Have anyone checked the content in rest_spm_slice_vol?

Submitted by leemon on

YAN Chao-Gan

Mon, 03/31/2014 - 15:20

Hi Meng,

Sorry for the delay.

Have you checked your files "/databank/Ketamine/Ramona_preprocRest/FunImgARWSF/zr76_3_Messung"? How big is it?

In the next version, it will turn to call SPM functions directly, the 4D file reading speed will be enhanced.

Best,

Chao-Gan

Thanks for your reply, Chao-Gan.
I have checked the size, it's around 2.2 GB. It's not too small, but too big:-) Our server is quite powerful to handle the data with this  size. 

Another suggestion, the template images created by DARTEL will be saved in the same folder of first subject in current version of DPARSFA. Maybe it's better to created a new sub-folder for the template and related files.  

All the best
Meng


On Mon, Mar 31, 2014 at 5:20 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Meng,

Sorry for the delay.

Have you checked your files "/databank/Ketamine/Ramona_preprocRest/FunImgARWSF/zr76_3_Messung"? How big is it?

In the next version, it will turn to call SPM functions directly, the 4D file reading speed will be enhanced.

Best,

Chao-Gan


Online version of this post: http://rfmri.org/comment/3050#comment-3050


Hi Meng,

Yes, it's too big. We do have figured it out in a close test version. We hope to release it soon -- there are several pieces haven't finish yet. Very sorry for the delay.

Thanks for your suggestion, it's just following the DARTEL behavior in SPM. We may change it according to your suggestion in a future release. But as for now, just focus on the several pieces and release one first. :)

Best,

Chao-Gan

Hi everyone, When I regressed out covariates in DPARSFA (version 2.3), I encounter the following errors: Resample Masks (/databank/Ketamine/DPARSF_V2.3_130615/Templates/BrainMask_05_91x109x91.img) to the resolution of functional images. Resample Masks (/databank/Ketamine/DPARSF_V2.3_130615/Templates/CsfMask_07_91x109x91.img) to the resolution of functional images. Resample Masks (/databank/Ketamine/DPARSF_V2.3_130615/Templates/WhiteMask_09_91x109x91.img) to the resolution of functional images. Resample Masks (/databank/Ketamine/DPARSF_V2.3_130615/Templates/GreyMask_02_91x109x91.img) to the resolution of functional images. Extracting ROI signals... Read 3D EPI functional images: "/databank/Ketamine/Ramona_preprocRest/FunImgARWSF/zr76_3_Messung".??? Error using ==> rest_spm_slice_vol File too small. Error in ==> rest_spm_read_vols at 34 Y(:,:,p,i) = rest_spm_slice_vol(V(i),rest_spm_matrix([0 0 p]),V(i).dim(1:2),0); Error in ==> rest_ReadNiftiImage at 110 Data = rest_spm_read_vols(V); Error in ==> rest_readfile at 71 [Outdata,Header]= rest_ReadNiftiImage(hname,volumeIndex); Error in ==> rest_to4d at 103 [theOneNiiFileTimePoint, VoxelSize, Header] = rest_readfile(theFilename, 'all'); Error in ==> y_ExtractROISignal at 56 [AllVolume,VoxelSize,theImgFileList, Header] =rest_to4d(AllVolume); Error in ==> DPARSFA_run>(parfor body) at 2910 y_ExtractROISignal([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName,filesep,AutoDataProcessParameter.SubjectI Error in ==> parallel_function at 473 F(base, limit); Error in ==> DPARSFA_run at 2780 parfor i=1:AutoDataProcessParameter.SubjectNum Error in ==> DPARSFA>pushbuttonRun_Callback at 1601 [Error]=DPARSFA_run(handles.Cfg); Error in ==> gui_mainfcn at 96 feval(varargin{:}); Error in ==> DPARSFA at 33 gui_mainfcn(gui_State, varargin{:}); ??? Error while evaluating uicontrol Callback I traced the sources and repeated the error, which was caused by rest_spm_read_vols. >> for i=1:n, for p=1:V(1).dim(3) Y(:,:,p,i) = rest_spm_slice_vol(V(i),rest_spm_matrix([0 0 p]),V(i).dim(1:2),0); end, end ??? Error using ==> rest_spm_slice_vol File too small. I checked the content of this matlab function and found it's quite strange in my computer. So any ideas on this? The content of spm_read_vols is the same as rest_spm_read_vols, which is listed as followings. function varargout = spm_slice_vol(varargin) % returns a slice through a memory mapped image - a compiled routine % FORMAT X = spm_slice_vol(V,A,dim,hold); % V - is a memory mapped image volume % A - is a 4 x 4 transformation matrix % dim - [i j] defines the two dimensions of the output image. The % coordinates in 3-D space of the voxels in this image are assumed % to range from 1,1,0 to i,j,0. % hold - sets the interpolation method for the resampling. % 0 Zero-order hold (nearest neighbour). % 1 First-order hold (trilinear interpolation). % 2->127 Higher order Lagrange (polynomial) interpolation using % different holds (second-order upwards). % -127 - -1 Different orders of sinc interpolation. % X - output image %_______________________________________________________________________ % % spm_slice_vol returns a section through a memory mapped image volume % on disk. This section is the transverse slice at z = 0 after linear % transformation according to matrix A % % see also spm_sample_vol.m % %_______________________________________________________________________ % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging % John Ashburner % $Id: spm_slice_vol.m 1143 2008-02-07 19:33:33Z spm $ %-This is merely the help file for the compiled routine error('spm_slice_vol.c not compiled - see Makefile') All the best Meng