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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]<mailto:[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]<mailto:[log in to unmask]>> on behalf of Mark Jenkinson <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Friday, 25 August 2017 10:27:39 PM
To: [log in to unmask]<mailto:[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]<mailto:[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>