help > error opening image in pickatlas results gui
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Jan 13, 2016  10:01 AM | Elliot Brown
error opening image in pickatlas results gui
Hi, 

I am trying to open an FSL image in the WFU-pickatlas Results GUI window, but keep getting this error:

13-Jan-2016 11:04:17 | ERROR | wfu_results_viewer.m | MException thrown. Stack follows:
13-Jan-2016 11:04:17 | ERROR | wfu_results_import_screen | Line 0176: Function is not defined for 'matlab.ui.Figure' inputs.
13-Jan-2016 11:04:17 | ERROR | loadGeneric | Line 0076
13-Jan-2016 11:04:17 | ERROR | loadSelect | Line 0109
13-Jan-2016 11:04:17 | ERROR | File_Open_Callback | Line 0467
13-Jan-2016 11:04:17 | ERROR | gui_mainfcn | Line 0095
13-Jan-2016 11:04:17 | ERROR | wfu_results_viewer | Line 0070
13-Jan-2016 11:04:17 | ERROR | @(hObject,eventdata)wfu_results_viewer('File_Open_Callback',hObject,eventdata,guidata(hObject)) | Line 0000

It seems to happen regardless of the type of image I try to open, so guessing it is not a problem with my FSL image. I tried with the cope image, the t-stat image and the z-stat image, and all gave the same error. 

I also get this warning coming up every time I press on the "RESULTS" button to open the WFU-pickatlas Results GUI window:

Using SPM8_lite, adding (spm_lite) to path.
Warning: Name is nonexistent or not a directory: spm_lite
> In path (line 109)
In addpath (line 86)
In wfu_results_defaults (line 31)
In wfu_results_viewer>wfu_results_OpeningFcn (line 103)
In gui_mainfcn (line 220)
In wfu_results_viewer (line 70)
In wfu_pickatlas>paresults_Callback (line 3007)
In wfu_pickatlas (line 110)
In @(hObject,eventdata)wfu_pickatlas('paresults_Callback',hObject,eventdata,guidata(hObject))

I am running SPM12 and Pickatlas ver. 3.0.5 in matlab 2015a on a mac. 

Can anyone help?

Thanks, 

Elliot.
Jan 13, 2016  12:01 PM | Benjamin Wagner - UT Southwestern Medical Center
RE: error opening image in pickatlas results gui
Hi Elliot,
  You've got a couple things working against you.  The first is that PickAtlas has not been well tested on Mac.  There are occasional glitches with this.  The second is that you are using 2015a.  I believe that was the version of matlab where they implemented the new figure drawing system.  I've not tested on that platform.  So, if possible, drop back to 2014 or before.

  The SPM_LITE error make me wonder about your installation.  spm_lite should be under wfu_tbx_common.  First, are you using SPM?  Second, do you have three directories in you PA installation:  wfu_pickatlas, wfu_results, and wfu_tbx_common?

Hope this helps,
Ben
Jan 14, 2016  02:01 PM | Elliot Brown
RE: error opening image in pickatlas results gui
Hi Ben, 

Thanks for the reply. This was a great help. I managed to make some progress using a Windows machine and an older version of MATLAB (2010a), but got as far as loading the FEAT directory, but then got this error:

14-Jan-2016 14:51:16 | ERROR | wfu_results_viewer.m | MException thrown. Stack follows:
14-Jan-2016 14:51:16 | ERROR | spm_getSPM | Line 0214: Cannot read C:\Users\Elliot\Desktop\Thalamo\Thalamocort_grp_results_AOO\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\SPM.mat
14-Jan-2016 14:51:16 | ERROR | wfu_results_compute | Line 0209
14-Jan-2016 14:51:16 | ERROR | File_Open_Callback | Line 0468
14-Jan-2016 14:51:16 | ERROR | gui_mainfcn | Line 0096
14-Jan-2016 14:51:16 | ERROR | wfu_results_viewer | Line 0070
14-Jan-2016 14:51:16 | ERROR | @(hObject,eventdata)wfu_results_viewer('File_Open_Callback',hObject,eventdata,guidata(hObject)) | Line 0000

Do you have any idea where this error is coming from?

There is no SPM.mat file in my FEAT directory.  

There is a progress bar ("Create xSPM structure") that is also on screen when this error comes up, but the bar only reaches halfway.

Thanks, 

Elliot.
Jan 15, 2016  06:01 AM | Benjamin Wagner - UT Southwestern Medical Center
RE: error opening image in pickatlas results gui
Hi Elliot,
  Could you please do the following and send me the output.  In the command window before opening the results viewer, type these commands.  The last will open the viewer itself.

global WFU_LOG
WFU_LOG=wfu_LOG;
WFU_LOG.on
WFU_LOG.level('info')
wfu_results_viewer

Then try to open your FEAT again.  When the error happens, please send the results of the LOG output.

Thanks,
Ben
Jan 15, 2016  11:01 AM | Elliot Brown
RE: error opening image in pickatlas results gui
Hi Ben, 

Thanks a lot for the reply.

Here is the error message I am getting following your instructions:

>> wfu_results_viewer
15-Jan-2016 12:01:21 | INFO | wfu_results_viewer.m | Entered function $Revision: 1.25 $
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'Results_Slider_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'Brain_Slider_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'ROI_PopUpMenu_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'Contrast_PopUpMenu_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'Atlas_Group_3_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'Atlas_Group_2_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'Atlas_Group_1_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'Extent_Edit_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Cmd: 'Threshold_Edit_CreateFcn' called
15-Jan-2016 12:01:22 | INFO | wfu_results_viewer.m | Creating Main Display
15-Jan-2016 12:01:22 | INFO | wfu_results_defaults.m | Entered function $Revision: 1.12 $
Using SPM8_lite, adding (spm_lite) to path.
Warning: Name is nonexistent or not a directory: spm_lite.
> In path at 110
In addpath at 87
In wfu_results\private\wfu_results_defaults at 31
In wfu_results_viewer>wfu_results_OpeningFcn at 103
In gui_mainfcn at 221
In wfu_results_viewer at 70
15-Jan-2016 12:01:23 | INFO | wfu_require_tbxs.m | Entered function $Revision: 1.2 $
15-Jan-2016 12:01:23 | INFO | wfu_require_tbxs.m | adding C:\Users\Elliot\Documents\MATLAB\spm12\toolbox\wfu_results to path

15-Jan-2016 12:01:23 | INFO | wfu_results_defaults.m | Using Atlas selected in PickAtlas
15-Jan-2016 12:01:23 | INFO | wfu_results_defaults.m | Reading Preferences
15-Jan-2016 12:01:23 | INFO | wfu_results_defaults.m | Reorienting results flip setting to match pick_atlas
15-Jan-2016 12:01:23 | INFO | wfu_resultsProgress.m | setting defaults
15-Jan-2016 12:01:24 | INFO | loadAtlas.m | Entered function $Revision: 1.3 $
15-Jan-2016 12:01:24 | INFO | wfu_results_viewer.m | Cmd: 'WFU_Results_Window_ResizeFcn' called
15-Jan-2016 12:01:24 | INFO | wfu_results_viewer.m | Cmd: 'WFU_Results_Window_ResizeFcn' called
15-Jan-2016 12:01:24 | INFO | wfu_resultsProgress.m | Loading Atlas Images & Data
15-Jan-2016 12:01:25 | INFO | loadTemplate.m | Entered function $Revision: 1.3 $
15-Jan-2016 12:01:25 | INFO | wfu_resultsProgress.m | Setting Background Image
15-Jan-2016 12:01:25 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:01:25 | INFO | createSlices.m | Entered function $Revision: 1.2 $
15-Jan-2016 12:01:25 | INFO | voxelImageConversion.m | Entered function $Revision: 1.3 $
15-Jan-2016 12:01:25 | INFO | updateBrain.m | Entered function $Revision: 1.4 $
15-Jan-2016 12:01:26 | INFO | wfu_resultsProgress.m |
15-Jan-2016 12:01:26 | INFO | wfu_results_viewer.m | Entered Functioning Program
15-Jan-2016 12:01:33 | INFO | wfu_results_viewer.m | Cmd: 'File_Callback' called
15-Jan-2016 12:01:33 | INFO | wfu_results_viewer.m | Cmd: 'File_Open_Callback' called
15-Jan-2016 12:01:34 | INFO | loadSelect.m | Entered function $Revision: 1.7 $
15-Jan-2016 12:01:50 | INFO | resultsClearSetDataFields.m | Entered function $Revision: 1.2 $
15-Jan-2016 12:01:50 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:01:50 | INFO | wfu_uncompress_nifti.m | There are 1 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:01:50 | INFO | loadSelect.m | fslRank: 3
15-Jan-2016 12:01:51 | INFO | loadSelect.m | afniRank: 0
15-Jan-2016 12:01:51 | INFO | loadSelect.m | processType: fsl
15-Jan-2016 12:01:51 | INFO | loadFSL.m | Entered function $Revision: 1.6 $
15-Jan-2016 12:01:52 | INFO | loadFSL.m | Found design.con file in: C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat
15-Jan-2016 12:01:55 | INFO | loadFSL.m | Found controls (tstat1 image) as C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\stats\tstat1.nii.gz
15-Jan-2016 12:01:55 | INFO | loadFSL.m | Found patients (tstat2 image) as C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\stats\tstat2.nii.gz
15-Jan-2016 12:01:55 | INFO | loadFSL.m | Found C>P (tstat3 image) as C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\stats\tstat3.nii.gz
15-Jan-2016 12:01:55 | INFO | loadFSL.m | Found P>C (tstat4 image) as C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\stats\tstat4.nii.gz
15-Jan-2016 12:01:55 | INFO | loadFSL.m | Overlay used as controls (zstat1 image)
15-Jan-2016 12:01:55 | INFO | loadFSL.m | Found patients (zstat2 image) as C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\stats\zstat2.nii.gz
15-Jan-2016 12:01:55 | INFO | loadFSL.m | Found C>P (zstat3 image) as C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\stats\zstat3.nii.gz
15-Jan-2016 12:01:55 | INFO | loadFSL.m | Found P>C (zstat4 image) as C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\stats\zstat4.nii.gz
15-Jan-2016 12:01:55 | INFO | wfu_results_import_screen.m | Entered function $Revision: 1.7 $
15-Jan-2016 12:02:02 | INFO | wfu_resultsProgress.m | Getting handles
15-Jan-2016 12:02:02 | INFO | wfu_resultsProgress.m | Checking ERDF
15-Jan-2016 12:02:02 | INFO | wfu_resultsProgress.m | Checking Contrasts
15-Jan-2016 12:02:02 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | There are 2 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | There are 3 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | There are 4 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | There are 5 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | There are 6 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | There are 7 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:03 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:04 | INFO | wfu_uncompress_nifti.m | There are 8 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:04 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:04 | INFO | wfu_uncompress_nifti.m | There are 9 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:04 | INFO | wfu_resultsProgress.m | Checking FWHM
15-Jan-2016 12:02:04 | INFO | wfu_resultsProgress.m | Checking Mask
15-Jan-2016 12:02:04 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:04 | INFO | wfu_uncompress_nifti.m | There are 10 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:04 | INFO | wfu_resultsProgress.m | Checking Mask
15-Jan-2016 12:02:04 | INFO | wfu_resultsProgress.m | Checking FWHM against Mask
15-Jan-2016 12:02:04 | INFO | wfu_resultsProgress.m | Reading Mask
15-Jan-2016 12:02:04 | INFO | wfu_resultsProgress.m | Creating Stats structure
15-Jan-2016 12:02:04 | INFO | wfu_uncompress_nifti.m | Entered function $Revision: 1.5 $
15-Jan-2016 12:02:05 | INFO | wfu_uncompress_nifti.m | There are 11 file(s) registered with wfu_uncompress_nifti.
15-Jan-2016 12:02:05 | INFO | wfu_results_compute.m | Entered function $Revision: 1.9 $
15-Jan-2016 12:02:05 | INFO | wfu_resultsProgress.m | Initializing Calculations
15-Jan-2016 12:02:05 | INFO | wfu_resultsProgress.m | Preparing Mask
15-Jan-2016 12:02:06 | INFO | wfu_resultsProgress.m | Create xSPM structure
15-Jan-2016 12:02:06 | ERROR | wfu_results_compute.m | locations of spm_getSPM and wfu_spm_getSPM8 are not the same!!! (C:\Users\Elliot\Documents\MATLAB\spm12 != C:\Users\Elliot\Documents\MATLAB\spm12\toolbox\wfu_pickatlas)
15-Jan-2016 12:02:06 | ERROR | wfu_results_compute.m | locations of spm_getSPM and wfu_spm_getSPM8 are not the same!!! (C:\Users\Elliot\Documents\MATLAB\spm12 != C:\Users\Elliot\Documents\MATLAB\spm12\toolbox\wfu_pickatlas)
15-Jan-2016 12:02:06 | ERROR | wfu_results_viewer.m | MException thrown. Stack follows:
15-Jan-2016 12:02:06 | ERROR | spm_getSPM | Line 0214: Cannot read C:\Users\Elliot\Desktop\Thalamo\group_results\Thalamo_Frontal_Scan_Age_Sex_BLThal_Group.gfeat\cope1.feat\SPM.mat
15-Jan-2016 12:02:06 | ERROR | wfu_results_compute | Line 0209
15-Jan-2016 12:02:06 | ERROR | File_Open_Callback | Line 0468
15-Jan-2016 12:02:06 | ERROR | gui_mainfcn | Line 0096
15-Jan-2016 12:02:06 | ERROR | wfu_results_viewer | Line 0070
15-Jan-2016 12:02:06 | ERROR | @(hObject,eventdata)wfu_results_viewer('File_Open_Callback',hObject,eventdata,guidata(hObject)) | Line 0000
15-Jan-2016 12:02:06 | INFO | wfu_results_viewer.m | Cmd: 'WFU_Results_Window_ResizeFcn' called
15-Jan-2016 12:02:10 | ERROR | wfu_results_viewer.m | Error opening data...
Jan 19, 2016  06:01 AM | Benjamin Wagner - UT Southwestern Medical Center
RE: error opening image in pickatlas results gui
Hi Elliot,

Thanks for the details messages. These lines tell of the problem:

15-Jan-2016 12:02:06 | ERROR | wfu_results_compute.m | locations of spm_getSPM and wfu_spm_getSPM8 are not the same!!! (C:\Users\Elliot\Documents\MATLAB\spm12 != C:\Users\Elliot\Documents\MATLAB\spm12\toolbox\wfu_pickatlas)
15-Jan-2016 12:02:06 | ERROR | wfu_results_compute.m | locations of spm_getSPM and wfu_spm_getSPM8 are not the same!!! (C:\Users\Elliot\Documents\MATLAB\spm12 != C:\Users\Elliot\Documents\MATLAB\spm12\toolbox\wfu_pickatlas)

Your SPM12 installation is listed in a higher precedence than the PickAtlas. I would use the pathtool and move pickatlas and its directories to the top.

Please let me know if you continue to have problems,
Ben
Jan 19, 2016  12:01 PM | Elliot Brown
RE: error opening image in pickatlas results gui
Hi Ben, 

Problem solved! It's working fine now. 

Thanks a lot for all your help. Most appreciated. 

Elliot.