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=
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ________________________________
>>>>>>
>>>>>> The materials in this message are private and may contain Protected
>>>>>> Healthcare Information or other information of a sensitive nature. If you
>>>>>> are not the intended recipient, be advised that any unauthorized use,
>>>>>> disclosure, copying or the taking of any action in reliance on the 
>>>>>> contents
>>>>>> of this information is strictly prohibited. If you have received this 
>>>>>> email
>>>>>> in error, please immediately notify the sender via telephone or return 
>>>>>> mail.
>>>>>>
>>>>>> _______________________________________________
>>>>>> HCP-Users mailing list
>>>>>> HCP-Users@humanconnectome.org
>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>> <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=sPzxLm_SMMk5275scURO0sERCdJS6N76AckPIzYZyXE&s=HA_OBAukOuMv6bzgh1-tFqC6ZSUAvEcYBLsoZuA9IOA&e=>
>>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> HCP-Users mailing list
>>>> HCP-Users@humanconnectome.org
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>> <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=>
>>>>
>>>
>>>
>>
>

_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Reply via email to