I was mistaken; the command gives this error when I use the option -T to run
TFCE, and palm runs smoothly when I do not use that option. Once again the
error is:
Building null distribution.
0.01% [Design 1/1, Contrast 1/1, Shuffling 1/10000, Modality 1/1]
Saving file: palm_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{:});
Would you have any suggestion for how I can run TFCE with palm here? Or is
anything else recommended for identifying clusters of activation?
Thank you,
Michael
________________________________
From: Michael F.W. Dreyfuss
Sent: Tuesday, September 13, 2016 12:25:03 PM
To: Burgess, Gregory
Cc: [email protected]; Anderson M. Winkler
Subject: Re: [HCP-Users] PALM with cifti files
Thank you very much. When I merge my cope files I was getting the same errors
as before when I ran the following command:
palm -i TGNGcope1.dtseries.nii -transposedata -fdr -d
$LevelThreeFEATDir/design.mat -t $LevelThreeFEATDir/design.con -T -ise
When I removed the "-t $LevelThreeFEATDir/design.con" then palm appears to run
smoothly, so the problem was coming from there. I thought that argument was
necessary to indicate that this was a one-sample t-test, but I the .mat file is
sufficient.
By the way, are the materials for the course available somewhere now? I'd love
to see them. I am also not familiar with palm_vestwrite, and I haven't been
able to any documentation online.
Thank you,
Michael
________________________________
From: Burgess, Gregory <[email protected]>
Sent: Tuesday, September 13, 2016 10:24:14 AM
To: Michael F.W. Dreyfuss
Cc: [email protected]; Anderson M. Winkler
Subject: Re: [HCP-Users] PALM with cifti files
Hi Michael,
I assume that each cope map is viewable in Connectome Workbench... that is to
say that each CIFTI cope has 91282 rows and 1 column.
For the recent HCP Course, we suggested merging the individual subject copes
into a dtseries with 91282 rows x S columns, where S was the number of subjects.
# Start an empty variable to store the list of arguments:
args=""
# For each subject:
for subj in $(cat list101.txt) ; do
# Append the respective arguments to the list (below it’s all a single line):
args="${args} -cifti
${PRACTICALS}/day3-tuesday/tfMRI/DATA/${subj}/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s2_level2_Glasser.feat/ParcellatedStats/cope11.feat/cope1.ptseries.nii
-column 1"
done
# Run the wb_command to merge all into a single file:
wb_command -cifti-merge Y.ptseries.nii ${args}
Then set the merged CIFTI output as the single input file with the -i option.
The .mat and .con can be written using palm_vestwrite, but I believe that PALM
will work directly with the output of FSL's GLM GUI as well.
Give that a try.
--Greg
____________________________________________________________________
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience
Phone: 314-362-7864<tel:314-362-7864>
Email: [email protected]<mailto:[email protected]>
On Sep 12, 2016, at 1:50 PM, Burgess, Gregory
<[email protected]<mailto:[email protected]>> wrote:
Hi Michael,
I just want to verify that you are trying to use PALM for “higher-level” group
analyses. PALM is not currently able to conduct “lower-level” timeseries
analyses. You currently need to use the HCP task fMRI pipelines for that.
If you are attempting group analyses, it might be helpful to know the error
messages that you are receiving.
Thanks,
--Greg
____________________________________________________________________
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: [email protected]<mailto:[email protected]>
On Sep 12, 2016, at 1:40 PM, Glasser, Matthew
<[email protected]<mailto:[email protected]>> wrote:
Do you have the latest version of PALM? Does it work if you convert the files
to dscalar?
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of "Michael F.W. Dreyfuss"
<[email protected]<mailto:[email protected]>>
Date: Monday, September 12, 2016 at 1:15 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] PALM with cifti files
Hello,
I am getting errors when I try to use palm with cifti files. Is there an option
or options that I need to use with palm for it to read dtseries.nii files
appropriately? Are there any examples of simple implementations of palm on
cifti type fMRI data (task based especially)?
Thanks you,
Michael
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