I believe that was part of the process, however in order to get a standard set of grayordinates across subjects, many subjects' segmentations were combined to make an atlas parcellation. The minimal preprocessing pipelines paper has some related information, but I'm not sure it covers how the atlas parcel definitions was generated:
http://www.ncbi.nlm.nih.gov/pubmed/23668970 Tim On Tue, Sep 1, 2015 at 7:31 PM, Nomi, Jason <jxn...@miami.edu> wrote: > 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> 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> >> *Sent:* Tuesday, September 1, 2015 8:12 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 >> >> 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> 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> >>> *Sent:* Monday, August 31, 2015 9:12 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 >>> >>> 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> 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> >>>> *Sent:* Monday, August 31, 2015 6:45 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 >>>> >>>> -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> 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 >>>>> 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
