Hello,

I am an FSL and Windows user. I would like to make a mask (that I can use in FSL) of the medial temporal lobes (comprising the hippocampus, perirhinal, entorhinal and parahippocampal cortices) and was hoping that I could use pickatlas to do this.

I downloaded SPM8 for this purpose, and then downloaded WFU_PickAtlas_3.0.4 and extracted it (using Express Zip File Compression Software) within the SPM8 toolbox folder.

This produced the folder structure C:\Users\kat\Documents\MATLAB\spm8\spm8\toolbox\WFU_PickAtlas_3\WFU_PickAtlas_3.0.4\...
so I cut the wfu_pickatlas, wfu_results and wfu_tbx_common subfolders from within this folder and pasted them directly into
C:\Users\kat\Documents\MATLAB\spm8\spm8\toolbox, so that I would have the three folders:

C:\Users\kat\Documents\MATLAB\spm8\spm8\toolbox\wfu_pickatlas
C:\Users\kat\Documents\MATLAB\spm8\spm8\toolbox\wfu_results
C:\Users\kat\Documents\MATLAB\spm8\spm8\toolbox\wfu_tbx_common

(as well as retaining the C:\Users\kat\Documents\MATLAB\spm8\spm8\toolbox\WFU_PickAtlas_3\WFU_PickAtlas_3.0.4\ folder, containing the manuals etc).

I opened matlab and typed in the command window:
addpath('C:\Users\kat\Documents\MATLAB\spm8\spm8\toolbox\wfu_pickatlas')

and then :
wfu_pickatlas;

but got the error message:

Error using fileparts
Too many output arguments.

Error in wfu_require_spm_lite (line 59)
[tbxCommonPath f e j] = fileparts(mfilename('fullpath'));
Error in wfu_pickatlas (line 21)
wfu_require_spm_lite({'SPM5','SPM8'});

I would be very grateful if someone could let me know what I am doing wrong. One possibility is that my screen resolution max is 1280x800 (I know that this means that I won't be able to see all the buttons when the GUI does open, but I'm not sure if this can be the reason that the GUI isn't opening at all), and another is that my extraction software caused a problem (The user manual says that 'If you are using WINZIP to extract the tar file version of the distribution, you must turn off the "Tar file smart CR/LF conversion
option" (found under Options, Configuration, Miscellaneous, Other). If this option is not turned off, the wfu_pickatlas.fig will be corrupted and the program will not start.', but the programme I used was not called Winzip and I couldn't find an equivalent option to turn off. It looks to me like the error message might be related to SPM, but as I've never used SPM before, I'm not sure how to go about solving the problem. I would be very grateful for any advice.

Many thanks,
Kathryn

Hello Kathryn,
  That one skipped pass.  Please fine attached a corrected version of wfu_require_spm_lite.m.  Please download it and place in the wfu_tbx_common directory.  Please let me know if you still have problems.

Ben

Thank you so much, Ben. This has fixed the problem.
Best wishes,
Kathryn