We are using version 3.1.0, so this should work. You could try version 3.0, but either should work.
Duncan
On 8 Sep 2014, at 13:38, Paul Beach <[log in to unmask]> wrote:
> Hi Stephen,
>
> Sorry to pester, but do you think a different version/distribution would work?
>
>
> On Thu, Sep 4, 2014 at 4:52 PM, Paul Beach <[log in to unmask]> wrote:
> Do you think I should acquire a different version/distribution?
>
>
> On Thu, Sep 4, 2014 at 6:25 AM, Paul Beach <[log in to unmask]> wrote:
> Hmm.
>
> This was being ran using R v3.1.0, spring dance.
>
>
> On Thu, Sep 4, 2014 at 3:08 AM, Stephen Smith <[log in to unmask]> wrote:
> Hi - well, at our end the 1.061 FIX update fixed this problem that appeared with the latest version of R.
> Exactly which version/distribution of R are you using?
> Cheers.
>
>
> On 3 Sep 2014, at 21:38, Paul Beach <[log in to unmask]> wrote:
>
>> Stephen,
>>
>> Any word on whether this is likely a problem on my end?
>>
>> Cheers
>>
>>
>> On Wed, Sep 3, 2014 at 8:38 AM, Paul Beach <[log in to unmask]> wrote:
>> Yes. This is supposed to be FIX v1.061 I'm using. This is confirmed in the settings.sh file:
>> # Settings file for FIX
>> # Modify these settings based on your system setup
>> FIXVERSION=1.06
>> # (actually this version is 1.061 - see wiki page for details)
>>
>>
>>
>>
>> On Wed, Sep 3, 2014 at 8:32 AM, Stephen Smith <[log in to unmask]> wrote:
>> OK - hopefully this is a known bug with the latest version of R - which should be fixed by the latest FIX update - do you have that?
>> See:
>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX
>> Cheers.
>>
>>
>>
>> On 3 Sep 2014, at 13:31, Paul Beach <[log in to unmask]> wrote:
>>
>>> Ah, sorry, I missed the hidden file after doing that command.
>>>
>>> I've attached the content of the file: fix_2b_predict.log
>>>
>>> The error at the bottom is below. Not sure what it means.
>>>
>>> Error in RET@get_where(newdata = newdata, mincriterion = mincriterion) :
>>> INTEGER() can only be applied to a 'integer', not a 'double'
>>> Calls: eval ... treeresponse -> .local -> <Anonymous> -> <Anonymous> -> .Call
>>> Execution halted
>>>
>>>
>>>
>>> On Wed, Sep 3, 2014 at 8:25 AM, Stephen Smith <[log in to unmask]> wrote:
>>> Hi - please see my previous email.....
>>>
>>>
>>> On 3 Sep 2014, at 13:24, Paul Beach <[log in to unmask]> wrote:
>>>
>>>> Stephen,
>>>>
>>>> No. There's no sign of the .txt file in the subject's .feat directory. Nore are there any log files in the .feat directory.
>>>>
>>>> I tried re-running the analysis using the octave setup. No dice. Same output and lack of the fix4melview_TRAIN_thr.txt
>>>>
>>>> Current residing files/sub-directories in .feat directory are:
>>>> absbrainthresh.txt design.ppm reg
>>>> confoundevs.txt design.trg report.html
>>>> design.con example_func.nii.gz report_log.html
>>>> design_cov.png filtered_func_data.ica report_poststats.html
>>>> design_cov.ppm filtered_func_data.nii.gz report_prestats.html
>>>> design.frf fix report_reg.html
>>>> design.fsf logs report_stats.html
>>>> design.mat mask.nii.gz report_unwarp.html
>>>> design.min mc stats
>>>> design.png mean_func.nii.gz
>>>>
>>>>
>>>>
>>>> On Wed, Sep 3, 2014 at 8:11 AM, Stephen Smith <[log in to unmask]> wrote:
>>>> Hi - yes there's no sign of any errors there. The output file should be in the FEAT folder, not inside the fix subfolder - anything there?
>>>> Do
>>>> ls -lart
>>>> to see if there's any other useful log files there, if not.
>>>> Cheers.
>>>>
>>>>
>>>>
>>>> On 2 Sep 2014, at 19:06, Paul Beach <[log in to unmask]> wrote:
>>>>
>>>>> FSL experts,
>>>>>
>>>>> I ran FIX classification using the Standard.RData and a single subject's .feat directory (which has all the requisite files/directories in it as I ran all pre-processing through FEAT GUI). I selected the matlab compilation as my means of running FIX. There are no error logs and it looks like everything ran "properly," so to speak.
>>>>>
>>>>> However, I'm not seeing the classification output I'm expecting, i.e. the fix4melview_TRAIN_thr.txt file.
>>>>>
>>>>> My command and terminal output:
>>>>> [beachpau@gauss SUBJECTS]$ fix -c HS_001/RestState_1_FSL_LAS.feat /home/beachpau/.local/opt/fix1.061/training_files/Standard.RData 20
>>>>> FIX Classifying components in Melodic directory: HS_001/RestState_1_FSL_LAS.feat using training file: /home/beachpau/.local/opt/fix1.061/training_files/Standard.RData and threshold 20
>>>>> FIX features not already generated, so creating them now.
>>>>> FIX Feature extraction for Melodic output directory: HS_001/RestState_1_FSL_LAS.feat
>>>>> create edge masks
>>>>> run FAST
>>>>> registration of standard space masks
>>>>> extract features
>>>>>
>>>>> [beachpau@gauss SUBJECTS]$
>>>>>
>>>>> Looking in the resultant fix directory within the subject's .feat directory I seen the following output files:
>>>>> edge1.nii.gz features.mat std1mm2exfunc0.nii.gz
>>>>> edge2.nii.gz highres2std.mat std1mm2exfunc1dil2.nii.gz
>>>>> edge3.nii.gz hr2exf.nii.gz std1mm2exfunc1dil.nii.gz
>>>>> edge4.nii.gz hr2exfTMP.nii.gz std1mm2exfunc1.nii.gz
>>>>> edge5.nii.gz hr2exfTMP.txt std1mm2exfunc2dil2.nii.gz
>>>>> fastsg_mixeltype.nii.gz logMatlab.txt std1mm2exfunc2dil.nii.gz
>>>>> fastsg_pve_0.nii.gz maske1.nii.gz std1mm2exfunc2.nii.gz
>>>>> fastsg_pve_1.nii.gz maske2.nii.gz std1mm2exfunc3dil2.nii.gz
>>>>> fastsg_pve_2.nii.gz maske3.nii.gz std1mm2exfunc3dil.nii.gz
>>>>> fastsg_pveseg.nii.gz maske4.nii.gz std1mm2exfunc3.nii.gz
>>>>> fastsg_seg.nii.gz maske5.nii.gz std2exfunc.mat
>>>>> features.csv std1mm2exfunc0dil2.nii.gz std2highres.mat
>>>>> features_info.csv std1mm2exfunc0dil.nii.gz
>>>>>
>>>>> The only thing I could find with any kind of error was within the logMatlab.txt file. However, I'm not really sure why these errors would matter as I should be using the compiler setup for FIX.
>>>>>
>>>>> The error on the logMatlab.txt file is as follows:
>>>>> { Warning: Name is nonexistent or not a directory: /usr/local/fsl/etc/matlab.}
>>>>> { > In path at 110
>>>>> In startup at 1}
>>>>> { Warning: Name is nonexistent or not a directory: /usr/local/fmrib/fmt.}
>>>>> { > In path at 110
>>>>> In startup at 2}
>>>>>
>>>>> I've attached the full output file in case it helps.
>>>>>
>>>>>
>>>>> Thanks!
>>>>> --
>>>>> Paul Beach
>>>>> DO/PhD candidate - Year VI
>>>>> Michigan State University
>>>>> - College of Osteopathic Medicine
>>>>> - Neuroscience Program
>>>>> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
>>>>> <logMatlab.txt>
>>>>
>>>>
>>>> ---------------------------------------------------------------------------
>>>> Stephen M. Smith, Professor of Biomedical Engineering
>>>> Associate Director, Oxford University FMRIB Centre
>>>>
>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>> +44 (0) 1865 222726 (fax 222717)
>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>> ---------------------------------------------------------------------------
>>>>
>>>> Stop the cultural destruction of Tibet
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Paul Beach
>>>> DO/PhD candidate - Year VI
>>>> Michigan State University
>>>> - College of Osteopathic Medicine
>>>> - Neuroscience Program
>>>> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>> ---------------------------------------------------------------------------
>>>
>>> Stop the cultural destruction of Tibet
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Paul Beach
>>> DO/PhD candidate - Year VI
>>> Michigan State University
>>> - College of Osteopathic Medicine
>>> - Neuroscience Program
>>> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
>>> <fix_2b_predict.log>
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>>
>> Stop the cultural destruction of Tibet
>>
>>
>>
>>
>>
>>
>>
>> --
>> Paul Beach
>> DO/PhD candidate - Year VI
>> Michigan State University
>> - College of Osteopathic Medicine
>> - Neuroscience Program
>> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
>>
>>
>>
>> --
>> Paul Beach
>> DO/PhD candidate - Year VI
>> Michigan State University
>> - College of Osteopathic Medicine
>> - Neuroscience Program
>> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
>
>
>
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
>
>
>
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
>
>
>
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
--
Duncan Mortimer
Computing Officer, FMRIB Centre, University of Oxford
John Radcliffe Hospital, Oxford, UK
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