Hi Joseph,
I downloaded your files earlier today but couldn’t yet have a look.
It may be that the particular values in the permutation distribution caused the
tail fitting to fail (simply an unlucky scenario). If that is the case, try
running again with a different seed (there is an option for that, see among the
advanced options). The default is 0, so try with a different number (e.g., 1,
2, ...).
All the best,
Anderson
Sent from mobile. Please excuse brevity.
________________________________
From: Joseph Orr <joseph....@tamu.edu>
Sent: Monday, July 23, 2018 7:59:26 PM
To: HCP Users
Subject: Re: [HCP-Users] issues with palm tfce for HCP task func data
I inserted a breakpoint in palm_competitive at line 104 right before the error
(pasted below) occurred. In the first pass. dpv_tstat_fwep, tfce_tstat, and
tfce_tstat_uncp are saved (now in the folder linked above), but when i
continue, I get the NaN error. The vector dd is length n-permutation - 1, and
has a single NaN in row 2499. The workspace at the time of the error is saved
as post_tfce_uncorrp_workspace.mat in the linked folder.
100% [Design 1/1, Contrast 1/1, Shuffling 2500/2500, Modality 1/1]
Elapsed time with permutations: ~ 4438.79 seconds.
Computing p-values.
Saving p-values (uncorrected, and corrected within modality and within
contrast).
Saving file: motor_RH_results_L_test_dpv_tstat_uncp
104 if any(isnan(dd)),
Saving file: motor_RH_results_L_test_dpv_tstat_fwep
Saving file: motor_RH_results_L_test_tfce_tstat
Saving file: motor_RH_results_L_test_tfce_tstat_uncp
K>> any(isnan(dd))
ans =
logical
1
K>> sum(isnan(dd))
ans =
1
Error using palm_competitive (line 105)
Data cannot be sorted. Check for NaNs that might be present,
or precision issues that may cause over/underflow.
If you are using "-approx tail", consider adding "-nouncorrected".
Error in palm_datapval (line 67)
[~,cdfG,distp] = palm_competitive(Gvals(:),'descend',true);
Error in palm_saveall (line 303)
Ptosave =
palm_datapval(plm.Gtfce{y}{m}{c},plm.Gtfcemax{y}{m}{c},false);
Error in palm_core (line 2489)
palm_saveall(plm,opts);
Error in palm (line 81)
palm_core(varargin{:});
--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A&M Institute for Neuroscience
Texas A&M University
College Station, TX
On Mon, Jul 23, 2018 at 3:27 PM, Joseph Orr
<joseph....@tamu.edu<mailto:joseph....@tamu.edu>> wrote:
I'm having an issue running palm following the CIFTI example
(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/Examples#Example_10:_Using_CIFTI_files).
I've worked with PALM a lot, but this is the first time using CIFTI files. I
am analyzing several functional tasks from 219 participants in the HCP. I'm
running a one-sample t-test with two covariates. The subcortical statistics run
fine, but I am having issues with the cortical surfaces.
I was running 10000 permutations and after completing the permutations the job
would stall for 10+ hours. When I tried running less (e.g., 500) permutations I
get an error from palm_competitive about NaNs. The dpv fwe-corrected stats save
(and look reasonable), so the NaN appears during the tfce stage. For the
surface I'm using:
HCP_S1200_GroupAvg_v1/S1200.R.midthickness_MSMAll.32k_fs_LR.surf.gii along with
the mean surface vertex area of the 219 participants. Inspecting the data in
wb_view I don't see anything unusual, and no Inf/NaN are indicated in
wb_command -file-infomation.
Here are the options I am using (I've tried toggling accel, nouncorrected, and
logp in different combinations, but the results are always the same):
-i lang_story-math_data_L.func.gii
-d design_n219_mean.mat
-t design_n219_mean.con
-o lang_story-math_data_L_cort
-T
-tfce2D
-s L_midthickness.surf.gii L_area.func.gii
-logp
-n 10000
-ise
The relevant files for one example are available here:
https://drive.google.com/drive/folders/1uZPQK6Gy2MtTuOjZwin0ZToxBSUN9tct?usp=sharing
I've checked everything that I can think of to troubleshoot the issue, but I've
hit a wall, so I'd be grateful for any advise/insights. The last thing I'm
trying is using the sphere surface, and I'll update if that works.
Joe
--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A&M Institute for Neuroscience
Texas A&M University
College Station, TX
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