Hi Anderson,
yes, this helped, now the analysis works. Thanks a lot!
Pavel
On 23 February 2016 at 07:57, Anderson M. Winkler
<[log in to unmask]> wrote:
> Hi Pavel,
>
> PALM needs the input 4D data file to be entered with the option "-i". The
> option "-s" is for a surface geometry. In the context of an analysis using
> FreeSurfer data, the file that goes with -s can be lh.pial, or rh.white for
> instance (from the 'fsaverage' subject).
>
> Hope this helps.
>
> All the best,
>
> Anderson
>
>
> On 22 February 2016 at 18:05, Pavel Hok <[log in to unmask]> wrote:
>>
>> Dear FSL experts,
>>
>> I am trying to run PALM on a set of data saved as FreeSurfer 4D mgh
>> surface file but I get an error which I cannot solve. The PALM is
>> started from MATLAB v 2012b with the command below:
>>
>> palm -n 5000 -s rawdata/surf/fA+S+M_concat_surf.mgh -o
>> results/palm-test.rand/fA+S+M-palm-surf -C 2.5 -T -d
>> designs/A6+S7+M9.mat -t designs/A6+S7+M9.con
>>
>> The output from PALM:
>>
>> Running PALM alpha83 using MATLAB with the following options:
>> -n 5000
>> -s rawdata/surf/fA+S+M_concat_surf.mgh
>> -o results/palm-test.rand/fA+S+M-palm-surf
>> -C 2.5
>> -save1-p
>> -fdr
>> -d designs/A6+S7+M9.mat
>> -t designs/A6+S7+M9.con
>> Loading surface 1/1: rawdata/surf/fA+S+M_concat_surf.mgh
>> Reading design matrix and contrasts.
>> Reference to non-existent field 'N'.
>>
>> Error in palm_takeargs (line 1964)
>> if size(plm.Mset{m},1) ~= plm.N,
>>
>> Error in palm_core (line 32)
>> [opts,plm] = palm_takeargs(varargin{:});
>>
>> Error in palm (line 81)
>> palm_core(varargin{:});
>>
>>
>> Is it data or matrix related? Or is it related to wrong settings or
>> FreeSurfer/MATLAB/FSL version?
>>
>> Thanks in advance!
>>
>> Cheers
>>
>> Pavel
>>
>> --
>>
>> -------------------------------------------------------------------------------
>> -- MUDr. Pavel Hok
>>
>> -------------------------------------------------------------------------------
>> -- Laboratoř funkční magnetické rezonance
>> -- Neurologická klinika
>> -- Lékařská fakulta
>> -- Univerzita Palackého v Olomouci
>> -- Fakultní nemocnice Olomouc
>>
>> -------------------------------------------------------------------------------
>> -- Laboratory of functional magnetic resonance imaging
>> -- Department of Neurology
>> -- Faculty of Medicine and Dentistry
>> -- Palacky University Olomouc
>> -- University Hospital Olomouc
>> -- Czech Republic
>>
>> -------------------------------------------------------------------------------
>> -- I.P. Pavlova 6, 775 20 Olomouc
>> -- web: fmri.upol.cz
>> -- tel.: +420 588 443 418
>> -- e-mail: [log in to unmask]
>>
>> -------------------------------------------------------------------------------
>
>
--
-------------------------------------------------------------------------------
-- MUDr. Pavel Hok
-------------------------------------------------------------------------------
-- Laboratoř funkční magnetické rezonance
-- Neurologická klinika
-- Lékařská fakulta
-- Univerzita Palackého v Olomouci
-- Fakultní nemocnice Olomouc
-------------------------------------------------------------------------------
-- Laboratory of functional magnetic resonance imaging
-- Department of Neurology
-- Faculty of Medicine and Dentistry
-- Palacky University Olomouc
-- University Hospital Olomouc
-- Czech Republic
-------------------------------------------------------------------------------
-- I.P. Pavlova 6, 775 20 Olomouc
-- web: fmri.upol.cz
-- tel.: +420 588 443 418
-- e-mail: [log in to unmask]
-------------------------------------------------------------------------------
