dparsfa将dicom转nifti的问题

Submitted by cbreal on Tue, 12/03/2013 - 12:09

        REST版本号V1.8_130615 DPARSFA版本号V2.3_130615 spm版本为spm8 matlab为linux下2010a(我测试的操作系统分别为redhat el5.7和redhat el6.2 测试用户分别为root和普通用户,普通用户有rest和dparsf文件夹下的777权限) 我执行dicom文件转nifti时遇到下面的情况FunRaw转FunImg时,FunImg文件夹会产生,但是nifti格式文件不会产生,程序会一直等待,直到我ctrl+c终止。如果用后面的脚本可以解决这一问题

      这个问题我用fedora 14和opensuse 11.4测试过,同样版本的spm,matlab,REST和DPARSFA是可以转换的。但是我在虚拟机内安装的redhat el5.7就转换失败。请问是什么原因造成的?有没有可能是操作系统的内核问题?

      不知道我上面的问题是否描述清楚了,如果您还需要其他信息的话我再进行补充?

 

我看了y_Call_dcm2nii.m文件

OldDirTemp=pwd;

cd([ProgramPath,filesep,'dcm2nii']);

if ispc

    if strcmpi(Option,'DefaultINI')

        Option='-b dcm2nii.ini';

    end

    eval(['!dcm2nii.exe ',Option,' -o ',OutputDir,' ',InputFilename]);

elseif ismac

    if strcmpi(Option,'DefaultINI')

        Option='-b ./dcm2nii_linux.ini';

    end

    eval(['!./dcm2nii_mac ',Option,' -o ',OutputDir,' ',InputFilename]);

else

    if strcmpi(Option,'DefaultINI')

        Option='-b ./dcm2nii_linux.ini';

    end

    eval(['!chmod +x dcm2nii_linux']);

    eval(['!./dcm2nii_linux ',Option,' -o ',OutputDir,' ',InputFilename]);

end

cd(OldDirTemp);

应该执行的是最后的一个else语句

 

 

用脚本可以转换文件格式 

#!/bin/bash

rootdir="/home/***/frequency_ybk/analysis";

data_type="FunRaw";

for condition in {"EO","EC"};do

        subname=048

        if [ $data_type = "T1Raw" ];then

          data_type_dst="T1Imgtmp";

        elif [ $data_type = "FunRaw" ];then

          data_type_dst="FunImgtmp";

        elif [ $data_type = "3DT1Raw" ];then

          data_type_dst="3DT1Imgtmp";

        fi

        echo $data_type

        outrootdir="${rootdir}/${condition}/${data_type_dst}";

        mkdir $outrootdir;

        outdir="${outrootdir}/sub${subname}";

        mkdir $outdir

        datadir="${rootdir}/${condition}/${data_type}/sub${subname}";

        cd $datadir;

        fn="${datadir}/*.1"

        cd /***/DPARSF_V2.2_130309/dcm2nii;

        dcm2nii -b dcm2nii.ini -o ${outdir} ${fn};

    done

 

YAN Chao-Gan

Tue, 12/03/2013 - 15:29

Hi,

I guess your problem is caused by the general purpose mouse (gpm) service in linux. The gpm service provides mouse support in Linux virtual consoles. It is not very useful and can be shut down without any side effects. Then "calling other commands from MATLAB" will no longer choke the processing (since MATLAB will no longer wait for the mouse input by gpm).
 
Please simply input "/etc/rc.d/init.d/gpm stop" in terminal will stop gpm, or "rpm -e gpm" will remove it. However, only superuser can do that. 
 
Hope this helps.
 
Best,
 
Chao-Gan

Stephanie

Tue, 12/03/2013 - 15:40

Hi

I have been using DPARSF A for a while now. For some reason I am now getting the error message "too many nii.gz files in each subjects directory, should only keep one 4D .nii.gz files"

However I do not use 4D files, onle nii files. What could be the problem? Can anyone help?

Many thanks,

Stephanie

Hi Stephanie,
In your case, I think there may be something wrong with the Starting Directory. Could you post a snapshot of your parameter setting here?

Best,

Chao-Gan


On Tue, Dec 3, 2013 at 10:40 AM, 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 Stephanie Kullmann (Stephanie)

Hi

I have been using DPARSF A for a while now. For some reason I am now getting the error message "too many nii.gz files in each subjects directory, should only keep one 4D .nii.gz files"

However I do not use 4D files, onle nii files. What could be the problem? Can anyone help?

Many thanks,

Stephanie


Online version of this post: http://www.rfmri.org/comment/2980#comment-2980