Stella,
unless you ran these commands somewhere else it seems that the files
you're trying to pass to melodic as input don't exist. For denoising,
you need to run:
melodic -i <infile> --mix=<mixing matrix> --filter="<BLAH>" <other
options e.g. -o denoise.ica>
where
<infile> is the data file which you used as input for the original
melodic run (if you can't remember, just look in the melodic.log file
inside of Ver_melodic.ica)
<mixing matrix> is the mixing matrix from the original melodic run (i
guess it's ./Ver_melodic.ica/melodic_mix )
2 bits of advice: - you should only filter effects which are clearly
interpretable as nuisance artefacts, from your earlier email I see
that you filter everything apart from a single component, are you
sure that this is what you want?
- It seems you're running an old verison of FSL, you might want to
consider updating the local distribution
cheers
christian
On 10 Aug 2005, at 04:12, Stella de Bode wrote:
> Thanks, Christian, ICA file is in the end
>
>
> [Stella:~] sdebode% wc denoise.ica/melodic_mix
> wc: denoise.ica/melodic_mix: open: No such file or directory
> [Stella:~] sdebode% avwsize denoise
> ** ERROR: nifti_image_read(denoise): can't open header file
> ** ERROR: nifti_image_open(denoise): bad header info
> Error: failed to open file denoise
> ERROR: Could not open file
>
> [Stella:Pryor/Pre_USC/Language] sdebode% ls -l *
> -r-xr-xr-x 1 sdebode sdebode 348 24 Jul 14:28
> Veronica2_0724_VocalGo.hdr
> -r-xr-xr-x 1 sdebode sdebode 11272192 24 Jul 14:28
> Veronica2_0724_VocalGo.img
>
> Ver_Contrasts.feat:
> total 39256
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> cluster_mask_zstat1.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> cluster_mask_zstat1.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> cluster_mask_zstat2.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> cluster_mask_zstat2.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> cluster_mask_zstat3.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> cluster_mask_zstat3.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> cluster_mask_zstat4.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> cluster_mask_zstat4.img
> -rw-r--r-- 1 sdebode sdebode 1052 24 Jul 18:55
> cluster_zstat1.html
> -rw-r--r-- 1 sdebode sdebode 204 24 Jul 18:55
> cluster_zstat1.txt
> -rw-r--r-- 1 sdebode sdebode 1052 24 Jul 18:55
> cluster_zstat2.html
> -rw-r--r-- 1 sdebode sdebode 204 24 Jul 18:55
> cluster_zstat2.txt
> -rw-r--r-- 1 sdebode sdebode 3456 24 Jul 18:55
> cluster_zstat3.html
> -rw-r--r-- 1 sdebode sdebode 657 24 Jul 18:55
> cluster_zstat3.txt
> -rw-r--r-- 1 sdebode sdebode 2310 24 Jul 18:55
> cluster_zstat4.html
> -rw-r--r-- 1 sdebode sdebode 459 24 Jul 18:55
> cluster_zstat4.txt
> -rw-r--r-- 1 sdebode sdebode 379 24 Jul 18:48 design.con
> -rw-r--r-- 1 sdebode sdebode 11756 24 Jul 18:48 design.fsf
> -rw-r--r-- 1 sdebode sdebode 163509 24 Jul 18:48 design.gif
> -rw-r--r-- 1 sdebode sdebode 3719 24 Jul 18:48 design.mat
> -rw-r--r-- 1 sdebode sdebode 629961 24 Jul 18:48 design.ppm
> -rw-r--r-- 1 sdebode sdebode 1146 24 Jul 18:48 design.trg
> -rw-r--r-- 1 sdebode sdebode 128254 24 Jul 18:48 design_cov.gif
>
> -rw-r--r-- 1 sdebode sdebode 571965 24 Jul 18:48 design_cov.ppm
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:48
> example_func.hdr
> -rw-r--r-- 1 sdebode sdebode 262144 24 Jul 18:48
> example_func.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:51
> filtered_func_data.hdr
> -rw-r--r-- 1 sdebode sdebode 11272192 24 Jul 18:51
> filtered_func_data.img
> -rw-r--r-- 1 sdebode sdebode 119 24 Jul 18:55
> lmax_zstat1.txt
> -rw-r--r-- 1 sdebode sdebode 119 24 Jul 18:55
> lmax_zstat2.txt
> -rw-r--r-- 1 sdebode sdebode 714 24 Jul 18:55
> lmax_zstat3.txt
> -rw-r--r-- 1 sdebode sdebode 415 24 Jul 18:55
> lmax_zstat4.txt
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:50 mask.hdr
> -rw-r--r-- 1 sdebode sdebode 131072 24 Jul 18:50 mask.img
> drwxr-xr-x 11 sdebode sdebode 374 24 Jul 18:50 mc
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> rendered_thresh_zstat1.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> rendered_thresh_zstat1.img
> -rw-r--r-- 1 sdebode sdebode 114549 24 Jul 18:55
> rendered_thresh_zstat1.png
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> rendered_thresh_zstat2.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> rendered_thresh_zstat2.img
> -rw-r--r-- 1 sdebode sdebode 115044 24 Jul 18:55
> rendered_thresh_zstat2.png
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> rendered_thresh_zstat3.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> rendered_thresh_zstat3.img
> -rw-r--r-- 1 sdebode sdebode 118270 24 Jul 18:55
> rendered_thresh_zstat3.png
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> rendered_thresh_zstat4.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> rendered_thresh_zstat4.img
> -rw-r--r-- 1 sdebode sdebode 116907 24 Jul 18:55
> rendered_thresh_zstat4.png
> -rw-r--r-- 1 sdebode sdebode 4476 24 Jul 18:59 report.com
> -rw-r--r-- 1 sdebode sdebode 3974 24 Jul 18:58 report.html
> -rw-r--r-- 1 sdebode sdebode 6269 24 Jul 18:59 report.log
> drwxr-xr-x 68 sdebode sdebode 2312 24 Jul 18:54 stats
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> thresh_zstat1.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> thresh_zstat1.img
> -rw-r--r-- 1 sdebode sdebode 6 24 Jul 18:54
> thresh_zstat1.vol
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> thresh_zstat2.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> thresh_zstat2.img
> -rw-r--r-- 1 sdebode sdebode 6 24 Jul 18:54
> thresh_zstat2.vol
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> thresh_zstat3.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> thresh_zstat3.img
> -rw-r--r-- 1 sdebode sdebode 6 24 Jul 18:55
> thresh_zstat3.vol
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:55
> thresh_zstat4.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:55
> thresh_zstat4.img
> -rw-r--r-- 1 sdebode sdebode 6 24 Jul 18:55
> thresh_zstat4.vol
> drwxr-xr-x 102 sdebode sdebode 3468 24 Jul 18:58 tsplot
>
> Ver_No_Contrast.feat:
> total 35752
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> cluster_mask_zstat1.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> cluster_mask_zstat1.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> cluster_mask_zstat2.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> cluster_mask_zstat2.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> cluster_mask_zstat3.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> cluster_mask_zstat3.img
> -rw-r--r-- 1 sdebode sdebode 1057 24 Jul 18:29
> cluster_zstat1.html
> -rw-r--r-- 1 sdebode sdebode 210 24 Jul 18:29
> cluster_zstat1.txt
> -rw-r--r-- 1 sdebode sdebode 1060 24 Jul 18:29
> cluster_zstat2.html
> -rw-r--r-- 1 sdebode sdebode 212 24 Jul 18:29
> cluster_zstat2.txt
> -rw-r--r-- 1 sdebode sdebode 1058 24 Jul 18:29
> cluster_zstat3.html
> -rw-r--r-- 1 sdebode sdebode 212 24 Jul 18:29
> cluster_zstat3.txt
> -rw-r--r-- 1 sdebode sdebode 296 24 Jul 18:26 design.con
> -rw-r--r-- 1 sdebode sdebode 10375 24 Jul 18:26 design.fsf
> -rw-r--r-- 1 sdebode sdebode 144887 24 Jul 18:26 design.gif
> -rw-r--r-- 1 sdebode sdebode 3719 24 Jul 18:26 design.mat
> -rw-r--r-- 1 sdebode sdebode 558159 24 Jul 18:26 design.ppm
> -rw-r--r-- 1 sdebode sdebode 1146 24 Jul 18:26 design.trg
> -rw-r--r-- 1 sdebode sdebode 128254 24 Jul 18:26 design_cov.gif
> -rw-r--r-- 1 sdebode sdebode 571965 24 Jul 18:26 design_cov.ppm
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:26
> example_func.hdr
> -rw-r--r-- 1 sdebode sdebode 262144 24 Jul 18:26
> example_func.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:27
> filtered_func_data.hdr
> -rw-r--r-- 1 sdebode sdebode 11272192 24 Jul 18:27
> filtered_func_data.img
> -rw-r--r-- 1 sdebode sdebode 118 24 Jul 18:29 lmax_zstat1.txt
> -rw-r--r-- 1 sdebode sdebode 119 24 Jul 18:29 lmax_zstat2.txt
> -rw-r--r-- 1 sdebode sdebode 117 24 Jul 18:29 lmax_zstat3.txt
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:27 mask.hdr
> -rw-r--r-- 1 sdebode sdebode 131072 24 Jul 18:27 mask.img
> drwxr-xr-x 11 sdebode sdebode 374 24 Jul 18:27 mc
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> rendered_thresh_zstat1.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> rendered_thresh_zstat1.img
> -rw-r--r-- 1 sdebode sdebode 122537 24 Jul 18:29
> rendered_thresh_zstat1.png
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> rendered_thresh_zstat2.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> rendered_thresh_zstat2.img
> -rw-r--r-- 1 sdebode sdebode 122464 24 Jul 18:29
> rendered_thresh_zstat2.png
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> rendered_thresh_zstat3.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> rendered_thresh_zstat3.img
> -rw-r--r-- 1 sdebode sdebode 122217 24 Jul 18:29
> rendered_thresh_zstat3.png
> -rw-r--r-- 1 sdebode sdebode 3706 24 Jul 18:30 report.com
> -rw-r--r-- 1 sdebode sdebode 3722 24 Jul 18:30 report.html
> -rw-r--r-- 1 sdebode sdebode 5429 24 Jul 18:30 report.log
> drwxr-xr-x 58 sdebode sdebode 1972 24 Jul 18:28 stats
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> thresh_zstat1.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> thresh_zstat1.img
> -rw-r--r-- 1 sdebode sdebode 6 24 Jul 18:28
> thresh_zstat1.vol
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> thresh_zstat2.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> thresh_zstat2.img
> -rw-r--r-- 1 sdebode sdebode 6 24 Jul 18:28
> thresh_zstat2.vol
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:29
> thresh_zstat3.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:29
> thresh_zstat3.img
> -rw-r--r-- 1 sdebode sdebode 6 24 Jul 18:29
> thresh_zstat3.vol
> drwxr-xr-x 77 sdebode sdebode 2618 24 Jul 18:30 tsplot
>
> Ver_melodic.ica:
> total 53392
> -rw-r--r-- 1 sdebode sdebode 368 24 Jul 18:41 PPCA
> -rw-r--r-- 1 sdebode sdebode 463 24 Jul 18:41
> eigenvalues_adjusted
> -rw-r--r-- 1 sdebode sdebode 440 24 Jul 18:41
> eigenvalues_percent
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:40
> example_func.hdr
> -rw-r--r-- 1 sdebode sdebode 262144 24 Jul 18:40
> example_func.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:41
> filtered_func_data.hdr
> -rw-r--r-- 1 sdebode sdebode 11272192 24 Jul 18:41
> filtered_func_data.img
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 18:41 mask.hdr
> -rw-r--r-- 1 sdebode sdebode 524288 24 Jul 18:41 mask.img
> -rw-r--r-- 1 sdebode sdebode 7336 24 Jul 19:13 melodic.log
> -rw-r--r-- 1 sdebode sdebode 6013 24 Jul 19:13 melodic_FTmix
> -rw-r--r-- 1 sdebode sdebode 348 24 Jul 19:13 melodic_IC.hdr
> -rw-r--r-- 1 sdebode sdebode 15204352 24 Jul 19:13 melodic_IC.img
> -rw-r--r-- 1 sdebode sdebode 13558 24 Jul 19:13 melodic_mix
> drwxr-xr-x 323 sdebode sdebode 10982 24 Jul 19:13 report
> -rw-r--r-- 1 sdebode sdebode 7322 24 Jul 19:13 report.log
> -rw-r--r-- 1 sdebode sdebode 40 24 Jul 18:41 smoothest
>
>
>
> On Aug 9, 2005, at 12:24 PM, Christian Beckmann wrote:
>
>
>> Stella,
>>
>> well, is there a file denoise in the directory? Can you send me
>> the output of
>>
>> ls -l *
>>
>> wc denoise.ica/melodic_mix
>>
>> and
>>
>> avwsize denoise
>>
>> thanks
>> Christian
>>
>>
>> On 9 Aug 2005, at 17:08, Stella de Bode wrote:
>>
>>
>>> Hello
>>> i tried to use denoise after running Melodic and got this error
>>> message
>>>
>>>
>>> <denoise_FSL command line.tiff>
>>> Thank you!
>>> stella
>>>
>>
>> --
>> Christian F. Beckmann
>> Oxford University Centre for Functional
>> Magnetic Resonance Imaging of the Brain,
>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>> Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/
>> ~beckmann/
>> Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
>
--
Christian F. Beckmann
Oxford University Centre for Functional
Magnetic Resonance Imaging of the Brain,
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
|
