Re: [HCP-Users] rs-fMRI with-in subject comparison
I analysis the data of 100 subjects (one scan for each) Is it making sense that the mean correlation of the DMN is 0.28 ? (Primary and Secondary Visual are r=0.5) From: Glasser, Matthew [glass...@wustl.edu] Sent: Sunday, March 10, 2019 10:59 AM To: Tali Weiss; Harms, Michael; NEUROSCIENCE tim Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. You would need to ask those authors about that parcellation. 2. That is not a cortical areal parcellation, but could be used for dimensionality reduction. Matt. From: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Sunday, March 10, 2019 at 8:55 AM To: "Harms, Michael" mailto:mha...@wustl.edu>>, Timothy Coalson mailto:tsc...@mst.edu>>, Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison Thank you! 1. For cortical and sub-cortical I need to choose this file? CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR.dlabel.nii is the surface Q1-Q6_RelatedParcellation210 or Q1-Q6_RelatedValidation210? 2. btw, I also found this parcellation: Schaefer A, Kong R, Gordon EM, Laumann TO, Zuo XN, Holmes AJ, Eickhoff SB, Yeo BTT. Local-Global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI, Cerebral Cortex, 29:3095-3114, 2018 https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobalhttps://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal Tali From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>] Sent: Monday, March 04, 2019 9:08 PM To: NEUROSCIENCE tim; Tali Weiss Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison As for a version of the parcellation with network assignments, see here: https://github.com/ColeLab/ColeAnticevicNetPartition cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Monday, March 4, 2019 at 12:38 PM To: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison There isn't a dedicated command to get the parcel names, but they are in the output of wb_command -file-information on the parcellated file, or you can take them from -cifti-label-export-table on the dlabel file. Tim On Mon, Mar 4, 2019 at 1:55 AM Tali Weiss mailto:tali.we...@weizmann.ac.il>> wrote: i did wb_command -cifti-parcellate wb_command -cifti-convert -to-text (to be continued in matlab) 1. Where I can find the titles of each of the 360 parcels? 2. I want to classify the parcel to networks (DMN, visual...)? is there a script in HCP that do it? From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Sunday, March 03, 2019 5:12 PM To: Tali Weiss; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. The HCP-YA data were not variance normalized. 2. wb_command -cifti-parcellate 3. There isn’t a good sub-cortical parcellation like the cortical parcellation yet unfortunately. If you are comparing functional connectivity across runs within a subject, you don’t need to concatenate or variance normalize the runs. Matt. From: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Sunday, March 3, 2019 at 4:28 AM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison Thank you Mattew! 1. Download Packages: State fMRI FIX-Denoised (Compact) {Subject}_REST/MNINonLinear/Results/{fMRIName}/{fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii - The raw data were zscore (overall standard deviation) and then cleaned by sICA+FIX? - In wb there is a layer: .dynconn.nii. Is it for each of the 4 rs-scan of each subject? 2. I’m not sure which command I need to use to extract the timecourse of each parcel and then to apply correlation bet
Re: [HCP-Users] rs-fMRI with-in subject comparison
1. You would need to ask those authors about that parcellation. 2. That is not a cortical areal parcellation, but could be used for dimensionality reduction. Matt. From: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Sunday, March 10, 2019 at 8:55 AM To: "Harms, Michael" mailto:mha...@wustl.edu>>, Timothy Coalson mailto:tsc...@mst.edu>>, Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison Thank you! 1. For cortical and sub-cortical I need to choose this file? CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR.dlabel.nii is the surface Q1-Q6_RelatedParcellation210 or Q1-Q6_RelatedValidation210? 2. btw, I also found this parcellation: Schaefer A, Kong R, Gordon EM, Laumann TO, Zuo XN, Holmes AJ, Eickhoff SB, Yeo BTT. Local-Global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI, Cerebral Cortex, 29:3095-3114, 2018 https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobalhttps://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal Tali From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>] Sent: Monday, March 04, 2019 9:08 PM To: NEUROSCIENCE tim; Tali Weiss Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison As for a version of the parcellation with network assignments, see here: https://github.com/ColeLab/ColeAnticevicNetPartition cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Monday, March 4, 2019 at 12:38 PM To: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison There isn't a dedicated command to get the parcel names, but they are in the output of wb_command -file-information on the parcellated file, or you can take them from -cifti-label-export-table on the dlabel file. Tim On Mon, Mar 4, 2019 at 1:55 AM Tali Weiss mailto:tali.we...@weizmann.ac.il>> wrote: i did wb_command -cifti-parcellate wb_command -cifti-convert -to-text (to be continued in matlab) 1. Where I can find the titles of each of the 360 parcels? 2. I want to classify the parcel to networks (DMN, visual...)? is there a script in HCP that do it? From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Sunday, March 03, 2019 5:12 PM To: Tali Weiss; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. The HCP-YA data were not variance normalized. 2. wb_command -cifti-parcellate 3. There isn’t a good sub-cortical parcellation like the cortical parcellation yet unfortunately. If you are comparing functional connectivity across runs within a subject, you don’t need to concatenate or variance normalize the runs. Matt. From: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Sunday, March 3, 2019 at 4:28 AM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison Thank you Mattew! 1. Download Packages: State fMRI FIX-Denoised (Compact) {Subject}_REST/MNINonLinear/Results/{fMRIName}/{fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii - The raw data were zscore (overall standard deviation) and then cleaned by sICA+FIX? - In wb there is a layer: .dynconn.nii. Is it for each of the 4 rs-scan of each subject? 2. I’m not sure which command I need to use to extract the timecourse of each parcel and then to apply correlation between all parcel of each network. input_label= Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii wb_command -cifti-all-labels-to-rois $input_label 1 ROIvalidation210.dscalar.nii what I need to do next? 3. I like to create correlation also between subcortical (volume). I read your article https://www.ncbi.nlm.nih.gov/pubmed/29925602 What is your recommendation to define
Re: [HCP-Users] rs-fMRI with-in subject comparison
Thank you! 1. For cortical and sub-cortical I need to choose this file? CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR.dlabel.nii is the surface Q1-Q6_RelatedParcellation210 or Q1-Q6_RelatedValidation210? 2. btw, I also found this parcellation: Schaefer A, Kong R, Gordon EM, Laumann TO, Zuo XN, Holmes AJ, Eickhoff SB, Yeo BTT. Local-Global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI, Cerebral Cortex, 29:3095-3114, 2018 https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobalhttps://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal Tali From: Harms, Michael [mha...@wustl.edu] Sent: Monday, March 04, 2019 9:08 PM To: NEUROSCIENCE tim; Tali Weiss Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison As for a version of the parcellation with network assignments, see here: https://github.com/ColeLab/ColeAnticevicNetPartition cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of Timothy Coalson Date: Monday, March 4, 2019 at 12:38 PM To: Tali Weiss Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison There isn't a dedicated command to get the parcel names, but they are in the output of wb_command -file-information on the parcellated file, or you can take them from -cifti-label-export-table on the dlabel file. Tim On Mon, Mar 4, 2019 at 1:55 AM Tali Weiss mailto:tali.we...@weizmann.ac.il>> wrote: i did wb_command -cifti-parcellate wb_command -cifti-convert -to-text (to be continued in matlab) 1. Where I can find the titles of each of the 360 parcels? 2. I want to classify the parcel to networks (DMN, visual...)? is there a script in HCP that do it? From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Sunday, March 03, 2019 5:12 PM To: Tali Weiss; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. The HCP-YA data were not variance normalized. 2. wb_command -cifti-parcellate 3. There isn’t a good sub-cortical parcellation like the cortical parcellation yet unfortunately. If you are comparing functional connectivity across runs within a subject, you don’t need to concatenate or variance normalize the runs. Matt. From: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Sunday, March 3, 2019 at 4:28 AM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison Thank you Mattew! 1. Download Packages: State fMRI FIX-Denoised (Compact) {Subject}_REST/MNINonLinear/Results/{fMRIName}/{fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii - The raw data were zscore (overall standard deviation) and then cleaned by sICA+FIX? - In wb there is a layer: .dynconn.nii. Is it for each of the 4 rs-scan of each subject? 2. I’m not sure which command I need to use to extract the timecourse of each parcel and then to apply correlation between all parcel of each network. input_label= Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii wb_command -cifti-all-labels-to-rois $input_label 1 ROIvalidation210.dscalar.nii what I need to do next? 3. I like to create correlation also between subcortical (volume). I read your article https://www.ncbi.nlm.nih.gov/pubmed/29925602 What is your recommendation to define subcortical volume? My analysis is “within subject” paradigm (comparing the scans in different days). From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, February 28, 2019 3:39 AM To: Tali Weiss; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. You would need to post the full path and filename. 2. This will be handled by multi-run sICA+FIX in the future. We will recommend all data be cleaned with sICA+FIX. Really you want to be dividing by the unstructured noise standard deviation, rather than the overall standard deviation. 3. Parcels have more statistical power than grayordinates. The HCP’s multi-modal parcellation is here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Tali Weiss
Re: [HCP-Users] rs-fMRI with-in subject comparison
As for a version of the parcellation with network assignments, see here: https://github.com/ColeLab/ColeAnticevicNetPartition cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of Timothy Coalson Date: Monday, March 4, 2019 at 12:38 PM To: Tali Weiss Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison There isn't a dedicated command to get the parcel names, but they are in the output of wb_command -file-information on the parcellated file, or you can take them from -cifti-label-export-table on the dlabel file. Tim On Mon, Mar 4, 2019 at 1:55 AM Tali Weiss mailto:tali.we...@weizmann.ac.il>> wrote: i did wb_command -cifti-parcellate wb_command -cifti-convert -to-text (to be continued in matlab) 1. Where I can find the titles of each of the 360 parcels? 2. I want to classify the parcel to networks (DMN, visual...)? is there a script in HCP that do it? From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Sunday, March 03, 2019 5:12 PM To: Tali Weiss; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. The HCP-YA data were not variance normalized. 2. wb_command -cifti-parcellate 3. There isn’t a good sub-cortical parcellation like the cortical parcellation yet unfortunately. If you are comparing functional connectivity across runs within a subject, you don’t need to concatenate or variance normalize the runs. Matt. From: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Sunday, March 3, 2019 at 4:28 AM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison Thank you Mattew! 1. Download Packages: State fMRI FIX-Denoised (Compact) {Subject}_REST/MNINonLinear/Results/{fMRIName}/{fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii - The raw data were zscore (overall standard deviation) and then cleaned by sICA+FIX? - In wb there is a layer: .dynconn.nii. Is it for each of the 4 rs-scan of each subject? 2. I’m not sure which command I need to use to extract the timecourse of each parcel and then to apply correlation between all parcel of each network. input_label= Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii wb_command -cifti-all-labels-to-rois $input_label 1 ROIvalidation210.dscalar.nii what I need to do next? 3. I like to create correlation also between subcortical (volume). I read your article https://www.ncbi.nlm.nih.gov/pubmed/29925602 What is your recommendation to define subcortical volume? My analysis is “within subject” paradigm (comparing the scans in different days). From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, February 28, 2019 3:39 AM To: Tali Weiss; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. You would need to post the full path and filename. 2. This will be handled by multi-run sICA+FIX in the future. We will recommend all data be cleaned with sICA+FIX. Really you want to be dividing by the unstructured noise standard deviation, rather than the overall standard deviation. 3. Parcels have more statistical power than grayordinates. The HCP’s multi-modal parcellation is here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Wednesday, February 27, 2019 at 7:26 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] rs-fMRI with-in subject comparison Dear Prof.Smith, I really appreciate your help. I like to compare the second rs-fmri scan (from two different days) of the same subject. 1.when i open MSMAII_hp2000_clean.dtseries in WB, I get also a layer "dynconn", for example: rfMRI_REST1_LR_Atlas_MSMAII_hp2000_clean.dynconn.nii Are those group average? 2. It is recommended in the HCP Users FAQ: "demean and normalize the individual timeseries." wb_command -cifti-math '(x - mean) / stdev' I am confused because it is writing demean andnormalize. (zscore include demean, am I missing something?). My design is "within", so should I only apply demean? or because it is in a di
Re: [HCP-Users] rs-fMRI with-in subject comparison
There isn't a dedicated command to get the parcel names, but they are in the output of wb_command -file-information on the parcellated file, or you can take them from -cifti-label-export-table on the dlabel file. Tim On Mon, Mar 4, 2019 at 1:55 AM Tali Weiss wrote: > i did > wb_command -cifti-parcellate > wb_command -cifti-convert -to-text (to be continued in matlab) > > 1. Where I can find the titles of each of the 360 parcels? > 2. I want to classify the parcel to networks (DMN, visual...)? is there a > script in HCP that do it? > -- > *From:* Glasser, Matthew [glass...@wustl.edu] > *Sent:* Sunday, March 03, 2019 5:12 PM > *To:* Tali Weiss; hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] rs-fMRI with-in subject comparison > > 1. The HCP-YA data were not variance normalized. > 2. wb_command -cifti-parcellate > 3. There isn’t a good sub-cortical parcellation like the cortical > parcellation yet unfortunately. > > If you are comparing functional connectivity across runs within a subject, > you don’t need to concatenate or variance normalize the runs. > > Matt. > > From: Tali Weiss > Date: Sunday, March 3, 2019 at 4:28 AM > To: Matt Glasser , "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison > > Thank you Mattew! > > > > 1. Download Packages: State fMRI FIX-Denoised (Compact) > > {Subject}_REST/MNINonLinear/Results/{fMRIName}/{fMRIName} > _Atlas_MSMAll_hp2000_clean.dtseries.nii > > - The raw data were zscore (overall standard deviation) and then cleaned > by sICA+FIX? > > - In wb there is a layer: .dynconn.nii. Is it for each of the 4 rs-scan of > each subject? > > > > 2. I’m not sure which command I need to use to extract the timecourse of > each parcel and then to apply correlation between all parcel of each > network. > > > > input_label= > Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii > > wb_command -cifti-all-labels-to-rois $input_label 1 > ROIvalidation210.dscalar.nii > > > > what I need to do next? > > > > 3. I like to create correlation also between subcortical (volume). > > I read your article > > https://www.ncbi.nlm.nih.gov/pubmed/29925602 > > > > What is your recommendation to define subcortical volume? > > My analysis is “within subject” paradigm (comparing the scans in different > days). > > > -- > *From:* Glasser, Matthew [glass...@wustl.edu] > *Sent:* Thursday, February 28, 2019 3:39 AM > *To:* Tali Weiss; hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] rs-fMRI with-in subject comparison > > 1. You would need to post the full path and filename. > 2. This will be handled by multi-run sICA+FIX in the future. We will > recommend all data be cleaned with sICA+FIX. Really you want to be > dividing by the unstructured noise standard deviation, rather than the > overall standard deviation. > 3. Parcels have more statistical power than grayordinates. The HCP’s > multi-modal parcellation is here: https://balsa.wustl.edu/file/show/3VLx > > Matt. > > From: on behalf of Tali Weiss < > tali.we...@weizmann.ac.il> > Date: Wednesday, February 27, 2019 at 7:26 AM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] rs-fMRI with-in subject comparison > > Dear Prof.Smith, > > I really appreciate your help. > I like to compare the second rs-fmri scan (from two different days) of > the same subject. > > 1.when i open MSMAII_hp2000_clean.dtseries in WB, I get also a layer > "dynconn", > for example: rfMRI_REST1_LR_Atlas_MSMAII_hp2000_clean.dynconn.nii > Are those *group* average? > > 2. It is recommended in the *HCP Users FAQ*: "demean and normalize the > individual timeseries." > wb_command -cifti-math '(x - mean) / stdev' > I am confused because it is writing demean *and*normalize. (zscore > include demean, am I missing something?). > > My design is "within", so should I only apply demean? or because it is in > a different day I should apply zscore? > > 3. I believe that statistically there are not enough time points in one > scan to use all grayordinates. > Thus, I will need to chose parcels/ROI. > What is the best parcels/ROI I can use? (I like to focus on the > attentional network, working memory and DMN) > Is there an easy way to get those ROIs from the tasks? > > Thank you > Tali > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectom
Re: [HCP-Users] rs-fMRI with-in subject comparison
i did wb_command -cifti-parcellate wb_command -cifti-convert -to-text (to be continued in matlab) 1. Where I can find the titles of each of the 360 parcels? 2. I want to classify the parcel to networks (DMN, visual...)? is there a script in HCP that do it? From: Glasser, Matthew [glass...@wustl.edu] Sent: Sunday, March 03, 2019 5:12 PM To: Tali Weiss; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. The HCP-YA data were not variance normalized. 2. wb_command -cifti-parcellate 3. There isn’t a good sub-cortical parcellation like the cortical parcellation yet unfortunately. If you are comparing functional connectivity across runs within a subject, you don’t need to concatenate or variance normalize the runs. Matt. From: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Sunday, March 3, 2019 at 4:28 AM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison Thank you Mattew! 1. Download Packages: State fMRI FIX-Denoised (Compact) {Subject}_REST/MNINonLinear/Results/{fMRIName}/{fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii - The raw data were zscore (overall standard deviation) and then cleaned by sICA+FIX? - In wb there is a layer: .dynconn.nii. Is it for each of the 4 rs-scan of each subject? 2. I’m not sure which command I need to use to extract the timecourse of each parcel and then to apply correlation between all parcel of each network. input_label= Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii wb_command -cifti-all-labels-to-rois $input_label 1 ROIvalidation210.dscalar.nii what I need to do next? 3. I like to create correlation also between subcortical (volume). I read your article https://www.ncbi.nlm.nih.gov/pubmed/29925602 What is your recommendation to define subcortical volume? My analysis is “within subject” paradigm (comparing the scans in different days). From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, February 28, 2019 3:39 AM To: Tali Weiss; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. You would need to post the full path and filename. 2. This will be handled by multi-run sICA+FIX in the future. We will recommend all data be cleaned with sICA+FIX. Really you want to be dividing by the unstructured noise standard deviation, rather than the overall standard deviation. 3. Parcels have more statistical power than grayordinates. The HCP’s multi-modal parcellation is here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Wednesday, February 27, 2019 at 7:26 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] rs-fMRI with-in subject comparison Dear Prof.Smith, I really appreciate your help. I like to compare the second rs-fmri scan (from two different days) of the same subject. 1.when i open MSMAII_hp2000_clean.dtseries in WB, I get also a layer "dynconn", for example: rfMRI_REST1_LR_Atlas_MSMAII_hp2000_clean.dynconn.nii Are those group average? 2. It is recommended in the HCP Users FAQ: "demean and normalize the individual timeseries." wb_command -cifti-math '(x - mean) / stdev' I am confused because it is writing demean andnormalize. (zscore include demean, am I missing something?). My design is "within", so should I only apply demean? or because it is in a different day I should apply zscore? 3. I believe that statistically there are not enough time points in one scan to use all grayordinates. Thus, I will need to chose parcels/ROI. What is the best parcels/ROI I can use? (I like to focus on the attentional network, working memory and DMN) Is there an easy way to get those ROIs from the tasks? Thank you Tali ___ 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.
Re: [HCP-Users] rs-fMRI with-in subject comparison
1. The HCP-YA data were not variance normalized. 2. wb_command -cifti-parcellate 3. There isn’t a good sub-cortical parcellation like the cortical parcellation yet unfortunately. If you are comparing functional connectivity across runs within a subject, you don’t need to concatenate or variance normalize the runs. Matt. From: Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Sunday, March 3, 2019 at 4:28 AM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] rs-fMRI with-in subject comparison Thank you Mattew! 1. Download Packages: State fMRI FIX-Denoised (Compact) {Subject}_REST/MNINonLinear/Results/{fMRIName}/{fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii - The raw data were zscore (overall standard deviation) and then cleaned by sICA+FIX? - In wb there is a layer: .dynconn.nii. Is it for each of the 4 rs-scan of each subject? 2. I’m not sure which command I need to use to extract the timecourse of each parcel and then to apply correlation between all parcel of each network. input_label= Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii wb_command -cifti-all-labels-to-rois $input_label 1 ROIvalidation210.dscalar.nii what I need to do next? 3. I like to create correlation also between subcortical (volume). I read your article https://www.ncbi.nlm.nih.gov/pubmed/29925602 What is your recommendation to define subcortical volume? My analysis is “within subject” paradigm (comparing the scans in different days). From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, February 28, 2019 3:39 AM To: Tali Weiss; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. You would need to post the full path and filename. 2. This will be handled by multi-run sICA+FIX in the future. We will recommend all data be cleaned with sICA+FIX. Really you want to be dividing by the unstructured noise standard deviation, rather than the overall standard deviation. 3. Parcels have more statistical power than grayordinates. The HCP’s multi-modal parcellation is here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Wednesday, February 27, 2019 at 7:26 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] rs-fMRI with-in subject comparison Dear Prof.Smith, I really appreciate your help. I like to compare the second rs-fmri scan (from two different days) of the same subject. 1.when i open MSMAII_hp2000_clean.dtseries in WB, I get also a layer "dynconn", for example: rfMRI_REST1_LR_Atlas_MSMAII_hp2000_clean.dynconn.nii Are those group average? 2. It is recommended in the HCP Users FAQ: "demean and normalize the individual timeseries." wb_command -cifti-math '(x - mean) / stdev' I am confused because it is writing demean andnormalize. (zscore include demean, am I missing something?). My design is "within", so should I only apply demean? or because it is in a different day I should apply zscore? 3. I believe that statistically there are not enough time points in one scan to use all grayordinates. Thus, I will need to chose parcels/ROI. What is the best parcels/ROI I can use? (I like to focus on the attentional network, working memory and DMN) Is there an easy way to get those ROIs from the tasks? Thank you Tali ___ 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. 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 ret
Re: [HCP-Users] rs-fMRI with-in subject comparison
Thank you Mattew! 1. Download Packages: State fMRI FIX-Denoised (Compact) {Subject}_REST/MNINonLinear/Results/{fMRIName}/{fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii - The raw data were zscore (overall standard deviation) and then cleaned by sICA+FIX? - In wb there is a layer: .dynconn.nii. Is it for each of the 4 rs-scan of each subject? 2. I’m not sure which command I need to use to extract the timecourse of each parcel and then to apply correlation between all parcel of each network. input_label= Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii wb_command -cifti-all-labels-to-rois $input_label 1 ROIvalidation210.dscalar.nii what I need to do next? 3. I like to create correlation also between subcortical (volume). I read your article https://www.ncbi.nlm.nih.gov/pubmed/29925602 What is your recommendation to define subcortical volume? My analysis is “within subject” paradigm (comparing the scans in different days). From: Glasser, Matthew [glass...@wustl.edu] Sent: Thursday, February 28, 2019 3:39 AM To: Tali Weiss; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] rs-fMRI with-in subject comparison 1. You would need to post the full path and filename. 2. This will be handled by multi-run sICA+FIX in the future. We will recommend all data be cleaned with sICA+FIX. Really you want to be dividing by the unstructured noise standard deviation, rather than the overall standard deviation. 3. Parcels have more statistical power than grayordinates. The HCP’s multi-modal parcellation is here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Wednesday, February 27, 2019 at 7:26 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] rs-fMRI with-in subject comparison Dear Prof.Smith, I really appreciate your help. I like to compare the second rs-fmri scan (from two different days) of the same subject. 1.when i open MSMAII_hp2000_clean.dtseries in WB, I get also a layer "dynconn", for example: rfMRI_REST1_LR_Atlas_MSMAII_hp2000_clean.dynconn.nii Are those group average? 2. It is recommended in the HCP Users FAQ: "demean and normalize the individual timeseries." wb_command -cifti-math '(x - mean) / stdev' I am confused because it is writing demean andnormalize. (zscore include demean, am I missing something?). My design is "within", so should I only apply demean? or because it is in a different day I should apply zscore? 3. I believe that statistically there are not enough time points in one scan to use all grayordinates. Thus, I will need to chose parcels/ROI. What is the best parcels/ROI I can use? (I like to focus on the attentional network, working memory and DMN) Is there an easy way to get those ROIs from the tasks? Thank you Tali ___ 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
Re: [HCP-Users] rs-fMRI with-in subject comparison
1. You would need to post the full path and filename. 2. This will be handled by multi-run sICA+FIX in the future. We will recommend all data be cleaned with sICA+FIX. Really you want to be dividing by the unstructured noise standard deviation, rather than the overall standard deviation. 3. Parcels have more statistical power than grayordinates. The HCP’s multi-modal parcellation is here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Tali Weiss mailto:tali.we...@weizmann.ac.il>> Date: Wednesday, February 27, 2019 at 7:26 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] rs-fMRI with-in subject comparison Dear Prof.Smith, I really appreciate your help. I like to compare the second rs-fmri scan (from two different days) of the same subject. 1.when i open MSMAII_hp2000_clean.dtseries in WB, I get also a layer "dynconn", for example: rfMRI_REST1_LR_Atlas_MSMAII_hp2000_clean.dynconn.nii Are those group average? 2. It is recommended in the HCP Users FAQ: "demean and normalize the individual timeseries." wb_command -cifti-math '(x - mean) / stdev' I am confused because it is writing demean andnormalize. (zscore include demean, am I missing something?). My design is "within", so should I only apply demean? or because it is in a different day I should apply zscore? 3. I believe that statistically there are not enough time points in one scan to use all grayordinates. Thus, I will need to chose parcels/ROI. What is the best parcels/ROI I can use? (I like to focus on the attentional network, working memory and DMN) Is there an easy way to get those ROIs from the tasks? Thank you Tali ___ 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] rs-fMRI with-in subject comparison
Dear Prof.Smith, I really appreciate your help. I like to compare the second rs-fmri scan (from two different days) of the same subject. 1.when i open MSMAII_hp2000_clean.dtseries in WB, I get also a layer "dynconn", for example: rfMRI_REST1_LR_Atlas_MSMAII_hp2000_clean.dynconn.nii Are those group average? 2. It is recommended in the HCP Users FAQ: "demean and normalize the individual timeseries." wb_command -cifti-math '(x - mean) / stdev' I am confused because it is writing demean and normalize. (zscore include demean, am I missing something?). My design is "within", so should I only apply demean? or because it is in a different day I should apply zscore? 3. I believe that statistically there are not enough time points in one scan to use all grayordinates. Thus, I will need to chose parcels/ROI. What is the best parcels/ROI I can use? (I like to focus on the attentional network, working memory and DMN) Is there an easy way to get those ROIs from the tasks? Thank you Tali ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users