That was the problem - sorry about that. I have extracted the mean time series for the left amygdala now.
Thanks so much for the help! I have one final question: I assume that this ROI is from the freesurfer subcortical segmentation? ________________________________ From: Timothy Coalson <tsc...@mst.edu> Sent: Tuesday, September 1, 2015 9:20 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file Your second command is different than the one I posted - specifically, the -volume option to -cifti-create-dense-from-template has a bug in v1.1 and v1.1.1, which causes it to do the wrong thing even when it doesn't error, use -volume-all instead (which does not take a structure name). Tim On Tue, Sep 1, 2015 at 7:08 PM, Nomi, Jason <jxn...@miami.edu<mailto:jxn...@miami.edu>> wrote: When I do the third step, I now get the error: ERROR: roi column is empty The first command: wb_command -cifti-separate 30_min.dtseries.nii COLUMN -volume AMYGDALA_LEFT output_left_amygdala.nii.gz -roi roi_left_amygdala.nii.gz The second command: wb_command -cifti-create-dense-from-template 30_min.dtseries.nii roi_left_amygdala.dscalar.nii -volume AMYGDALA_LEFT roi_left_amygdala.nii.gz The third command: wb_command -cifti-stats 30_min.dtseries.nii -reduce MEAN -roi roi_left_amygdala.dscalar.nii Thanks for your patience on this Tim - ________________________________ From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Sent: Tuesday, September 1, 2015 8:12 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file That is a bug in -cifti-create-dense-from-template we hadn't caught, sorry. To work around it, you can remove the -crop option from the -cifti-separate command (warning, may use a lot of memory, you could take only the first frame with -cifti-merge before doing -cifti-separate, as for this method you don't need the data volume output), and then use the -volume-all option to -cifti-create-dense-from-template instead of the -volume option, like so: #get the roi in the full volume space wb_command -cifti-separate tfMRI_EMOTION_LR_Atlas.dtseries.nii COLUMN -volume AMYGDALA_LEFT output_left_amygdala.nii.gz -roi roi_left_amygdala.nii.gz #turn the ROI into cifti wb_command -cifti-create-dense-from-template tfMRI_EMOTION_LR_Atlas.dtseries.nii roi_left_amygdala.dscalar.nii -volume-all roi_left_amygdala.nii.gz #stats prints a number per column to standard output wb_command -cifti-stats tfMRI_EMOTION_LR_Atlas.dtseries.nii -reduce MEAN -roi roi_left_amygdala.dscalar.nii Tim On Tue, Sep 1, 2015 at 9:57 AM, Nomi, Jason <jxn...@miami.edu<mailto:jxn...@miami.edu>> wrote: Hi Tim, When doing the second step (turn the ROI into cifti), I get the following error: ERROR: input volume doesn't match volume space and dimensions in CIFTI The code I am using for the first step: wb_command -cifti-separate 30_min.dtseries.nii COLUMN -volume AMYGDALA_LEFT output_left_amygdala.nii.gz -roi roi_left_amygdala.nii.gz -crop The code I am using for the second step: wb_command -cifti-create-dense-from-template 30_min.dtseries.nii roi_left_amygdala.dscalar.nii -volume AMYGDALA_LEFT roi_left_amygdala.nii.gz -from-cropped Any advice on what is happening? Jason ________________________________ From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Sent: Monday, August 31, 2015 9:12 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file That file contains all the voxels of the structure, plus zero voxels out to the bounding box of the structure, so you probably also need the ROI volume to get it to do the right thing. I'm not all that familiar with fsl tools. The tfMRI_EMOTION_LR_Atlas.dtseries.nii file is the same as the input in the first step. The roi_left_amygdala.dscalar.nii file is written out by the second step, for use in the third step. Tim On Mon, Aug 31, 2015 at 7:07 PM, Nomi, Jason <jxn...@miami.edu<mailto:jxn...@miami.edu>> wrote: Thank you for the quick reply Tim! I was wondering if I could simplify things by applying the fsl command "fslmeants" to the output from the first step, on the "output_left_amygdala.nii.gz" file? That should get me the mean of all the voxels included in that file right? If that file contains only the voxels of the left amygdala, then I figure that would get me the averaged time series. If that is not possible, I am unclear where the file in the second step, "tfMRI_EMOTION_LR_Atlas.dtseries.nii roi_left_amygdala.dscalar.nii", comes from. Thanks for the help - Jason ________________________________ From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Sent: Monday, August 31, 2015 6:45 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file -cifti-separate can't do any averaging, that isn't its purpose. Instead, you can use -cifti-stats and the roi of the amygdala to do such an average: #what you already did, for the purpose of getting the ROI wb_command -cifti-separate tfMRI_EMOTION_LR_Atlas.dtseries.nii COLUMN -volume AMYGDALA_LEFT output_left_amygdala.nii.gz -roi roi_left_amygdala.nii.gz -crop #turn the ROI into cifti wb_command -cifti-create-dense-from-template tfMRI_EMOTION_LR_Atlas.dtseries.nii roi_left_amygdala.dscalar.nii -volume AMYGDALA_LEFT roi_left_amygdala.nii.gz -from-cropped #stats prints a number per column to standard output wb_command -cifti-stats tfMRI_EMOTION_LR_Atlas.dtseries.nii -reduce MEAN -roi roi_left_amygdala.dscalar.nii If you were using a surface structure, you should use -cifti-weighted-stats instead as the last step with -spatial-weights to account for differences in vertex area. Tim On Mon, Aug 31, 2015 at 1:33 PM, Nomi, Jason <jxn...@miami.edu<mailto:jxn...@miami.edu>> wrote: Dear Experts, I am trying to acquire the averaged volume time series for subcortical structures in text file form. >From this post >http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01184.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg01184.html&d=BQMFaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=ZJUDSwWP05vEvMBUQZ8FbQ&m=BmKcM4Yzl6xcnzSTeNcIEuHvRFAqTKTTeOiGiMbb7UQ&s=rMIzyQLLAXu4Qo1sXKKB9Rx2BEZhsmIRPFso5N-9d_0&e=> > , I assume that doing these commands : wb_command -cifti-separate tfMRI_EMOTION_LR_Atlas.dtseries.nii COLUMN -volume AMYGDALA_LEFT output_left_amygdala.nii.gz -roi roi_left_amygdala.nii.gz -crop gives me a nifti file with *all* the voxels from the left amygdala (output_left_amygdala.nii.gz). Is there a way to get the *averaged* time series for all left amygdala voxels into a nifti file using the -cifti-separate command? If so, I suppose that I could then use the -nifti-information command to extract the time series from that averaged nifti file into a text file. Or, is there another way that I should do this? Thanks in advance! Jason _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=BQMFaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=ZJUDSwWP05vEvMBUQZ8FbQ&m=BmKcM4Yzl6xcnzSTeNcIEuHvRFAqTKTTeOiGiMbb7UQ&s=eIqQcGiHAP8KDaMKQ5LBktP1HatoITSdGPtrXN1YFqs&e=> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
