In that case I recommend learning a bit more about ICA and perhaps the command line, as you do need to understand what it means to set the ICA dimensionality (how many components are you asking for) to use ICA and many of the most powerful neuroimaging tools are command line-based.
Peace, Matt. From: stargazy pie <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Monday, May 29, 2017 at 8:56 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: 回复： 回复：答复: 答复: 答复: [HCP-Users] GIFTI surface data Hi, I don't know how to set ICA dimensionality with -d flag, so I just added --CIFTI after input file name. ./melodic -i /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii --CIFTI -o /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstica.ica Could not open file /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstica.ica/eigenvalues_percent for writing terminate called after throwing an instance of 'cifti::CiftiException' what(): error opening file '/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstica.ica/melodic_IC.nii' Aborted (core dumped) By the way, the data's dimenstion is 91282(grayordinate)*420(time point) after I converted it to GIFTI, how long does it take to run ICA? how do I set the -d flag? In my opinion, after ICA, the result will be something like A(smaller than 91282)*420, right? Thanks. ------------------ 原始邮件 ------------------ 发件人: "Glasser, Matthew";<glass...@wustl.edu<mailto:glass...@wustl.edu>>; 发送时间: 2017年5月29日(星期一) 晚上10:37 收件人: "stargazy pie"<1257735...@qq.com<mailto:1257735...@qq.com>>; "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>; 主题: Re: 回复：答复: 答复: 答复: [HCP-Users] GIFTI surface data You will need to set the --CIFTI flag and specify an ICA dimensionality with the -d flag. Peace, Matt. From: stargazy pie <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Monday, May 29, 2017 at 9:04 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: 回复：答复: 答复: 答复: [HCP-Users] GIFTI surface data Hi, I use the latest version, v5.0.10 Thanks. ---原始邮件--- 发件人: "Glasser, Matthew"<glass...@wustl.edu<mailto:glass...@wustl.edu>> 发送时间: 2017年5月29日 10:11:33 收件人: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>;"wtj"<1257735...@qq.com<mailto:1257735...@qq.com>>; 主题: Re: 答复: 答复: 答复: [HCP-Users] GIFTI surface data What version of FSL are you using? Peace, Matt. From: wtj <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Sunday, May 28, 2017 at 1:34 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: 答复: 答复: 答复: [HCP-Users] GIFTI surface data Hi, I add the –o option, but there are more errors now. ./melodic -i /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii -o /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstica.ica ** ERROR: nifti_convert_nhdr2nim: bad datatype ** ERROR (nifti_image_read): cannot create nifti image from header '/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii' ** ERROR: nifti_image_open(/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries): bad header info ERROR: failed to open file /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries Image Exception : #22 :: ERROR: Could not open image /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries An exception has been thrown ERROR: Could not open image /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseriesTrace: read_volumeROI. Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年5月27日 22:56 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> 主题: Re: 答复: 答复: [HCP-Users] GIFTI surface data Perhaps you should specify a specific output directory with -o. Peace, Matt. From: wtj <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Friday, May 26, 2017 at 11:51 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: 答复: 答复: [HCP-Users] GIFTI surface data Hi, I use melodic commandline of latest version FSL and my command line scrpt is: melodic –i /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii An exception has been thrown Cannot create directory /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.ica++++++++++++++++++++ What’s the problem? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年5月25日 8:27 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> 主题: Re: 答复: [HCP-Users] GIFTI surface data You might need to use the command line version of the latest FSL. The latest version of melodic does natively work with CIFTI. Peace, Matt. From: wtj <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Wednesday, May 24, 2017 at 7:21 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: 答复: [HCP-Users] GIFTI surface data Hi, When I do ICA using MELODIC ICA button in FSL,I selected a .dtseries.nii file, then something went wrong. child process exited abnormally child process exited abnormally while executing "exec sh -c "${FSLDIR}/bin/fslnvols $thefile 2> /dev/null" " (procedure "feat5:updateimageinfo" line 9) invoked from within "feat5:updateimageinfo $w $i 1" (procedure "feat5:multiple_check" line 63) invoked from within "feat5:multiple_check .r 0 1 1 d" invoked from within ".dialog1.cancel invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .dialog1.cancel" (command bound to event) Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年5月24日 9:54 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> 主题: Re: [HCP-Users] GIFTI surface data No you would use the CIFTI file. It would be called ${StudyFolder}/${Subject]/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas.dtseries.nii. You would ideally run it through ICA+FIX first before analyzing it. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of wtj <1257735...@qq.com<mailto:1257735...@qq.com>> Date: Tuesday, May 23, 2017 at 8:49 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] GIFTI surface data Hi, I use the lifespan rfMRI data. After preprocessing, there is a file in /subject/MNINonLinear/Results/rfMRI_REST1_LR named rfMRI_REST1_LR.L.native.func.gii with size, for example, 130576*420. Is this file the cortical BOLD signal time series data? Can I use it to do rfMRI analysis? Thanks. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
