Hi Conor,
Can you upload the problematic file ( prefiltered_func_data_thresh.nii.gz ) to the oxfile link ( https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF ) so I can check what is happening?
Kind Regards
Matthew
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 30 Aug 2017, at 01:19, Conor Owens-Walton <[log in to unmask]> wrote:
>
> Dear Mark,
>
> Sorry I should have said I am using fslversion 5.0.9
>
> Kind regards,
> Conor
> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Conor Owens-Walton <[log in to unmask]>
> Sent: Tuesday, 29 August 2017 4:05:31 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Data type query
>
> Dear Mark,
>
> When I navigate into the nonan.feat folder and run that command I get a 'Segmentation fault: 11' printed to terminal.
>
> I am using FSL 5.0 on macOS Sierra (Version 10.12.1).
>
> Sorry to take more of your time.
>
> Kind regards,
>
> Conor
> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
> Sent: Tuesday, 29 August 2017 12:19:05 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Data type query
>
> Hi,
>
> It looks like the problem is in this command:
>
> /usr/local/fsl/bin/susan prefiltered_func_data_thresh 44.14088925 2.12314225053 3 1 1 mean_func 44.14088925 prefiltered_func_data_smooth
>
> What happens if you try to run this yourself from the command line?
>
> Also, what version of FSL are you running and what are the specs of the machine you are using?
>
> All the best,
> Mark
>
>
>
>> On 26 Aug 2017, at 03:24, Conor Owens-Walton <[log in to unmask]> wrote:
>>
>> Dear Mark (/FSL Community),
>>
>> Thanks so much for your response. I tried using fslmaths with -nan followed by my basic preprocessing feat analysis, but to no avail.
>>
>> I ran a feat preprocessing as follows (including only changes from default settings):
>>
>> First-level analysis - Preprocessing
>>
>> Data:
>> • 4D data: PID_nonan
>> Pre-stats:
>> • MELODIC ICA data exploration
>> Registration:
>> • Main structural image: PID_brain
>> • Nonlinear registration
>>
>> Attached is the log file (also as a text file) and another log text from the Output directory.
>>
>> I would be so grateful for any help that you guys can give me.
>>
>> Kindest regards,
>>
>> Conor
>>
>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
>> Sent: Friday, 25 August 2017 10:27:39 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Data type query
>>
>> Hi,
>>
>> This all looks fine, and there is no problem with the data type.
>> What can be a problem sometimes (though I can't tell if it is in this case or not) is the presence of NaN values in the image. FSL is not happy with these values, though they can be easily removed. Just run:
>>
>> fslmaths Pid_FUNC -nan Pid_FUNC_nonan
>>
>> and then try again with the new file (Pid_FUNC_nonan).
>>
>> Hopefully that will fix the problem.
>> If not please email back but provide more details about exactly what you have run and more information from the error (e.g., the log file).
>>
>> All the best,
>> Mark
>>
>>
>>
>> > On 25 Aug 2017, at 03:26, Conor Owens-Walton <[log in to unmask]> wrote:
>> >
>> > Dear FSL community,
>> >
>> > I have some processed and censored FUNC data that I want to use for a resting-state analysis.
>> >
>> > I have tried running FEAT analysis on the data but I always get a "child process exited abnormally" error. Unfortunately I am not able to fix the problem with the physicist who implemented the preprocessing steps.
>> >
>> > Attached is the fslhd info and a screen shot of the data.
>> >
>> > Would anyone be able to point me in the right direction on how I could get the data working properly?
>> >
>> > Thank you so much in advance.
>> >
>> > Kind regards,
>> > Conor
>> >
>> >
>> > <pid_sample.png>filename Pid_FUNC.nii.gz
>> >
>> > sizeof_hdr 348
>> > data_type FLOAT32
>> > dim0 4
>> > dim1 61
>> > dim2 73
>> > dim3 61
>> > dim4 250
>> > dim5 1
>> > dim6 1
>> > dim7 1
>> > vox_units Unknown
>> > time_units Unknown
>> > datatype 16
>> > nbyper 4
>> > bitpix 32
>> > pixdim0 0.000000
>> > pixdim1 3.000000
>> > pixdim2 3.000000
>> > pixdim3 3.000000
>> > pixdim4 1.000000
>> > pixdim5 1.000000
>> > pixdim6 1.000000
>> > pixdim7 1.000000
>> > vox_offset 352
>> > cal_max 0.0000
>> > cal_min 0.0000
>> > scl_slope 1.000000
>> > scl_inter 0.000000
>> > phase_dim 0
>> > freq_dim 0
>> > slice_dim 0
>> > slice_name Unknown
>> > slice_code 0
>> > slice_start 0
>> > slice_end 0
>> > slice_duration 0.000000
>> > time_offset 0.000000
>> > intent Unknown
>> > intent_code 0
>> > intent_name
>> > intent_p1 0.000000
>> > intent_p2 0.000000
>> > intent_p3 0.000000
>> > qform_name Unknown
>> > qform_code 0
>> > qto_xyz:1 3.000000 0.000000 0.000000 0.000000
>> > qto_xyz:2 0.000000 3.000000 0.000000 0.000000
>> > qto_xyz:3 0.000000 0.000000 3.000000 0.000000
>> > qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>> > qform_xorient Left-to-Right
>> > qform_yorient Posterior-to-Anterior
>> > qform_zorient Inferior-to-Superior
>> > sform_name Aligned Anat
>> > sform_code 2
>> > sto_xyz:1 -3.000000 -0.000000 0.000000 90.000000
>> > sto_xyz:2 -0.000000 3.000000 -0.000000 -126.000000
>> > sto_xyz:3 0.000000 0.000000 3.000000 -72.000000
>> > sto_xyz:4 0.000000 0.000000 0.000000 1.000000
>> > sform_xorient Right-to-Left
>> > sform_yorient Posterior-to-Anterior
>> > sform_zorient Inferior-to-Superior
>> > file_type NIFTI-1+
>> > file_code 1
>> > descrip
>> > aux_file
>> >
>> <report_log.html><report_log.txt><feat1>
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