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<mailto: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<mailto:andersonwink...@gmail.com>
<andersonwink...@gmail.com<mailto:andersonwink...@gmail.com>> on behalf of
Anderson M. Winkler <wink...@fmrib.ox.ac.uk<mailto: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<mailto: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.midthickness.32k_fs_LR.surf.gii
Is that correct?
Thanks again,
Michael
________________________________
From: Timothy Coalson <tsc...@mst.edu<mailto: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<mailto: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<mailto: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/master/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<mailto: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<mailto: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.php?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<mailto: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_fsaverage/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<mailto:andersonwink...@gmail.com>
<andersonwink...@gmail.com<mailto:andersonwink...@gmail.com>> on behalf of
Anderson M. Winkler <wink...@fmrib.ox.ac.uk<mailto: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<mailto: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<mailto: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<mailto: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<mailto:do...@wustl.edu>>
Sent: Wednesday, September 14, 2016 11:09:04 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org<mailto: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<mailto: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
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