Re: [HCP-Users] Palm with TFCE on Cifti data
Hi Michael, That's right, no _tfce_ in the file names in the Example 9. Fixed, thanks. All the best, Anderson On 21 September 2016 at 00:54, Timothy Coalson <tsc...@mst.edu> wrote: > 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-templ >> ate? >> >> >> 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:
Re: [HCP-Users] Palm with TFCE on Cifti data
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<mailto: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_tstat_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 MaximumMean Sample Dev % Positive % Negative Inf/NaN Map Name 1 0.000 0.000 0.0000.0000.0000.000 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 verti
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_ > tstat_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 MaximumMean Sample Dev % Positive % Negative > Inf/NaN Map Name > > 1 0.000 0.000 0.000 0.0000.0000.000 > 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 >
Re: [HCP-Users] Palm with TFCE on Cifti data
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>
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<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=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=XBMPF2RHrxNWP8kAzlc8VR5C9A5jl6wCaLfoCs3cJ6w=44LdqlN7nRABsWwWMwVK8JKXAOcyWg8mdM9QX1micco=>.
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=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=XBMPF2RHrxNWP8kAzlc8VR5C9A5jl6wCaLfoCs3cJ6w=44LdqlN7nRABsWwWMwVK8JKXAOcyWg8mdM9QX1micco=>
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=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=gm0rcNwkH04qTmxXiPGQwA3Er4v-XqQRWQCJbV5Zi88=KMqdCUnTb-qhBGGQ9cCd5Wznv0uOWbk0cJlvRZfefIA=>
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:
Th
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 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_fsaverage/fs_ > LR.L.midthickness_va_avg.32k_fs_LR.shape.gii > > > 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=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=sPzxLm_SMMk5275scURO0sERCdJS6N76AckPIzYZyXE=1VAqCh8ViCwPk9iSx03nPlQ4XvNFdEQYQ-SGgB3Ywk0=> > > 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
Re: [HCP-Users] Palm with TFCE on Cifti data
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
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=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=sPzxLm_SMMk5275scURO0sERCdJS6N76AckPIzYZyXE=1VAqCh8ViCwPk9iSx03nPlQ4XvNFdEQYQ-SGgB3Ywk0=>
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 1/1, 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
>
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
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 1/1, 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=DQIGaQ=lb
>> 62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf9
>> 9IoNsmxWf1JolkKMmL6bXnYFSwg=r90wcW3hZmEtN5Op3za0BAuX5uqah-
>> NHkwg8a_Q7XII=3G_GSd6Y2Hl4j0R9IXFYn7JG7IJ5qEetuM339dG1HHg=
>>
>>
>>
>>
>>
>>
>>
>> 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
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>>
>
>
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Re: [HCP-Users] Palm with TFCE on Cifti data
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 1/1, 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.
> humanconnectome.org_mailman_listinfo_hcp-2Dusers=DQIGaQ&
> c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_
> z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=r90wcW3hZmEtN5Op3za0BAuX5uqah-
> NHkwg8a_Q7XII=3G_GSd6Y2Hl4j0R9IXFYn7JG7IJ5qEetuM339dG1HHg=
>
>
>
>
>
>
>
> 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
>
___
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[HCP-Users] Palm with TFCE on Cifti data
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 1/1, 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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