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
---------------------------------------------------------------------------
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