External Email - Use Caution
Dear Freesurfer Community, Drs. Winkler, Greve, Fischl, et al.
*My apologies if this reposts, but this is my first time emailing the
listserv, and I'm not sure if my earlier email went through*
Could anyone help me understand which palm options are needed in order to
produce tfce and clustere NPC results that are fwe-corrected across
contrasts (i.e., npc_fisher_cfwep_)?
I'm analyzing area and thickness and have four one-tailed contrasts of
interest (e.g., C1+, C1-, C2+, C2-). Currently, I am only able to get the
"output'_dpv_npc_fisher_cfwep_c[1234]" results, but the palm log ends
abruptly after saving these files and does not save the _tfce_ or
_clustere_ versions:
Saving p-values for NPC between modalities (uncorrected and corrected
within contrasts).
Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c1
Saving file: wordadhd_npc_lh_clustere_npc_fisher_c1
Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c1
Saving file: wordadhd_npc_lh_tfce_npc_fisher_c1
Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c1
Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c2
Saving file: wordadhd_npc_lh_clustere_npc_fisher_c2
Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c2
Saving file: wordadhd_npc_lh_tfce_npc_fisher_c2
Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c2
Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c3
Saving file: wordadhd_npc_lh_clustere_npc_fisher_c3
Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c3
Saving file: wordadhd_npc_lh_tfce_npc_fisher_c3
Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c3
Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c4
Saving file: wordadhd_npc_lh_clustere_npc_fisher_c4
Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c4
Saving file: wordadhd_npc_lh_tfce_npc_fisher_c4
Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c4
Saving p-values for NPC between modalities (corrected across contrasts).
Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c1
Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c2
Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c3
Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c4
>>
The error log contains the following text, and my efforts to read through
these source files have been in vain:
{^HCell contents reference from a non-cell array object.
Error in palm_saveall (line 1043)
distmax(:,j) = plm.Tclumax{m}{c};
Error in palm_core (line 2489)
palm_saveall(plm,opts);
Error in palm (line 81)
palm_core(varargin{:});
}^H
^G
I have essentially permuted the various -corr(con/mod) and -npc(con/mod)
options, as well as various combinations of -T & -C {z}, -Tuni & -Cuni {z},
and -Tnpc & -Cnpc {z}, using a small number of permutations to assess the
number of output maps and whether jobs finish appropriately.
Here's an example of one of the palm commands that resulted in these output
and error logs (with line-breaks for legibility):
fsl_sub -l $logdir palm -designperinput
-i {area_dir}/292_${hemi}.area_stack.mgh
-d {design_dir}/wordadhd_npc_areatotal.mat
-t {design_dir}/wordadhd_npc_areatotal.con
-i {thickness_dir}/292_${hemi}.thickness_stack.mgh
-d {design_dir}/wordadhd_npc_thickmean.mat
-t {design_dir}/wordadhd_npc_thickmean.con
-m {base_dir}/palm/input/${hemi}mask.mgz
-s ${surf_dir}/${hemi}.white ${surf_dir}/${hemi}.white.avg.area.mgh
-o wordadhd_npc_${hemi}
-eb ${EB} -corrcon -corrmod
-logp -ise -npc -T -C 1.64485 -n 5
If knowing versions helps at all:
PALM alpha109
MATLAB 8.3.0.532 (R2014a)
FreeSurfer 5.3.0
FSL 5.0.8
Any advice you could provide on this particular error, why my input doesn't
produce the tfce_npc_fisher_cfwep or clustere__npc_fisher_cfwep results, or
other problem-solving suggestions would be greatly appreciated!
With gratitude,
Dan
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
