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.



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,


On 16 September 2016 at 16:32, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:


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,



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<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,


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 

Is that correct?

Thanks again,


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, 
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 

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.


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 
 Use preferably the midthickness." Where "here" is a link to :


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,


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, 

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:


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).


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:


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:


wb_command -surface-vertex-areas data_L.func.gii


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!


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; 

Subject: Re: [HCP-Users] Palm with TFCE on Cifti data

Hi Michael,

Please see an example in this page: 

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,


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,


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,


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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