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
