Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file
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 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 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 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 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 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 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 __
Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file
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 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 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 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 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 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_E
Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file
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 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 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 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 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=eIqQcGiHAP8KDa
Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file
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 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 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
[HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file
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 , 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
[HCP-Users] auto-correlations
Dear Experts, I was just reading in the Smith et al. (2013) paper about correcting for autocorrelations (footnote 7) and was wondering if there were any type of corrections you would advise. I am aware that I should demean, and then normalize the individual time series before concatenating across sessions (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ - point 3), but I am wondering if there are any suggestions about mixture-model corrections or pre whitening. I am interested in creating a parcellated connectome using the surface based data based off of an ROI atlas and was wondering if concerns about autocorrelations would be a problem when exploring dynamic functional connections between the ROI time series. Thanks in advance! Jason ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Creating a parcellated connectome from a label file
I was able to extract the time series for each label from the .ptseries.nii file in the terminal window using the wb_command -nifti-information with the -print-matrix option and then I exported that to a single text file. Thanks Matt!! Jason From: Glasser, Matthew Sent: Sunday, April 26, 2015 11:57 PM To: Nomi, Jason; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating a parcellated connectome from a label file wb_command -cifti-parcellate is indeed the first step. The next step you could load the resulting .ptseries.nii file into matlab or use wb_command -nifti-information with the -print-matrix option to output the terminal window, which you could redirect to a text file. I don't know if this is in the released version yet, but the development version has the ability to use wb_command -cifti-convert to convert the file -to-text. Peace, Matt. From: , Jason mailto:jxn...@miami.edu>> Date: Sunday, April 26, 2015 at 3:53 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Creating a parcellated connectome from a label file Dear Experts, I am trying to create a parcellated connectome from a label file based off of the Gordon et al., 2014 (Cerebral Cortex) paper. They have provided a dlabel.nii file consisting of 333 parcels in both the left (162 parcels) and right (172 parcels) hemispheres (http://www.nil.wustl.edu/labs/petersen/Resources.html). Eventually, I would like to acquire the time series for subcortical and cerebellar areas for a whole brain parcellated connectome, but this would be the first step. I would like to get a series of text files (or even better: a single text file with each parcel/ROI as a single column) for each subject based off of the label file provided by Gordon et al. I am not sure exactly what to do here. I have been reading through the posts on the forum and assume I might perhaps start with the -cifti-parcellate command: wb_command -cifti-parcellate COLUMN I assume (hope?) the output file contains the average time series for each parcel as defined from the gordon_LR.dlabel.nii file?? However, I am unsure how I would acquire the time series information in text file form from this output file. Am I even in the right ballpark here?? Any help would be appreciated as I have not worked with surface data yet. Thanks in advance! best, Jason ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Creating a parcellated connectome from a label file
Dear Experts, I am trying to create a parcellated connectome from a label file based off of the Gordon et al., 2014 (Cerebral Cortex) paper. They have provided a dlabel.nii file consisting of 333 parcels in both the left (162 parcels) and right (172 parcels) hemispheres (http://www.nil.wustl.edu/labs/petersen/Resources.html). Eventually, I would like to acquire the time series for subcortical and cerebellar areas for a whole brain parcellated connectome, but this would be the first step. I would like to get a series of text files (or even better: a single text file with each parcel/ROI as a single column) for each subject based off of the label file provided by Gordon et al. I am not sure exactly what to do here. I have been reading through the posts on the forum and assume I might perhaps start with the -cifti-parcellate command: wb_command -cifti-parcellate COLUMN I assume (hope?) the output file contains the average time series for each parcel as defined from the gordon_LR.dlabel.nii file?? However, I am unsure how I would acquire the time series information in text file form from this output file. Am I even in the right ballpark here?? Any help would be appreciated as I have not worked with surface data yet. Thanks in advance! best, Jason ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Parcellated Connectome
Thank you Steve! Yes - I was speaking about the group-ICA spatial maps. I have noticed that I can threshold the group-ICA spatial maps for each component at a much higher level than other ICAs that I have done on non-HCP data. Your explanation about strong CNR makes sense. I am still a little unclear about the relationship of instantiating a strong threshold on the group-ICA spatial maps relative to the time series. For example, if I threshold a component's spatial map at a lower level, more areas of activation will naturally show up. Does the time series represent all voxels in the spatial map when there is no thresholding? Or, does the time series represent only the strongest voxels of activation? Thus, when I apply a strong threshold for image presentation to "clean up" the image a little, does the time series also include those voxels that are not visible due to high thresholding? Thanks again! Jason From: Stephen Smith Sent: Saturday, April 11, 2015 3:29 AM To: Nomi, Jason Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Parcellated Connectome Hi - there are many factors that affect overall scaling - more below: On 10 Apr 2015, at 14:22, Nomi, Jason mailto:jxn...@miami.edu>> wrote: Dear Experts, I have noticed that the time-series for individual subjects from the dual regression output in the parcellated connectome (100 comp ICA) has a much larger range than I am used to seeing. The range for time series values are approximately -800 to 800 while dual regression outputs that I have conducted myself are usually around -5 to 5. I also notice that I can set the threshold much higher for the independent components when isolating activation compared to dual regression analyses that I have done myself. This "cleans up" the component representation substantially. My questions are: 1) Is there a particular reason for this large increase in ranges? In this case most likely because we set the max of the group maps used in dualreg stage 1 to be 1. This causes output timeseries to have larger scaling - but the overall scaling is arbitrary anyway. 2) Does the larger threshold for component activation have any influence on the time series that is being produced? Does the time series from the dual regression output only represent the areas from the independent component with the most intense activation? I would like to ensure that my presentation of component images using a much higher threshold is actually representative of the time series that I am analyzing. Do you mean the group-ICA spatial maps or maps output by diualreg stage 2? The group-ICA maps have high peaks (compared with the background scaling) for a couple of reasons: a) because there are so many subjects being combined that the ICA components are strong, and b) the group-PCA reduction has removed a lot of unstructured noise before the PCA+ICA step. But despite the maps having strong "CNR", they are still valid maps. Cheers, Steve. Thanks! Jason ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk> http://www.fmrib.ox.ac.uk/~steve --- Stop the cultural destruction of Tibet<http://smithinks.net> ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Dense Connectome Time Courses
Dear HCP Experts, I have a question regarding the text files found in the dense connectome release. Are the columns found in the text files for the node time courses ordered in the same way as the melodic_IC_sum.nii.gz file? That is, I assume that column 1 in the text file represents the time course for component 0 in the melodic file, column 2 = component 1, column 3 = component 2, etc, etc. Also, for the 4800 time points listed in the text file, how does the ordering of the resting state acquisition scans go? I know that there are four 15 minute resting state scans (1200 volumes each), 2 L-R and 2 R-L acquired. But, how are they ordered in the text file? Are the first 2400 volumes L-R and R-L? Or, are the first 2400 volumes both L-R, or both R-L? I would like to cut the file in half for an analysis (30 minute resting state scan) but want to ensure that I use a counterbalanced L-R and R-L acquisition parameter. Thank you for the help - Jason ? ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Using Connectome Workbench Commands
Hi Tim, You are absolutely right. I was missing the -repeat after the -var option for mean for my own command. The code works perfectly now. Thanks! Jason From: Timothy Coalson Sent: Tuesday, October 28, 2014 5:47 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Using Connectome Workbench Commands That is the error I would expect if you removed the -repeat after the -var option for mean (yes, it needs 2 -repeat options, they each associate with one -var option) - could you paste the command you actually ran? Tim On Tue, Oct 28, 2014 at 11:30 AM, Nomi, Jason mailto:jxn...@miami.edu>> wrote: Hi Tim, Thank you for the help with the workbench and the code. Yes, it is a mac osx. Sorry for the mix up. Also, I can get the first two commands to work for "MEAN" and "STDEV", but the last command gives me an error message: wb_command -volume-math '((x - mean) / stdev)' normalized.nii.gz -fixnan 0 -var x -var mean mean.nii.gz -repeat -var stdev stdev.nii.gz -repeat ERROR: volume file for variable 'mean' has 1 subvolume(s), but previous volume files have 1200 subvolume(s) requested to be used Any help would be appreciated. best, Jason Jason S. Nomi, Ph.D. Post-Doctoral Researcher (BCCL Lab) Department of Psychology University of Miami 5151 San Amaro Drive: Room 114A Website: http://www.psy.miami.edu/bccl/ Email: jxn...@miami.edu<mailto:jxn...@miami.edu> From: Timothy Coalson mailto:tsc...@mst.edu>> Sent: Monday, October 27, 2014 5:38 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Using Connectome Workbench Commands Inline replies. Tim On Mon, Oct 27, 2014 at 10:26 AM, Nomi, Jason mailto:jxn...@miami.edu>> wrote: Dear Experts, I am trying to use the workbench commands but cannot get them to work. After opening the “wb_command” file in my linux terminal, I get the message printed below. Linux terminal? The output shows that you successfully executed the Mac OS X binary, is there a linux system involved? However, none of the commands work and nothing comes up when I type in the command by itself to get help. I have tried all the various combinations. With the “-“, without it. With “wb_command” to start, without it, etc. Try entering this at the command line: /Applications/workbench/bin_macosx64/wb_command -volume-reduce If you want to use it without entering that path each time, you'll need to add "/Applications/workbench/bin_macosx64/" to your PATH environment variable. How to do this depends on what shell you are using. Also, I would like to conduct variance normalization on some of the .nii files from the ICA-Fix dataset. Would using the command, “-volume-reduce" with the VARIANCE operation accomplish this? No, among other things, variance is nonlinear with the spread of the data. If the files you are looking at end in .dtseries.nii, they are not volume files, but rather CIFTI files (there are other 2-part extensions that signify CIFTI files, but ICA-FIX should be using dtseries). This thread contains the steps for normalizing (including demeaning) along timeseries while in CIFTI format: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00444.html Similar commands apply if you are actually dealing with volume file timeseries: wb_command -volume-reduce MEAN mean.nii.gz wb_command -volume-reduce STDEV stdev.nii.gz wb_command -volume-math '(x - mean) / stdev' normalized.nii.gz -fixnan 0 -var x -var mean mean.nii.gz -repeat -var stdev stdev.nii.gz -repeat Thank you very much for you help. best, Jason UM-46JNG5RP:~ admin$ /Applications/workbench/bin_macosx64/wb_command ; exit & Why do you have "; exit &" on the end? Connectome Workbench Version: 1.0 Qt Compiled Version: 4.8.3 Qt Runtime Version: 4.8.3 commit: dfd2086d37612ccf2369b85b5f5f0f5987369339 commit date: 2014-09-09 13:23:57 -0500 Compiler: clang2++ (/usr/local/clang-openmp-opt/llvm/build/Release/bin) Compiler Version: Compiled Debug: NO Operating System: Apple OSX Information options: -help print this help info -arguments-help explain how to read the help info for subcommands -version print version information only -list-commandsprint all non-information (processing) subcommands -all-commands-helpprint all non-information (processing) subcommands and their help info - VERY LONG Global options (can be added to any command): -disable-provenance don't generate provenance info in output files If the first argument is not recognized, all processing commands that start with the argument are displayed ___ HCP-Users mailing lis
Re: [HCP-Users] Using Connectome Workbench Commands
Hi Tim, Thank you for the help with the workbench and the code. Yes, it is a mac osx. Sorry for the mix up. Also, I can get the first two commands to work for "MEAN" and "STDEV", but the last command gives me an error message: wb_command -volume-math '((x - mean) / stdev)' normalized.nii.gz -fixnan 0 -var x -var mean mean.nii.gz -repeat -var stdev stdev.nii.gz -repeat ERROR: volume file for variable 'mean' has 1 subvolume(s), but previous volume files have 1200 subvolume(s) requested to be used Any help would be appreciated. best, Jason Jason S. Nomi, Ph.D. Post-Doctoral Researcher (BCCL Lab) Department of Psychology University of Miami 5151 San Amaro Drive: Room 114A Website: http://www.psy.miami.edu/bccl/ Email: jxn...@miami.edu From: Timothy Coalson Sent: Monday, October 27, 2014 5:38 PM To: Nomi, Jason Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Using Connectome Workbench Commands Inline replies. Tim On Mon, Oct 27, 2014 at 10:26 AM, Nomi, Jason mailto:jxn...@miami.edu>> wrote: Dear Experts, I am trying to use the workbench commands but cannot get them to work. After opening the “wb_command” file in my linux terminal, I get the message printed below. Linux terminal? The output shows that you successfully executed the Mac OS X binary, is there a linux system involved? However, none of the commands work and nothing comes up when I type in the command by itself to get help. I have tried all the various combinations. With the “-“, without it. With “wb_command” to start, without it, etc. Try entering this at the command line: /Applications/workbench/bin_macosx64/wb_command -volume-reduce If you want to use it without entering that path each time, you'll need to add "/Applications/workbench/bin_macosx64/" to your PATH environment variable. How to do this depends on what shell you are using. Also, I would like to conduct variance normalization on some of the .nii files from the ICA-Fix dataset. Would using the command, “-volume-reduce" with the VARIANCE operation accomplish this? No, among other things, variance is nonlinear with the spread of the data. If the files you are looking at end in .dtseries.nii, they are not volume files, but rather CIFTI files (there are other 2-part extensions that signify CIFTI files, but ICA-FIX should be using dtseries). This thread contains the steps for normalizing (including demeaning) along timeseries while in CIFTI format: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00444.html Similar commands apply if you are actually dealing with volume file timeseries: wb_command -volume-reduce MEAN mean.nii.gz wb_command -volume-reduce STDEV stdev.nii.gz wb_command -volume-math '(x - mean) / stdev' normalized.nii.gz -fixnan 0 -var x -var mean mean.nii.gz -repeat -var stdev stdev.nii.gz -repeat Thank you very much for you help. best, Jason UM-46JNG5RP:~ admin$ /Applications/workbench/bin_macosx64/wb_command ; exit & Why do you have "; exit &" on the end? Connectome Workbench Version: 1.0 Qt Compiled Version: 4.8.3 Qt Runtime Version: 4.8.3 commit: dfd2086d37612ccf2369b85b5f5f0f5987369339 commit date: 2014-09-09 13:23:57 -0500 Compiler: clang2++ (/usr/local/clang-openmp-opt/llvm/build/Release/bin) Compiler Version: Compiled Debug: NO Operating System: Apple OSX Information options: -help print this help info -arguments-help explain how to read the help info for subcommands -version print version information only -list-commandsprint all non-information (processing) subcommands -all-commands-helpprint all non-information (processing) subcommands and their help info - VERY LONG Global options (can be added to any command): -disable-provenance don't generate provenance info in output files If the first argument is not recognized, all processing commands that start with the argument are displayed ___ 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
[HCP-Users] Using Connectome Workbench Commands
Dear Experts, I am trying to use the workbench commands but cannot get them to work. After opening the “wb_command” file in my linux terminal, I get the message printed below. However, none of the commands work and nothing comes up when I type in the command by itself to get help. I have tried all the various combinations. With the “-“, without it. With “wb_command” to start, without it, etc. Also, I would like to conduct variance normalization on some of the .nii files from the ICA-Fix dataset. Would using the command, “-volume-reduce" with the VARIANCE operation accomplish this? Thank you very much for you help. best, Jason UM-46JNG5RP:~ admin$ /Applications/workbench/bin_macosx64/wb_command ; exit & Connectome Workbench Version: 1.0 Qt Compiled Version: 4.8.3 Qt Runtime Version: 4.8.3 commit: dfd2086d37612ccf2369b85b5f5f0f5987369339 commit date: 2014-09-09 13:23:57 -0500 Compiler: clang2++ (/usr/local/clang-openmp-opt/llvm/build/Release/bin) Compiler Version: Compiled Debug: NO Operating System: Apple OSX Information options: -help print this help info -arguments-help explain how to read the help info for subcommands -version print version information only -list-commandsprint all non-information (processing) subcommands -all-commands-helpprint all non-information (processing) subcommands and their help info - VERY LONG Global options (can be added to any command): -disable-provenance don't generate provenance info in output files If the first argument is not recognized, all processing commands that start with the argument are displayed ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] More questions about Fix-preprocessed rs-fMRI data
? Dear Experts, I have a follow up question regarding this earlier thread about Fix-preprocessed rs-fMRI data. http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00596.html There are 4 runs for the fix data each consisting of a 15 minute resting state .nii volume file: Rest1: LR Rest1: RL Rest2: LR Rest2: RL >From the earlier thread it seems like all 4 runs should be concatenated? In >other words, I should combine all 4 15 minute runs into a single 60 minute >run? Or, should I merge them to make a single 15 minute run? I do not understand what to do with the 4 runs. There is a PNAS paper where they simply chose one of the 15 minute runs (Rest2: LR): http://www.pnas.org/content/111/28/10341.full.pdf Is this acceptable? Or, is it absolutely necessary to combine/concatenate/merge (I don't know what the proper term/operation is here!) the 4 runs? best, Jason ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
