. Dreyfuss <
> mid2...@med.cornell.edu> wrote:
>
>> Thank you very much.
>>
>>
>> Sorry,  I don't think I was clear about what I was suggesting. I was
>> proposing using the midthickness surface file generated for each
>> participant rather than an average in separate -s arguments, so something
>> like:
>>
>>
>> palm -i sub1.L.surf.gii -i sub2.L.surf.gii -i sub3.L.surf.gii {...} -s
>> sub1.L.midthickness.surf.gii -s sub2.L.midthickness.surf.gii -s sub3.L.
>> midthickness.surf.gii {...}
>>
>>
>> such that each subject's input file is matched by their own
>> corrresponding midthickness surface file. I tried this and palm was able to
>> run. Would you recommend creating a group average or using the average from
>> the HCP data over this approach? If you recommend a local group average,
>> what would be the wb_command to do that on the midthickness data?
>>
>>
>> Sorry, I wasn't sure what you were referring to about compiling and
>> skipping the conversion. What is that in reference to?
>>
>>
>> Thank you again,
>>
>> Michael
>>
>>
>> *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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>>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> HCP-Users mailing list
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>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=gm0rcNwkH04qTmxXiPGQwA3Er4v-XqQRWQCJbV5Zi88&s=7g9DRC7Ln3QDWsQrolOjQEkJRgmnGCLAtgCvYNcdtQU&e=>
>>>>>
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