help > GZIP/GUNZIP Issues.
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Oct 6, 2015  05:10 PM | Jamie Hanson
GZIP/GUNZIP Issues.

Hello GTG community,



I was just getting back into resting state analyses after a short break and was running into some issues with GTG, when attempting to preprocess some data. After attempting to motion censor my data (just to make sure I was specifying inputs, etc. correctly), I ran into an error. After I run into the error, the functional file then looks to be corrupted. I tried this in two subjects (one of which I checked the file integrity on before running GTG) and had the same issue. I'm using a newer version of Matlab (R2015a), so I am not sure if that is related to things. This is the error output... 



>> GTG

Error using gunzipwgunzipwrite (line 227)

Unexpected end of input stream when attempting to GUNZIP the file

"/Users/jamielarshanson/Desktop/GTG_TEST/20110316_12445/20110316_12445_run004_02_SWAP_mcf_MNI.nii".



Error in gunzipEgunzipEntries (line 147)

names{k} = gunzipwrite(entries(k).file, outputDir, baseName, streamCopier);

Error in gunzip (line 89)

names = gunzipEntries(entries, outputDir);

Error in load_nii_gz (line 66)

gunzip(filename);

Error in GTG_preprocess_GUI>preprocess_for_graph (line 1823)

func_data = load_nii_gz(func_filename);

Error in GTG_preprocess_GUI>Start_pushbutton_Callback (line 1385)

[out.ts{currsub,1},out.num_censored_vols(currsub,1),out.num_censored_vols_FD(currsub,1),out.num_censored_vols_DVARS(currsub,1),out.GCOR(currsub,1),out.mean_FD(currsub,1),out.mean_DVARS(currsub,1)]

=

preprocess_for_graph(out,sub,logfile_fid,img_ext,func_filename,parc_filename,funcmask_filename,WM_filename,vent_filename,parc_warp_filename,WM_warp_filename,vent_warp_filename,par_filename);

Error in gui_mainfcn (line 95)

feval(varargin{:});

Error in GTG_preprocess_GUI (line 134)

gui_mainfcn(gui_State, varargin{:});

Error in @(hObject,eventdata)GTG_preprocess_GUI('Start_pushbutton_Callback',hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback



====



Again, I was just trying to specify some basic parameters. For this test, I was just using functional data already in 2mm MNI space (with MNI masks as my Functional Brain Mask and ROI Mask. I attached my log file, but it didn't have much information. 

Thoughts? 

Any suggestions are greatly appreciated!

Thanks much,

Jamie.

Oct 6, 2015  06:10 PM | Jamie Hanson
RE: GZIP/GUNZIP Issues.
Apologies for omitted that info... Mac os (10.10.5, 14F27)
Oct 6, 2015  06:10 PM | Jeffrey Spielberg
RE: GZIP/GUNZIP Issues.
Thanks for posting, Jamie.  The issue may be with matlab's implementation of gunzip/gzip, which uses JAVA and has been known to cause problems.  Since you are using OXS, let's try the native gunzip/gzip instead.  Try using the attached file (replace the old version in GTG/dependencies/handle_nifti)....
Attachment: load_nii_gz.m