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Bug 2456 - ft_volumerealign gives no output

Reported 2014-01-26 22:30:00 +0100
Modified 2019-08-10 12:28:06 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Windows
Importance: P5 critical
Assigned to: Haiteng Jiang
Depends on:
See also:

Sara Rombetto - 2014-01-26 22:30:52 +0100

I use the fieldtrip-20140114 on a 64 bit pc, OS windows7, RAM memory 6 GB Here I past a snippet of my script I was not able to attach the file PIERPAOL_0101.raw as it is too big rawdataname = 'H:\MaterialeSara\MEG\Tracciati\PIERPAOL_01\PIERPAOL_0101.raw'; hdr = ft_read_header(rawdataname); %% chooses channels cfg = []; cfg.dataset = rawdataname; = {'MAG_*', 'REF_*', '-MAG_021', '-MAG_026', '-MAG_066', '-MAG_075', '-MAG_099', '-MAG_100','-MAG_104', '-MAG_110', '-MAG_112', '-MAG_113', '-MAG_117', '-MAG_122', '-MAG_124', '-MAG_125', '-MAG_128', '-MAG_131', '-MAG_135', '-MAG_138', 'ELEC_007'};%valido per saramed02'ELEC_*'}; %% cfg.trialfun ='ft_trialfun_general'; % cfg.trialdef.triallength = 5; % duration in seconds cfg.trialdef.ntrials = inf; % number of trials, inf results in as many as possible cfg = ft_definetrial(cfg); % The output of ft_definetrial can be used for ft_preprocessing. %% preprocessing cfg.preproc.dftfilter = 'yes'; cfg.preproc.bpfilter ='yes'; cfg.preproc.bpfreq= [2 100]; data = ft_preprocessing(cfg); %% cfg.refchannel = 'REF_*'; = 'MAG_*'; cfg.zscore = 'no'; cfg.pertrial = 'no'; cfg.trials = 'all'; [dataout] = ft_denoise_pca(cfg, data) ; %% cfg = []; cfg.output = 'pow'; % cfg.output = 'powandcsd'; cfg.method = 'mtmfft'; cfg.pad = 'maxperlen'; % means maximal number of samples cfg.taper = 'hanning'; % window function cfg.xlim = 'maxmin'; % defines frequency band of the display cfg.tapsmofrq = 1; % taper to smooth frequencies cfg.foilim = [2 49]; [freq] = ft_freqanalysis(cfg, dataout); mri = ft_read_mri('H:\MaterialeSara\ModifiedBurkhardStay\matlab\Subject01.mri'); %this is downloaded from fieldtrip! %[mri] = ft_convert_coordsys(mri, 'spm', 2) %this gives an error message, as it is not implemented yet cfg=[]; cfg.method = 'interactive'; [mri2] = ft_volumerealign(cfg, mri); %this gives no output

Jan-Mathijs Schoffelen - 2014-01-27 09:01:50 +0100

Hi Haiteng, Would you mind taking this one? The usual course of action is to first reproduce the bug. Sara had problems uploading the relevant data, but it seems that she just uses Subject01.mri (you can find this one somewhere on /home/common/matlab/fieldtrip/data). I suspect that the bug is a problem on her end, but we should try first. If it indeed happens to lie at the user's end, verify whether the function has been properly used (i.e. did Sara press 'q' when exiting, or did she just close the figure? The former is how it should be, the latter probably will produce no output).

Haiteng Jiang - 2014-01-29 15:02:23 +0100

(In reply to Jan-Mathijs Schoffelen from comment #1) Hi JM, Yes, I think Sara only needs mri . I just test it and everything is fine. At this moment , Sara probably doesn't have enough RAM memory to proceed since (data/dataout/) could be very large. Sara, Could you please add clear data dataout (it is not used later anyway) before ft_read_mri? Let me know whether it works. Haiteng

Jörn M. Horschig - 2014-01-29 17:12:28 +0100

since you specify cfg.interactive='yes', could it be that you just need to press 'q' to quit the interactive mode?

Sara Rombetto - 2014-01-29 17:53:47 +0100

I press the q key, but after that there is no output. At the momenti I am in a different lab, so I cannot check my RAm...but If I am right it should be 8 GB. How much RAM do you have? I can try to send you the dataout, but I guess it is bigger that 1MB. Do you have a ftp site where I can charge it? Regards Sara Rombetto

Haiteng Jiang - 2014-02-01 15:41:42 +0100

(In reply to Sara Rombetto from comment #4) Hi Sara, What do you mean by 'no output'. After you identify it by pressing either n/l/r for fiducials ,then press 'q' to save and exit. The Fiduicals are stored in MRI2. Have you ever see the plot of the anatomical mri before you identify fiducials ? This issue is not related to the data.

Sara Rombetto - 2014-02-02 11:57:59 +0100

Now I can see the fiducials in different colors (blu, red and green) and I can see the output. I cannot understand where was the problem...but it looks like it is solved now! thanks

Robert Oostenveld - 2014-03-26 17:12:41 +0100

it seems that it has been resolved, so I'll change the status accordingly.

Haiteng Jiang - 2014-03-26 21:35:22 +0100

Yes, It is not a bug actually ....(In reply to Robert Oostenveld from comment #7)

Robert Oostenveld - 2019-08-10 12:28:06 +0200

This closes a whole series of bugs that have been resolved (either FIXED/WONTFIX/INVALID) for quite some time. If you disagree, please file a new issue describing the issue on