[HCP-Users] Downloading HCP data to a shared computing cluster
Dear HCP experts, I was wondering if it is possible to download HCP data directly to a shared computing cluster (e.g. the openmind.mit.edu cluster). Since data is downloaded via Aspera Connect, there is no link that one can copy and paste to download data directly to the cluster. Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] 900 group average: are individual subjects the "S500 Release Subjects" + the "S900 New Subjects"
Thank you! I noticed (and this is also seen in the image Jenn attached) that the total number of subjects with 100% tasks and 100% resting state is 788 (not 787, which is the number of subjects in the S900 group average). Is there a subject that was excluded from the S900 group average for another reason? Thank you very much, Xavier. From: Elam, Jennifer [e...@wustl.edu] Sent: Friday, February 03, 2017 11:12 AM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] 900 group average: are individual subjects the "S500 Release Subjects" + the "S900 New Subjects" Mike just answered while I was writing this, but for everyone's benefit who need to do something similar: To get the list of subjects that were included in the S900 group average task analysis, you need to go to the subject dashboard (click on Explore All Family Subjects to get there from the Public Connectome Data page) and filter all subjects for those that have 3T Resting state Percent complete = 100 AND 3T Task fMRI Percent Complete = 100, like this: [cid:9cc36f61-309e-453e-9e8e-95b6de6d46a9] Once you have that filter set, you can click "Save Group" to save this group and "Download CSV" to download this group and all it's behavioral and demographic data in a spreadsheet. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Xavier Guell Paradis <xavie...@mit.edu> Sent: Friday, February 3, 2017 9:41:31 AM To: hcp-users@humanconnectome.org Subject: [HCP-Users] 900 group average: are individual subjects the "S500 Release Subjects" + the "S900 New Subjects" Dear HCP experts, In order to get the level2 data from the individual subjects which were included in the 900 subjects group average, should we put together the subjects of the "S500 Release Subjects" with the "S900 New Subjects"? Thank you, Xavier. ___ HCP-Users mailing list 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
Re: [HCP-Users] How many voxels in the cerebellum?
Great, thank you very much!! From: Glasser, Matthew [glass...@wustl.edu] Sent: Thursday, February 02, 2017 11:34 AM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How many voxels in the cerebellum? 2mm standard CIFTI files (with 91282 grayordinates) have the following: CortexLeft: 29696 out of 32492 vertices CortexRight:29716 out of 32492 vertices AccumbensLeft: 135 voxels AccumbensRight: 140 voxels AmygdalaLeft: 315 voxels AmygdalaRight: 332 voxels BrainStem: 3472 voxels CaudateLeft:728 voxels CaudateRight: 755 voxels CerebellumLeft: 8709 voxels CerebellumRight:9144 voxels DiencephalonVentralLeft:706 voxels DiencephalonVentralRight: 712 voxels HippocampusLeft:764 voxels HippocampusRight: 795 voxels PallidumLeft: 297 voxels PallidumRight: 260 voxels PutamenLeft:1060 voxels PutamenRight: 1010 voxels ThalamusLeft: 1288 voxels ThalamusRight: 1248 voxels Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Thursday, February 2, 2017 at 10:30 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] How many voxels in the cerebellum? This one: HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar Thanks, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, February 02, 2017 11:28 AM To: Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] How many voxels in the cerebellum? What file? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Thursday, February 2, 2017 at 10:26 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] How many voxels in the cerebellum? Dear HCP experts, Is there a way to know how many voxels does the cerebellum have in a given file? Thank you very much, Xavier. ___ 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 return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] How many voxels in the cerebellum?
Dear HCP experts, Is there a way to know how many voxels does the cerebellum have in a given file? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.?
Hi Greg, Thank you for your reply. Would you recommend the following commands to analyze the data as you suggested?: 1) -cifti-merge all level2 cope files of RH (create "mergedcopeMOTORRHONLY.dtseries.nii") 2) -cifti-merge all level2 cope files of CUE (create "mergedcopeMOTORCUEONLY.dtseries.nii") 3) calculate RH minus CUE cope file as follows: -cifti-math '(x) - (y)' /mergedcopeMOTORRHMINUSCUE.dtseries.nii -var x /mergedcopeMOTORRHONLY.dtseries.nii -var y /mergedcopeMOTORCUEONLY.dtseries.nii 4) then obtain Cohen's d as follows: -cifti-reduce /mergedcopeMOTORTMINUSCUE.dtseries.nii MEAN /meancopeMOTORTMINUSCUE.dscalar.nii; -cifti-reduce /mergedcopeMOTORHMINUSCUE.dtseries.nii STDEV /stdevcopeMOTORTMINUSCUE.dscalar.nii; -cifti-math '(mean) / stdev' /cohendmapMOTORTMINUSCUE.dscalar.nii -var mean /meancopeMOTORTMINUSCUE.dscalar.nii -var stdev /stdevcopeMOTORTMINUSCUE.dscalar.nii Thank you very much, Xavier. From: Burgess, Gregory [gburg...@wustl.edu] Sent: Monday, February 06, 2017 5:18 PM To: Xavier Guell Paradis Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.? I thought that contrasting each effector against the average of the others (e.g., RH-AVG) was a more-effective control to isolate motor-specific regions. If you are still interested in contrasting each effector versus the cue (controlling for visual activation without controlling for other task-related processes), it is possible for you to create it yourself by subtracting the cope maps for ‘CUE’ from the cope for each effector. --Greg Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Psychiatry Phone: 314-362-7864 Email: gburg...@wustl.edu > On Feb 3, 2017, at 4:25 PM, Xavier Guell Paradis <xavie...@mit.edu> wrote: > > Dear HCP experts, > I was wondering if there is any reason why motor contrasts of one motor task > minus cue (e.g. RH-Cue) were not calculated. > Thank you very much, > Xavier. > ___ > HCP-Users mailing list > 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] 900 group average: are individual subjects the "S500 Release Subjects" + the "S900 New Subjects"
Dear HCP experts, In order to get the level2 data from the individual subjects which were included in the 900 subjects group average, should we put together the subjects of the "S500 Release Subjects" with the "S900 New Subjects"? Thank you, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Hi Michael, This has worked wonderfully. Thank you all for your very helpful messages. Xavier. From: Harms, Michael [mha...@wustl.edu] Sent: Tuesday, January 31, 2017 11:01 AM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Yes. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders 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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Tuesday, January 31, 2017 at 9:59 AM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Michael, Thank you so much for all your help. I have seen that for each task, each subject has multiple cope1 files (under different cope folders; for example for the EMOTION task subject 100206 has the following folders, each with a cope1.dtseries.nii file: cope1.feat, cope2.feat, cope3.feat, cope4.feat, cope5.feat, cope6.feat). The Contrasts.txt file for EMOTION shows the following: FACES, SHAPES, FACES-SHAPES, neg_FACES, neg_SHAPES, SHAPES-FACES. If I am interested in FACES-SHAPES, should I use the cope1.dtseries.nii file that is inside the cope3.feat folder (given that FACES-SHAPES is the third contrast listed in the Contrasts.txt file)? Thank you, Xavier. From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>] Sent: Monday, January 30, 2017 9:11 PM To: Xavier Guell Paradis; Glasser, Matthew; Elam, Jennifer; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? No, we were proposing this: M = cifti map of mean(of Level 2 individual subject copes) S = cifti map of std(of Level 2 individual subject copes) Cohen’s d = M/S cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders 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: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, January 30, 2017 at 6:41 PM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? I think this would be done from a level3 file; maybe I'm wrong. If I understand this correctly, the three steps below would give a Cohen's d map. Have I understood it right?: 1st) take this file: HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar.nii 2nd) transform this file into a cope1 file (Michael said he may be able to make this file available; "I can make the equivalent “cope1” file from the Level 3 ‘flameo’ available via Box") 3rd) in the cope1 file, do (x-mean)/SD for every data point Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Monday, January 30, 2017 7:26 PM To: Xavier Guell Paradis; Harms, Michael; Elam, Jennifer; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? I assumed you were talking about level3 files. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> D
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Dear Matt, Thank you again for your reply. I have been able to find cope1 files for single subject task contrasts (e.g. cope1 file for working memory contrasts of subject 996782), but not for the S900 group (e.g. I have not been able to find a cope1 file for the S900 group for working memory contrasts). I was wondering: a) Is there any task contrast effect size map available for the S900 group? (even if they are not optimally scaled) b) If not, would it be possible to generate a task contrast effect size map by using available S900 group data (e.g. the task contrasts zstat maps of the S900 group), or would it be necessary to go back to the data of each individual subject? c) If it is necessary to go back to the data of each individual subject, which approach would you suggest to combine all cope1 files of each subject of the S900 group into one effect size map of all subjects? Would something like normalizing the cope1 file of each subject (using wb_command as written below) and then averaging all normalized cope1 files work? Or would something as simple as averaging all cope1 files work? wb_command -cifti-reduce MEAN mean.dtseries.nii wb_command -cifti-reduce STDEV stdev.dtseries.nii wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -var mean mean.dtseries.nii -select 1 1 -repeat -var stdev stdev.dtseries.nii -select 1 1 -repeat Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Thursday, January 26, 2017 6:53 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? The files called cope1 or beta are an effect size measure, however the released versions are not optimally scaled (because of a non-optimal intensity bias field correction). We plan to correct this in the future. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Thursday, January 26, 2017 at 5:41 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Matt, Thank you very much for your very helpful reply. I will have to investigate this topic more, but is there any approach you would suggest to obtain effect size maps from the S900 group HCP data? I was wondering if the zstat data of the S900 group task contrasts could be converted to effect size values without having to go back to the individual subjects. Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, January 26, 2017 5:33 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Standard error scales with sample size, standard deviation does not. Things like Z, t, and p all also scale with sample size and are measures of statistical significance via various transformations. Thus for a large group of subjects, Z and t will be very high and p will be very low. Z, t and p are thus all not biologically interpretable, as their values also depend on the amount and quality of the data. In the limit with infinite amounts of data, the entire brain will be significant for any task, but wether a region is statistically significant tells us little about its importance functionally. Measures like appropriately scaled GLM regression betas, %BOLD change, or Cohen’s d are biologically interpretable measures of effect size because their values should not change as sample size and data amount go up (rather the uncertainty on their estimates goes down). Regions with a large effect size in a task are likely important to that task (and will probably also meet criteria for statistical significance given a reasonable amount of data). A common problem in neuroimaging studies is showing thresholded statistical significance maps rather than effect size maps (ideally unthresholded with an indication of which portions meet tests of statistical significance), and in general focusing on statistically significant blobs rather than the effect size in identifiable brain areas (which should often show stepwise changes in activity at their borders). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Dear Matt, Thanks for the reply. Did you mean that the pipelines produce group average effect size map and that these must be somewhere as part of the HCP public data; or were you referring to the individual subject effect size maps? Thanks, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Friday, January 27, 2017 3:01 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? I assume these are available somewhere because the pipelines produce them, but I didn’t make these group average results. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Friday, January 27, 2017 at 10:04 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Matt, Thank you again for your reply. I have been able to find cope1 files for single subject task contrasts (e.g. cope1 file for working memory contrasts of subject 996782), but not for the S900 group (e.g. I have not been able to find a cope1 file for the S900 group for working memory contrasts). I was wondering: a) Is there any task contrast effect size map available for the S900 group? (even if they are not optimally scaled) b) If not, would it be possible to generate a task contrast effect size map by using available S900 group data (e.g. the task contrasts zstat maps of the S900 group), or would it be necessary to go back to the data of each individual subject? c) If it is necessary to go back to the data of each individual subject, which approach would you suggest to combine all cope1 files of each subject of the S900 group into one effect size map of all subjects? Would something like normalizing the cope1 file of each subject (using wb_command as written below) and then averaging all normalized cope1 files work? Or would something as simple as averaging all cope1 files work? wb_command -cifti-reduce MEAN mean.dtseries.nii wb_command -cifti-reduce STDEV stdev.dtseries.nii wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -var mean mean.dtseries.nii -select 1 1 -repeat -var stdev stdev.dtseries.nii -select 1 1 -repeat Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, January 26, 2017 6:53 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? The files called cope1 or beta are an effect size measure, however the released versions are not optimally scaled (because of a non-optimal intensity bias field correction). We plan to correct this in the future. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Thursday, January 26, 2017 at 5:41 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Matt, Thank you very much for your very helpful reply. I will have to investigate this topic more, but is there any approach you would suggest to obtain effect size maps from the S900 group HCP data? I was wondering if the zstat data of the S900 group task contrasts could be converted to effect size values without having to go back to the individual subjects. Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, January 26, 2017 5:33 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Standard error scales with sample size, standard deviation does not. Things like Z, t, and p all also scale with sample size and are measures of statistical significance via various transformations. Thus for a large group of subjects, Z and t will be very high and p will be very low. Z, t and p are thus all not bio
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Thank you again for the reply. Is there a way to access data that was produced but not packaged up? Thank you for your help, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Friday, January 27, 2017 3:21 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? It was produced, whether or not it was packaged up is a separate matter. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Friday, January 27, 2017 at 2:18 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Matt, Thanks for the reply. Did you mean that the pipelines produce group average effect size map and that these must be somewhere as part of the HCP public data; or were you referring to the individual subject effect size maps? Thanks, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Friday, January 27, 2017 3:01 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? I assume these are available somewhere because the pipelines produce them, but I didn’t make these group average results. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Friday, January 27, 2017 at 10:04 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Matt, Thank you again for your reply. I have been able to find cope1 files for single subject task contrasts (e.g. cope1 file for working memory contrasts of subject 996782), but not for the S900 group (e.g. I have not been able to find a cope1 file for the S900 group for working memory contrasts). I was wondering: a) Is there any task contrast effect size map available for the S900 group? (even if they are not optimally scaled) b) If not, would it be possible to generate a task contrast effect size map by using available S900 group data (e.g. the task contrasts zstat maps of the S900 group), or would it be necessary to go back to the data of each individual subject? c) If it is necessary to go back to the data of each individual subject, which approach would you suggest to combine all cope1 files of each subject of the S900 group into one effect size map of all subjects? Would something like normalizing the cope1 file of each subject (using wb_command as written below) and then averaging all normalized cope1 files work? Or would something as simple as averaging all cope1 files work? wb_command -cifti-reduce MEAN mean.dtseries.nii wb_command -cifti-reduce STDEV stdev.dtseries.nii wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -var mean mean.dtseries.nii -select 1 1 -repeat -var stdev stdev.dtseries.nii -select 1 1 -repeat Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, January 26, 2017 6:53 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? The files called cope1 or beta are an effect size measure, however the released versions are not optimally scaled (because of a non-optimal intensity bias field correction). We plan to correct this in the future. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Thursday, January 26, 2017 at 5:41 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Dear Michael and Matthew, Thank you very much for all your replies, your comments were extremely helpful. Xavier. From: Harms, Michael [mha...@wustl.edu] Sent: Monday, January 30, 2017 12:30 PM To: Elam, Jennifer; Glasser, Matthew; Xavier Guell Paradis; hcp-users@humanconnectome.org Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Hi, Just wanted to mention that I’m not promoting the computation of Cohen’s d effect size maps by dividing the z-stat maps by sqrt(N) as a “formal” solution. Since the z-stat are computed using ‘flameo’ and multi-level variance modeling, I think the “proper” way to compute Cohen’s d effect size maps would be from first principles — i.e., the mean (across subjects) divided by the std (across subjects), of the Level 2 copes. And even that might have some issues, due to the family structure (resulting in a underestimate of the std across subjects). We’ll give this some thought, and aim to include Cohen’s d effect size maps of the task contrasts as part of the group average maps for the S1200 release. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders 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: "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>> Date: Monday, January 30, 2017 at 11:21 AM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Posting this off-list thread about computing effect size task maps for the S900 from the group average zstat maps back to the list in case looking through it is of interest to other users. If the discussion continues, please include the list address in the responses so others can follow. Thanks, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> ____ From: Harms, Michael Sent: Sunday, January 29, 2017 10:39 PM To: Glasser, Matthew; Xavier Guell Paradis Cc: Burgess, Gregory; Elam, Jennifer Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Or perhaps, rather than showing p=0.05 as a contour, show the Cohen’s d = XX contour, to get away from the problem where, with 787 subjects, huge chunks of cortex will have p<0.05, even if the Cohen’s d effect size is tiny in many places. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders 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: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Saturday, January 28, 2017 at 1:50 PM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Significance is a quantification of “likelihood of truth” whereas effect size is a quantification of “importance.” With large numbers of subjects, the uncertainty of the measure diminishes and thus it can be considered “true” in the absence of confounds, but that does not say whether we should care about it or not. As Mike says, it is unclear that there is a threshold of effect size that is anything other than arbitrary (just as with significance we by convention set an arbitr
[HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters
Dear HCP experts, After using -cifti-find-clusters, is there a way to know the size of the clusters that the command has found? We know that the clusters will be larger than the specified volume-value-threshold, but is there a way to know the mm^3 or number of voxels of the clusters identified? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Dear Michael, Wouldn't using the cope files have the problem that "the released versions are not optimally scaled (because of a non-optimal intensity bias field correction)" (as written by Matthew before in this conversation)? Or would this not matter if Cohen's d were calculated from cope1 files? Thanks, Xavier. From: Harms, Michael [mha...@wustl.edu] Sent: Monday, January 30, 2017 12:30 PM To: Elam, Jennifer; Glasser, Matthew; Xavier Guell Paradis; hcp-users@humanconnectome.org Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Hi, Just wanted to mention that I’m not promoting the computation of Cohen’s d effect size maps by dividing the z-stat maps by sqrt(N) as a “formal” solution. Since the z-stat are computed using ‘flameo’ and multi-level variance modeling, I think the “proper” way to compute Cohen’s d effect size maps would be from first principles — i.e., the mean (across subjects) divided by the std (across subjects), of the Level 2 copes. And even that might have some issues, due to the family structure (resulting in a underestimate of the std across subjects). We’ll give this some thought, and aim to include Cohen’s d effect size maps of the task contrasts as part of the group average maps for the S1200 release. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders 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: "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>> Date: Monday, January 30, 2017 at 11:21 AM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Posting this off-list thread about computing effect size task maps for the S900 from the group average zstat maps back to the list in case looking through it is of interest to other users. If the discussion continues, please include the list address in the responses so others can follow. Thanks, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: Harms, Michael Sent: Sunday, January 29, 2017 10:39 PM To: Glasser, Matthew; Xavier Guell Paradis Cc: Burgess, Gregory; Elam, Jennifer Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Or perhaps, rather than showing p=0.05 as a contour, show the Cohen’s d = XX contour, to get away from the problem where, with 787 subjects, huge chunks of cortex will have p<0.05, even if the Cohen’s d effect size is tiny in many places. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders 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: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Saturday, January 28, 2017 at 1:50 PM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>> Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Significance is a quantification of “likelihood of truth” whereas effect size is a quantification of “importance.” With large numbers of subjects, the uncertainty of the measure diminishes and thus it can be considered “true” in the absence of confounds, but that does
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Hi Matthew, I am sorry, I didn't fully understand your previous message. Do you mean that the two steps that I mentioned in my last message are correct? Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Monday, January 30, 2017 7:22 PM To: Xavier Guell Paradis; Harms, Michael; Elam, Jennifer; hcp-users@humanconnectome.org Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Those are the level 2 copes. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, January 30, 2017 at 6:20 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Matthew, Thank you very much for the suggestion. To make sure that I understand this correctly; would this be the correct analysis?: 1st) Obtain a group cope1 file of the S900 group task contrasts (in a previous message, Michael said he could make this available from the S900 group task contrasts zstat maps: "I can make the equivalent “cope1” file from the Level 3 ‘flameo’ available via Box" 2nd) For each data point of the group cope1 file, calculate (x-mean)/SD. This gives a Cohen's d map. Is this correct? Thank you, Xavier. ________ From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Monday, January 30, 2017 6:51 PM To: Xavier Guell Paradis; Harms, Michael; Elam, Jennifer; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? No because the non-optimal scaling will divide out in the mean(cope)/std(cope) ratio. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, January 30, 2017 at 4:35 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Michael, Wouldn't using the cope files have the problem that "the released versions are not optimally scaled (because of a non-optimal intensity bias field correction)" (as written by Matthew before in this conversation)? Or would this not matter if Cohen's d were calculated from cope1 files? Thanks, Xavier. From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>] Sent: Monday, January 30, 2017 12:30 PM To: Elam, Jennifer; Glasser, Matthew; Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Hi, Just wanted to mention that I’m not promoting the computation of Cohen’s d effect size maps by dividing the z-stat maps by sqrt(N) as a “formal” solution. Since the z-stat are computed using ‘flameo’ and multi-level variance modeling, I think the “proper” way to compute Cohen’s d effect size maps would be from first principles — i.e., the mean (across subjects) divided by the std (across subjects), of the Level 2 copes. And even that might have some issues, due to the family structure (resulting in a underestimate of the std across subjects). We’ll give this some thought, and aim to include Cohen’s d effect size maps of the task contrasts as part of the group average maps for the S1200 release. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington U
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
I think this would be done from a level3 file; maybe I'm wrong. If I understand this correctly, the three steps below would give a Cohen's d map. Have I understood it right?: 1st) take this file: HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar.nii 2nd) transform this file into a cope1 file (Michael said he may be able to make this file available; "I can make the equivalent “cope1” file from the Level 3 ‘flameo’ available via Box") 3rd) in the cope1 file, do (x-mean)/SD for every data point Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Monday, January 30, 2017 7:26 PM To: Xavier Guell Paradis; Harms, Michael; Elam, Jennifer; hcp-users@humanconnectome.org Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? I assumed you were talking about level3 files. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, January 30, 2017 at 6:25 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Hi Matthew, I am sorry, I didn't fully understand your previous message. Do you mean that the two steps that I mentioned in my last message are correct? Thank you very much, Xavier. ________ From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Monday, January 30, 2017 7:22 PM To: Xavier Guell Paradis; Harms, Michael; Elam, Jennifer; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Those are the level 2 copes. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, January 30, 2017 at 6:20 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Burgess, Gregory" <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> Subject: RE: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear Matthew, Thank you very much for the suggestion. To make sure that I understand this correctly; would this be the correct analysis?: 1st) Obtain a group cope1 file of the S900 group task contrasts (in a previous message, Michael said he could make this available from the S900 group task contrasts zstat maps: "I can make the equivalent “cope1” file from the Level 3 ‘flameo’ available via Box" 2nd) For each data point of the group cope1 file, calculate (x-mean)/SD. This gives a Cohen's d map. Is this correct? Thank you, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Monday, January 30, 2017 6:51 PM To: Xavier Guell Paradis; Harms, Michael; Elam, Jennifer; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Burgess, Gregory Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? No because the non-optimal scaling will divide out in the mean(cope)/std(cope) ratio. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, January 30, 2017 at 4:35 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: "Burgess, Gregory" <gburg.
[HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Dear HCP team, I have seen that the zstat values for tasks contrasts are very large in the HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar.nii file, to the point that one can observe areas of activation in task contrasts by setting very high z value thresholds (e.g., a z threshold of +14). I think (please correct me if I'm wrong) that the z values of the S900 file are very large because the group is very large, therefore the standard deviation is very small (given that there will be less variability in a group if one takes a very large group of people rather than a small group of people), and if the standard deviation is very small then even small differences from the mean will lead to very large z values. I was wondering what implication does this have in terms of statistical significance. A z value of 14 or larger would correspond to an extremely small p value, i.e. it would be extremely unlikely to observe by chance a measure which is 14 times the standard deviation away from the mean. Would it therefore be correct to assume that the areas that we can observe in the S900 tfMRI_ALLTASKS task contrasts with a very high zstat threshold (e.g., 14) are statistically significant, without having to worry about multiple comparisons or family structure? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?
Dear Matt, Thank you very much for your very helpful reply. I will have to investigate this topic more, but is there any approach you would suggest to obtain effect size maps from the S900 group HCP data? I was wondering if the zstat data of the S900 group task contrasts could be converted to effect size values without having to go back to the individual subjects. Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Thursday, January 26, 2017 5:33 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Standard error scales with sample size, standard deviation does not. Things like Z, t, and p all also scale with sample size and are measures of statistical significance via various transformations. Thus for a large group of subjects, Z and t will be very high and p will be very low. Z, t and p are thus all not biologically interpretable, as their values also depend on the amount and quality of the data. In the limit with infinite amounts of data, the entire brain will be significant for any task, but wether a region is statistically significant tells us little about its importance functionally. Measures like appropriately scaled GLM regression betas, %BOLD change, or Cohen’s d are biologically interpretable measures of effect size because their values should not change as sample size and data amount go up (rather the uncertainty on their estimates goes down). Regions with a large effect size in a task are likely important to that task (and will probably also meet criteria for statistical significance given a reasonable amount of data). A common problem in neuroimaging studies is showing thresholded statistical significance maps rather than effect size maps (ideally unthresholded with an indication of which portions meet tests of statistical significance), and in general focusing on statistically significant blobs rather than the effect size in identifiable brain areas (which should often show stepwise changes in activity at their borders). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Thursday, January 26, 2017 at 3:46 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance? Dear HCP team, I have seen that the zstat values for tasks contrasts are very large in the HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar.nii file, to the point that one can observe areas of activation in task contrasts by setting very high z value thresholds (e.g., a z threshold of +14). I think (please correct me if I'm wrong) that the z values of the S900 file are very large because the group is very large, therefore the standard deviation is very small (given that there will be less variability in a group if one takes a very large group of people rather than a small group of people), and if the standard deviation is very small then even small differences from the mean will lead to very large z values. I was wondering what implication does this have in terms of statistical significance. A z value of 14 or larger would correspond to an extremely small p value, i.e. it would be extremely unlikely to observe by chance a measure which is 14 times the standard deviation away from the mean. Would it therefore be correct to assume that the areas that we can observe in the S900 tfMRI_ALLTASKS task contrasts with a very high zstat threshold (e.g., 14) are statistically significant, without having to worry about multiple comparisons or family structure? Thank you very much, Xavier. ___ 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] Expected date of 1,200 subjects release?
Dear Jenn, Thank you for your reply. Will this release include all level 2 and level 3 analyses, or only the preprocessed or raw data of the individual subjects? Thank you, Xavier. From: Elam, Jennifer [e...@wustl.edu] Sent: Saturday, February 11, 2017 1:12 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: Expected date of 1,200 subjects release? Hi Xavier, Look for it in the next week or two, barring any last minute issues. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu www.humanconnectome.org From: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Xavier Guell Paradis <xavie...@mit.edu> Sent: Saturday, February 11, 2017 9:07:07 AM To: hcp-users@humanconnectome.org Subject: [HCP-Users] Expected date of 1,200 subjects release? Dear HCP tema, Is there an expected date for the release of the 1,200 subjects data? Thank you very much, Xavier. ___ HCP-Users mailing list 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
Re: [HCP-Users] Edit colors of palette in wb view?
It worked, thank you very much! Xavier. From: hcp-users-boun...@humanconnectome.org [hcp-users-boun...@humanconnectome.org] on behalf of Harwell, John [jharw...@wustl.edu] Sent: Monday, February 13, 2017 3:38 PM To: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Edit colors of palette in wb view? Your file appears to be a NIFTI volume file. Use the command “wb_command -volume-label-import”. This command adds labels to the volume file’s header and creates a new NIFTI volume that is viewable in wb_view. On Feb 13, 2017, at 1:43 PM, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote: Dear John, My file is a cerebellum map: Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii. This file contains integers from 1 to 7 for the cerebellar structures. I have tried -cifti-label-import and -metric-label-import but they do not seem to work. Which wb command would you recommend? Thank you very much, Xavier. From: hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> [hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>] on behalf of Harwell, John [jharw...@wustl.edu<mailto:jharw...@wustl.edu>] Sent: Monday, February 13, 2017 1:07 PM To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: [HCP-Users] Edit colors of palette in wb view? Hello, You will need to convert your data to the CIFTI Label File format using “wb_command". A label table contains a group of labels and each label consists of a text name, RGB color components, and an integer value. When the data is displayed, coloring is performed by matching data values to the integer values in the label table. Without knowing the format of your data, I am unable to suggest the best “wb_command” for you to use but one of these may be useful: * wb_command -cifti-create-label * wb_command -cifti-label-import * wb_command -metric-label-import Related questions have been asked previously and these are links to them from the HCP user archives: * http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02286.html * http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01919.html * http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02548.html John Harwell From: hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Sent: Monday, February 13, 2017 11:05 AM To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: [HCP-Users] Edit colors of palette in wb view? Dear HCP experts, Is it possible to edit the colors of the palette in wb view? For example, is it possible to define color A, color B and color C and tell wb view to show values=1 in color A, values=2 in color B, values=3 in color C, etc.? Thank you very much, Xavier. ___ 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<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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Edit colors of palette in wb view?
Dear HCP experts, Is it possible to edit the colors of the palette in wb view? For example, is it possible to define color A, color B and color C and tell wb view to show values=1 in color A, values=2 in color B, values=3 in color C, etc.? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Edit colors of palette in wb view?
Dear John, My file is a cerebellum map: Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii. This file contains integers from 1 to 7 for the cerebellar structures. I have tried -cifti-label-import and -metric-label-import but they do not seem to work. Which wb command would you recommend? Thank you very much, Xavier. From: hcp-users-boun...@humanconnectome.org [hcp-users-boun...@humanconnectome.org] on behalf of Harwell, John [jharw...@wustl.edu] Sent: Monday, February 13, 2017 1:07 PM To: hcp-users@humanconnectome.org Subject: [HCP-Users] Edit colors of palette in wb view? Hello, You will need to convert your data to the CIFTI Label File format using “wb_command". A label table contains a group of labels and each label consists of a text name, RGB color components, and an integer value. When the data is displayed, coloring is performed by matching data values to the integer values in the label table. Without knowing the format of your data, I am unable to suggest the best “wb_command” for you to use but one of these may be useful: * wb_command -cifti-create-label * wb_command -cifti-label-import * wb_command -metric-label-import Related questions have been asked previously and these are links to them from the HCP user archives: * http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02286.html * http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01919.html * http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02548.html John Harwell From: hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Sent: Monday, February 13, 2017 11:05 AM To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: [HCP-Users] Edit colors of palette in wb view? Dear HCP experts, Is it possible to edit the colors of the palette in wb view? For example, is it possible to define color A, color B and color C and tell wb view to show values=1 in color A, values=2 in color B, values=3 in color C, etc.? Thank you very much, Xavier. ___ 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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] d maps from cope files: first merge and then demean, or first demean and then merge?
Dear HCP experts, I have been calculating group Cohen's d maps as follows: 1) -cifti-merge all level2 cope files of a task contrast 2) -cifti-reduce mean, -cifti-reduce stdev and -cifti-math mean/stdev Is this the correct order, or should I have demeaned each individual subject before using -cifti-merge? I am asking this because I read that "you should never temporally concatenate without first demeaning the individual timeseries" here: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00444.html Thank you, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Expected date of 1,200 subjects release?
Dear HCP tema, Is there an expected date for the release of the 1,200 subjects data? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Seed-based RS functional connectivity for individual subject
Dear HCP team, I am trying to calculate resting-state functional connectivity for subject 100307 using a seed in the right cerebral cortex that I have defined using a ROI metric file. I have tried the following -cifti-correlation code: /Applications/workbench/bin_macosx64/wb_command -cifti-correlation /Users/xavierguell/Desktop/MRIFILES/HCPDATA/100307REST/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii /Users/xavierguell/Desktop/MRIFILES/HCPDATA/100307REST/UCTconn1003072BKseed.dconn.nii -roi-override -right-roi /Users/xavierguell/Desktop/MRIFILES/HCPDATA/HCP_S900_GroupAvg_v1/UCTconn1003072BKROI.func.gii The output file (UCTconn1003072BKseed.dconn.nii) is generated and I can open the file in workbench view. However, the file in workbench view does not show color in any brain area. Also, workbench view crashes very frequently after loading the UCTconn1003072BKseed.dconn.nii file. I would be grateful if you could tell me whether there is something wrong in the code I wrote. Thank you very much, Xavier. Xavier Guell Paradis, M.D. Visiting Scientist Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xavie...@mit.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Problem downloading data: "Destination path directory does not exist (Code: 6)"
Dear HCP team, I am trying to download individual subject data (100307_3T_tfMRI_MOTOR_analysis and 100307_3T_tfMRI_WM_analysis). The following message appears in the Aspera Connect window: "Error: Destination path directory does not exist (Code: 6)". Is there any solution? Thank you very much, Xavier. Xavier Guell Paradis, M.D. Visiting Scientist Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xavie...@mit.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Continuous border drawing holding "alt/option" key does not work
Dear HCP team, I am using wb_view version 1.2.3. I have noticed that it is not possible to draw a continuous line by holding down the alt/option key and the left mouse button while dragging the mouse. Drawing a border is possible only by drawing multiple points. Is this a known issue, or am I doing something wrong in my computer? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Workbench tutorial data download: "No such file or directory"
Dear HCP team, When trying to download the "Connectome Workbench Tutorial Data" file (from this page https://db.humanconnectome.org/data/projects/HCP_900) I get the following error message in the Aspera Connect window: "Error: Server aborted session: No such file or directory (Code: 43)". The same thing happens when I try to download the "900 Subjects Group Average Data" or the "500 Subjects Group Average Data" or the "820 Subjects, MSM-All Registered, Dense Connectome". How could I solve this? Thank you very much, Xavier. Xavier Guell Paradis, M.D. Postdoctoral Fellow Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xavie...@mit.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Threshold p value in workbench view
I think I cannot access this link https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf ; the following message appears: "This shared file or folder link has been removed or is unavailable to you. ". Is there an alternative way to access the information in this link? As for this image (https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=sharing), wouldn't this show z values from 0 to 0.05 (instead of p values from 0 to 0.05) if the file I am using is the "tfMRI_ALLTASKS_level3_zstat1" file? I guess it is first necessary to convert z values to p values using the wb_command. Is this explained in the wustl.box link that you sent? Thank you, Xavier. From: Dierker, Donna [do...@wustl.edu] Sent: Wednesday, December 28, 2016 10:11 AM To: Xavier Guell Paradis Subject: Re: [HCP-Users] Threshold p value in workbench view Does this link work? https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=sharing > On Dec 27, 2016, at 5:04 PM, Dierker, Donna <do...@wustl.edu> wrote: > > See if you can read this link, Xavier: > > https://wustl.box.com/s/uuxn06pjlnn6ts7nhak0zww53l33fxzf > > People also use metric- or cifti-math to convert to log p or 1-p. Whatever > works for you. > > >> On Dec 27, 2016, at 10:39 AM, Xavier Guell Paradis <xavie...@mit.edu> wrote: >> >> Dear Sir or Madam, >> When viewing task contrasts in workbench (the file is >> HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMSulc.dscalar.nii), is >> there a way to threshold areas of activation for a given p value (e.g. areas >> that, in the task contrast, have achieved a p<0.001)? >> A previous post in this mailing list asked the same question (the post was >> called "thresholding the data to p-value"), but the person that replied to >> the email included a screen capture which is not available in the mail >> archive. Without that screen capture, I cannot understand how to threshold >> data using p values. >> >> Thank you very much, >> Xavier. >> >> >> Xavier Guell Paradis, M.D. >> Visiting Scientist >> Massachusetts Institute of Technology >> McGovern Institute for Brain Research >> Office: 46-4033A >> Phone: (617) 324-4355 >> Email: xavie...@mit.edu >> ___ >> HCP-Users mailing list >> 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 > https://drive.google.com/file/d/0B76s53K6sr4Qa0Z6MHB3OXRxbW8/view?usp=sharingnot > 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 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] Threshold p value in workbench view
Dear Sir or Madam, When viewing task contrasts in workbench (the file is HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMSulc.dscalar.nii), is there a way to threshold areas of activation for a given p value (e.g. areas that, in the task contrast, have achieved a p<0.001)? A previous post in this mailing list asked the same question (the post was called "thresholding the data to p-value"), but the person that replied to the email included a screen capture which is not available in the mail archive. Without that screen capture, I cannot understand how to threshold data using p values. Thank you very much, Xavier. Xavier Guell Paradis, M.D. Visiting Scientist Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xavie...@mit.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Number of twins in group of subjects: would this be considered "publishing restricted data"?
Dear HCP experts, If we reported in a publication the number of twins in a group of subjects, would this be considered "publishing restricted data"? (e.g., "800 subjects completed all tasks. This group included 100 pairs of twins") Thank you, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] saving one of the .dconn maps as a separate cifti?
This is very useful, thank you very much for the quick and very helpful reply! Xavier. From: Elam, Jennifer [e...@wustl.edu] Sent: Thursday, July 13, 2017 11:21 AM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] saving one of the .dconn maps as a separate cifti? Hi Xavier, When you have the .dconn file open in wb_view and have clicked on the desired seed location, click on the Connectivity tab in the Overlay Toolbox, then click the "Copy" button next to the loaded .dconn file listed. [https://outlook.office.com/owa/?realm=wustl.edu] Then go to File -> Save/Manage Files. Your map of the connectivity should be listed there as a .dscalar file with the Save checkbox already checked. Click Save Checked Files to save with the default name, or click on the gear button in the More column to set a new file name, then click Save Checked Files. Let me know if you'd like some screenshots-- I don't think they will come through on the list. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Xavier Guell Paradis <xavie...@mit.edu> Sent: Thursday, July 13, 2017 9:56 AM To: hcp-users@humanconnectome.org Subject: [HCP-Users] saving one of the .dconn maps as a separate cifti? Dear HCP experts, I have the 33GB .dconn file, have clicked in one place in the cerebral cortex and now I am seeing a connectivity map in the cerebral cortex and subcortical structures. The map is called "Row: 27597, Node Index: 30393, Structure: CORTEX_LEFT". Is it possible to access this map separately as an independent file, or to save this map that I am seeing as a separate cifti file? I have been playing with "Save/Manage files" but cannot figure it out. I thought I could try -cifti-separate and look for the file called "Row: 27597, Node Index: 30393, Structure: CORTEX_LEFT", but -cifti-separate seems to require a lot of processing memory. Thank you very much, Xavier. Xavier Guell Paradis, M.D. Research Fellow Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xavie...@mit.edu ___ HCP-Users mailing list 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] saving one of the .dconn maps as a separate cifti?
Dear HCP experts, I have the 33GB .dconn file, have clicked in one place in the cerebral cortex and now I am seeing a connectivity map in the cerebral cortex and subcortical structures. The map is called "Row: 27597, Node Index: 30393, Structure: CORTEX_LEFT". Is it possible to access this map separately as an independent file, or to save this map that I am seeing as a separate cifti file? I have been playing with "Save/Manage files" but cannot figure it out. I thought I could try -cifti-separate and look for the file called "Row: 27597, Node Index: 30393, Structure: CORTEX_LEFT", but -cifti-separate seems to require a lot of processing memory. Thank you very much, Xavier. Xavier Guell Paradis, M.D. Research Fellow Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xavie...@mit.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Convert a .dscalar.nii to multiple nifti files?
Thank you very much for the reply. The .dscalar.nii file that I am interesting in converting to multiple nifti files contains only cerebellar data, which is not surface information. Would there be any way of converting that to multiple nifti files? Thank you very much, Xavier. From: Harms, Michael [mha...@wustl.edu] Sent: Wednesday, July 05, 2017 12:02 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Convert a .dscalar.nii to multiple nifti files? Hi, You can’t represent the surface information in a .dscalar.nii via a nifti file. The -cifti-convert -to-nifti command exists for converting a CIFTI to a “fake”-NIFTI file for use in external tools/analyses that can be conducted on a per-grayordinate basis (i.e., without any regard to spatial information). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders 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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Wednesday, July 5, 2017 at 10:55 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Convert a .dscalar.nii to multiple nifti files? Dear HCP experts, Is it possible to convert a .dscalar.nii which contains 4 different maps to 4 different nifti files (one for each map)? I have tried -cifti-convert -to-nifti but the output was a very strange nifti file. Thank you very much, Xavier. ___ 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] How can I convert subcortical nifti files to dlabel files?
Dear HCP experts, I have several subcortical nifti files, each containing one cluster. I would like to convert them to dlabel files, so that then I can use wb_view to see the functional connectivity from each of these clusters (using your group .dconn file). How can I convert subcortical nifti files to dlabel files? I have been exploring several wb_commands but I cannot figure it out. Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?
Dear Matt, Thank you for your reply. I have realized that a very curious thing happens: - If I open the dlabel file and right-click the cluster in wb_view, I do not see any option - If I open the dscalar file and right-click the cluster in wb_view, I do not see any option - If I open the dlabel file AND the dscalar file and right-click the cluster in wb_view (note that the cluster is now present twice: in the dlabel file and in the dscalar file), I see the "Show Data/Time Series Graph" but not the "Show Cifti Connectivity" option. I opened wb_view multiple times to make sure that this is true: I only see the "Show Data/Time Series Graph" once I have opened both files; but I still do not see the "Show Cifti Connectivity" option. This is a strange pattern, but perhaps it is a clue to find out what I am doing wrong. An extra piece of information that might be useful: when I open the dlabel file, I can see it listed in the "Labels" list of the "Features ToolBox". Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Wednesday, August 09, 2017 2:13 PM To: Xavier Guell Paradis; NEUROSCIENCE tim Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files? It should work if you skip the last step and use the dlabel file. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Wednesday, August 9, 2017 at 9:43 AM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] How can I convert subcortical nifti files to dlabel files? Dear Tim and Matt, Thank you very much for your reply. I tried -volume-label-import, followed by -cifti-create-label, followed by -cifti-all-labels-to-rois. After this, when I right-click the cluster in wb_view, I see the option "Show Data/Time Series Graph For Parcel [my cluster]" but I do not see the option "Show Cifti Connectivity For Parcel [my cluster]" (even though I can see this option for other parcels, such as the Yeo map). I have been trying different things but cannot figure it out. Some extra information in case it is useful: My clusters are a group average registered to the HCP "S900_Average_T1w_restore.nii", so at this point I am not concerned about comparison across subjects. I would like to calculate functional connectivity from each of my subcortical clusters using your S900 .dconn file. My original nifti file with the right cerebellum cluster is called "mycluster.nii". I created the file "textforvolumelabelimport.txt" with the following text: CEREBELLUM_RIGHT 1 1 1 1 Then I did the following: wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt mycluster_label.nii wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume mycluster_label.nii mycluster_label.nii wb_command -cifti-all-labels-to-rois mycluster_labelStep2.dlabel.nii 1 mycluster_labelStep3.dscalar.nii When I right-click "mycluster_labelStep3.dscalar.nii" in wb_view, I can see the option of "Show Data/Time Series Graph" but not the option of "Show Cifti Connectivity". Thank you very much, Xavier. From: Timothy Coalson [tsc...@mst.edu<mailto:tsc...@mst.edu>] Sent: Tuesday, August 08, 2017 4:39 PM To: Xavier Guell Paradis Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files? I'm assuming you want them to match a standard grayordinate space, so that they can be compared across subjects. The simple way that doesn't account for residual subject differences in subcortical locations is to first resample the data to the appropriate resolution/orientation MNI space (222 for the 91k grayordinates), then use -cifti-create-dense-from-template with the -volume-all option. The better but more involved way is to take the subject's subcortical structure labels from freesurfer, import them to workbench format with the names that -cifti-create-label specifies, use -cifti-create-label to make a subject-specific cifti file (you will also need to provide some dummy surface data for the next step to work), and then use -cifti-resample to use only the same-structure-overlap information, and dilate to fill in any holes if desired. We use this second method for fMRI data in the pipelines, see here: https://github.com/Washington-University/Pipelines/blob/master/fMRISurface/scripts/SubcorticalProcessing.sh#L40 Though t
Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?
Dear Tim, Thank you for your reply I have made sure that I have the group .dconn file opened, and I can see that it is correctly opened because I can see connectivity when I click on any structure. However, I still have the same problem: I do not see the option of "Show Cifti Connectivity" when I right-click the cluster of the dlabel file I have created (however, I can see the dlabel file in the "Labels" list of the "Features Toolbox"). These are the steps I followed to create the dlabel file; I imagine I did something wrong in these steps but I cannot figure out what: My original nifti file with the right cerebellum cluster is called "mycluster.nii". I created the file "textforvolumelabelimport.txt" with the following text: CEREBELLUM_RIGHT 1 1 1 1 Then I did the following: wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt mycluster_label.nii wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume mycluster_label.nii mycluster_label.nii The resulting dlabel file is "mycluster_labelStep2.dlabel.nii" Thank you very much, Xavier. From: Timothy Coalson [tsc...@mst.edu] Sent: Wednesday, August 09, 2017 4:57 PM To: Xavier Guell Paradis Cc: Glasser, Matthew; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files? You need to have a dtseries (or dconn) file open before you can see any kind of connectivity. If you only have the labels/rois open, how do you expect it to figure out connectivity information? Note that we only have options for averaging things inside a label, the ROI file will not be useful in the GUI for this purpose. Tim On Wed, Aug 9, 2017 at 3:42 PM, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote: Dear Matt, Thank you for your reply. I have realized that a very curious thing happens: - If I open the dlabel file and right-click the cluster in wb_view, I do not see any option - If I open the dscalar file and right-click the cluster in wb_view, I do not see any option - If I open the dlabel file AND the dscalar file and right-click the cluster in wb_view (note that the cluster is now present twice: in the dlabel file and in the dscalar file), I see the "Show Data/Time Series Graph" but not the "Show Cifti Connectivity" option. I opened wb_view multiple times to make sure that this is true: I only see the "Show Data/Time Series Graph" once I have opened both files; but I still do not see the "Show Cifti Connectivity" option. This is a strange pattern, but perhaps it is a clue to find out what I am doing wrong. An extra piece of information that might be useful: when I open the dlabel file, I can see it listed in the "Labels" list of the "Features ToolBox". Thank you very much, Xavier. ________ From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Wednesday, August 09, 2017 2:13 PM To: Xavier Guell Paradis; NEUROSCIENCE tim Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files? It should work if you skip the last step and use the dlabel file. Peace, Matt. From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Wednesday, August 9, 2017 at 9:43 AM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] How can I convert subcortical nifti files to dlabel files? Dear Tim and Matt, Thank you very much for your reply. I tried -volume-label-import, followed by -cifti-create-label, followed by -cifti-all-labels-to-rois. After this, when I right-click the cluster in wb_view, I see the option "Show Data/Time Series Graph For Parcel [my cluster]" but I do not see the option "Show Cifti Connectivity For Parcel [my cluster]" (even though I can see this option for other parcels, such as the Yeo map). I have been trying different things but cannot figure it out. Some extra information in case it is useful: My clusters are a group average registered to the HCP "S900_Average_T1w_restore.nii", so at this point I am not concerned about comparison across subjects. I would like to calculate functional connectivity from each of my subcortical clusters using your S900 .dconn file. My original nifti file with the right cerebellum cluster is called "mycluster.nii". I created the file "textforvolumelabelimport.txt" with the following text: CEREBELLUM_RIGHT 1 1 1 1 Then
Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?
Dear Tim and Matt, Thank you very much for your reply. I tried -volume-label-import, followed by -cifti-create-label, followed by -cifti-all-labels-to-rois. After this, when I right-click the cluster in wb_view, I see the option "Show Data/Time Series Graph For Parcel [my cluster]" but I do not see the option "Show Cifti Connectivity For Parcel [my cluster]" (even though I can see this option for other parcels, such as the Yeo map). I have been trying different things but cannot figure it out. Some extra information in case it is useful: My clusters are a group average registered to the HCP "S900_Average_T1w_restore.nii", so at this point I am not concerned about comparison across subjects. I would like to calculate functional connectivity from each of my subcortical clusters using your S900 .dconn file. My original nifti file with the right cerebellum cluster is called "mycluster.nii". I created the file "textforvolumelabelimport.txt" with the following text: CEREBELLUM_RIGHT 1 1 1 1 Then I did the following: wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt mycluster_label.nii wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume mycluster_label.nii mycluster_label.nii wb_command -cifti-all-labels-to-rois mycluster_labelStep2.dlabel.nii 1 mycluster_labelStep3.dscalar.nii When I right-click "mycluster_labelStep3.dscalar.nii" in wb_view, I can see the option of "Show Data/Time Series Graph" but not the option of "Show Cifti Connectivity". Thank you very much, Xavier. From: Timothy Coalson [tsc...@mst.edu] Sent: Tuesday, August 08, 2017 4:39 PM To: Xavier Guell Paradis Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files? I'm assuming you want them to match a standard grayordinate space, so that they can be compared across subjects. The simple way that doesn't account for residual subject differences in subcortical locations is to first resample the data to the appropriate resolution/orientation MNI space (222 for the 91k grayordinates), then use -cifti-create-dense-from-template with the -volume-all option. The better but more involved way is to take the subject's subcortical structure labels from freesurfer, import them to workbench format with the names that -cifti-create-label specifies, use -cifti-create-label to make a subject-specific cifti file (you will also need to provide some dummy surface data for the next step to work), and then use -cifti-resample to use only the same-structure-overlap information, and dilate to fill in any holes if desired. We use this second method for fMRI data in the pipelines, see here: https://github.com/Washington-University/Pipelines/blob/master/fMRISurface/scripts/SubcorticalProcessing.sh#L40 Though that script actually only outputs a volume file, and therefore it doesn't bother with having surface data in those temporary cifti files. Tim On Tue, Aug 8, 2017 at 3:19 PM, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote: Dear HCP experts, I have several subcortical nifti files, each containing one cluster. I would like to convert them to dlabel files, so that then I can use wb_view to see the functional connectivity from each of these clusters (using your group .dconn file). How can I convert subcortical nifti files to dlabel files? I have been exploring several wb_commands but I cannot figure it out. Thank you very much, Xavier. ___ 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] modify dconn file so that it only includes cerebellum values?
Dear HCP experts,
I am trying to modify the group average dconn file
(HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it only
includes data from the cerebellum (even though, of course, these data will
correspond to the connectivity of each cerebellum voxel to the rest of the
brain).
I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile -vol-roi
cerebellumatlas.nii
("cerebellumatlas.nii" is a cerebellum volume atlas which contains values for
the cerebellum only)
This has not worked.
I have also tried to use the -cerebellum-roi option of
-cifti-restrict-dense-map, without writing any metric file after
-cerebellum-roi. This also doesn't work.
Is there any way to tell wb_command that I only want to keep the cerebellar
data, without having to include any file which indicates where the cerebellum
is?
Thank you very much,
Xavier.
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Re: [HCP-Users] modify dconn file so that it only includes cerebellum values?
Thank you very much!
From: Timothy Coalson [tsc...@mst.edu]
Sent: Friday, May 05, 2017 4:58 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] modify dconn file so that it only includes cerebellum
values?
The command to do this is -cifti-separate with the -volume option and -roi
suboption, and the CEREBELLUM_LEFT and CEREBELLUM_RIGHT structures (we don't
use the CEREBELLUM label in the volume, instead we split the hemispheres),
however, it always outputs the data from the requested structure also, so you
don't want to run it on a dconn (especially not for volume structures).
Instead, run it on any dscalar or small dtseries file you have lying around
that uses the same dense mapping (or use -cifti-reduce to make one from the
dconn). Alternatively, if you are using a standard grayordinate space, you can
extract the cerebellum halves from the volume label file in the Pipelines
repository that defines the grayordinate voxels, with -volume-label-to-roi,
like this:
wb_command -volume-label-to-roi
Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz
cerebellum_left_roi.nii.gz -name CEREBELLUM_LEFT
wb_command -volume-label-to-roi
Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz
cerebellum_right_roi.nii.gz -name CEREBELLUM_RIGHT
Since either way of getting these ROIs has the halves separate, you then need
to combine them with -volume-math:
wb_command -volume-math 'x || y' cerebellum_all_roi.nii.gz -var x
cerebellum_left_roi.nii.gz -var y cerebellum_right_roi.nii.gz
Tim
On Fri, May 5, 2017 at 3:42 PM, Xavier Guell Paradis
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:
Thank you for your reply.
Runing -cifti-restrict-dense-map again with ROW direction has worked; now I see
cerebellum data only. However, I think it would be "cleaner" to do as you
suggested and "get the ROI of where cerebellum data exists from the cifti
file". How could I do this?
Thank you very much,
Xavier.
From: Timothy Coalson [tsc...@mst.edu<mailto:tsc...@mst.edu>]
Sent: Friday, May 05, 2017 4:32 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] modify dconn file so that it only includes cerebellum
values?
On Fri, May 5, 2017 at 3:09 PM, Xavier Guell Paradis
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:
Dear HCP experts,
I am trying to modify the group average dconn file
(HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it only
includes data from the cerebellum (even though, of course, these data will
correspond to the connectivity of each cerebellum voxel to the rest of the
brain).
I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile -vol-roi
cerebellumatlas.nii
("cerebellumatlas.nii" is a cerebellum volume atlas which contains values for
the cerebellum only)
This has not worked.
That should work, but you need to run it again on the output of that, this time
with the ROW direction, so that both directions are cerebellum-only. Please be
more specific than "has not worked", did you get an error (and if so, copy the
error message), or did its output not match what you expected?
I have also tried to use the -cerebellum-roi option of
-cifti-restrict-dense-map, without writing any metric file after
-cerebellum-roi. This also doesn't work.
This should have caused an error, as the current grayordinates space doesn't
use surfaces for cerebellum. Additionally, if you don't provide a required
argument to an option, you will get a different kind of error.
Is there any way to tell wb_command that I only want to keep the cerebellar
data, without having to include any file which indicates where the cerebellum
is?
No, this isn't a use case we expected, normally we want to match existing cifti
mappings (for instance, 91k grayordinates), not make new ones. It is possible
to get the ROI of where cerebellum data exists from the cifti file, but since
you say you already have that ROI...on the other hand, if the specific error
you got was something like "volume space doesn't match", then you actually
should derive the ROI from the cifti file, rather than using whatever you have.
Thank you very much,
Xavier.
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Re: [HCP-Users] modify dconn file so that it only includes cerebellum values?
Thank you for your reply.
Runing -cifti-restrict-dense-map again with ROW direction has worked; now I see
cerebellum data only. However, I think it would be "cleaner" to do as you
suggested and "get the ROI of where cerebellum data exists from the cifti
file". How could I do this?
Thank you very much,
Xavier.
From: Timothy Coalson [tsc...@mst.edu]
Sent: Friday, May 05, 2017 4:32 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] modify dconn file so that it only includes cerebellum
values?
On Fri, May 5, 2017 at 3:09 PM, Xavier Guell Paradis
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:
Dear HCP experts,
I am trying to modify the group average dconn file
(HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it only
includes data from the cerebellum (even though, of course, these data will
correspond to the connectivity of each cerebellum voxel to the rest of the
brain).
I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile -vol-roi
cerebellumatlas.nii
("cerebellumatlas.nii" is a cerebellum volume atlas which contains values for
the cerebellum only)
This has not worked.
That should work, but you need to run it again on the output of that, this time
with the ROW direction, so that both directions are cerebellum-only. Please be
more specific than "has not worked", did you get an error (and if so, copy the
error message), or did its output not match what you expected?
I have also tried to use the -cerebellum-roi option of
-cifti-restrict-dense-map, without writing any metric file after
-cerebellum-roi. This also doesn't work.
This should have caused an error, as the current grayordinates space doesn't
use surfaces for cerebellum. Additionally, if you don't provide a required
argument to an option, you will get a different kind of error.
Is there any way to tell wb_command that I only want to keep the cerebellar
data, without having to include any file which indicates where the cerebellum
is?
No, this isn't a use case we expected, normally we want to match existing cifti
mappings (for instance, 91k grayordinates), not make new ones. It is possible
to get the ROI of where cerebellum data exists from the cifti file, but since
you say you already have that ROI...on the other hand, if the specific error
you got was something like "volume space doesn't match", then you actually
should derive the ROI from the cifti file, rather than using whatever you have.
Thank you very much,
Xavier.
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http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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[HCP-Users] merge multiple dtseries.nii into one dscalar.nii?
Dear HCP experts, Is there a way I can create a dscalar.nii file which contains four cope.dtseries.nii files as four different maps? I have been exploring different possibilities with wb_command but can't find the way to do it. Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] How to transform all subcortical values to 0 in a dscalar?
Dear HCP experts, I have a dscalar file with one map of cortical and subcortical data. I would like to transform all subcortical values to 0, and leave the cortical surface values intact. I have explored the -cifti-stats and -volume-stats options as well as -cifti-create-dense-scalar but cannot figure out a way to do this. Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] How to transform all subcortical values to 0 in a dscalar?
Dear Tim, Thank you for your reply. I wanted the subcortical data to be 0 so that it would not interfere with some math operations I wanted to perform using cortical data only, but I agree with your idea that this is not the optimal approach (plus the 0's would still affect some of the math operations). In the end I imported the dscalar file with python as a matrix, excluded all the rows that did not belong to cortical vertices, and then did the math operations. Thank you very much, Xavier. From: Timothy Coalson [tsc...@mst.edu] Sent: Wednesday, October 04, 2017 4:09 PM To: Xavier Guell Paradis Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How to transform all subcortical values to 0 in a dscalar? You can use -cifti-replace-structure with the -volume-all option and a volume file of zeroes. If you have a lot of maps (or you want to do something similar to a long dtseries), you can make a cifti file with 1's in the surfaces and 0's in voxels, and use -cifti-math to multiply them together. For a small dscalar file, I would do it like this: wb_command -cifti-separate COLUMN -volume-all volspacetemp.nii.gz -crop wb_command -volume-math '0' zerovol.nii.gz -var x volspacetemp.nii.gz cp data_subcort_zeroed.dscalar.nii wb_command -cifti-replace-structure data_subcort_zeroed.dscalar.nii COLUMN -volume-all zerovol.nii.gz -from-cropped I am curious, why do you want the subcortical data to be zero? It won't make the file smaller, and processing commands will still think there is data there, it won't interact with the surface data regardless of whether it is zero, and you can choose not to display the subcortical stuff anyway... Tim On Wed, Oct 4, 2017 at 10:07 AM, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote: Dear HCP experts, I have a dscalar file with one map of cortical and subcortical data. I would like to transform all subcortical values to 0, and leave the cortical surface values intact. I have explored the -cifti-stats and -volume-stats options as well as -cifti-create-dense-scalar but cannot figure out a way to do this. Thank you very much, Xavier. ___ 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] Table indicating location of clusters according to a dlabel file?
Dear HCP experts, I have a thresholded functional connectivity map (dscalar), and the dlabel files from the Glasser 2016 multimodal cortical parcellation. I was wondering whether there is a wb_command that would automatically generate a table indicating which labels overlap with my functional connectivity map. I have been exploring the wb_command index as well as the HCP mail archive and cannot find anything like this. Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Table indicating location of clusters according to a dlabel file?
Thank you Matt and Tim for the very useful comments! Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Thursday, September 07, 2017 5:25 PM To: NEUROSCIENCE tim; Xavier Guell Paradis Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Table indicating location of clusters according to a dlabel file? Right. Basically we are suspicious of defining areas based on statistical thresholds, as these are unlikely to reflect biological boundaries in the brain, but rather the vagaries of the statistical thresholding approach and the noise distribution. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Thursday, September 7, 2017 at 4:22 PM To: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Table indicating location of clusters according to a dlabel file? The commands in wb_command are designed for scripting flexibility, they each do a small, low-level operation, to be chained together to achieve various tasks. However, they mainly output data files, there isn't much for text output currently. You could use -cifti-parcellate to parcellate your cluster maps, and any parcel with a nonzero value therefore has some overlap - you can view this file on the surface and click on any nonzero patch to check what area it is. You can also dump those values to text with -cifti-convert -to-text. Running -file-information on the parcellated file or the dlabel file will give you the order of the parcel names. We aren't big fans of thresholding, and we would also consider parcellating the timeseries before running the statistics, if your question is "which of this parcellation's areas are significantly activated?". Tim On Thu, Sep 7, 2017 at 3:59 PM, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote: Dear HCP experts, I have a thresholded functional connectivity map (dscalar), and the dlabel files from the Glasser 2016 multimodal cortical parcellation. I was wondering whether there is a wb_command that would automatically generate a table indicating which labels overlap with my functional connectivity map. I have been exploring the wb_command index as well as the HCP mail archive and cannot find anything like this. Thank you very much, Xavier. ___ 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<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
Re: [HCP-Users] Resampling freesurfer-HCP
I thought it might be useful to add that the initial .w file is thresholded and does not contain values for all cerebral cortical regions. Thank you very much, Xavier. From: hcp-users-boun...@humanconnectome.org [hcp-users-boun...@humanconnectome.org] on behalf of Xavier Guell Paradis [xavie...@mit.edu] Sent: Tuesday, September 12, 2017 2:05 PM To: hcp-users@humanconnectome.org Subject: [HCP-Users] Resampling freesurfer-HCP Dear HCP experts, I have an overlay freesurfer file (format is .w) which corresponds to a task activity surface map (group result). I have one .w file for each cerebral hemisphere. I would like to visualize these maps using wb_view, and have tried to follow the instructions you published (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?). As a first step I would need to convert the .w files into .func.gii files using mris_convert. Then I would use wb_command -metric-resample, as indicated in your instructions. This does not seem to work with my .w file: 1) mris_convert myfile.w myfile.func.gii This generates myfile.func.gii, but when I use wb_command -metric-resample I get the following error: ERROR: Parse error while reading: error occurred while parsing element, line number: 1 column number: 1 2) As an alternative approach, I opened myfile.w using Tksurfer and saved the overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then I do the following: mris_convert myfile.mgh myfile.func.gii This generates the myfile.func.gii file, but when I use wb_command -metric-resample with this file I get a different error: ERROR: All data arrays (columns) in the file must have the same number of rows. The first array (column) contains 163842 rows. Array 2 contains 327680 rows. Thank you very much for your help, Xavier. ___ HCP-Users mailing list 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] Resampling freesurfer-HCP
Dear HCP experts, I have an overlay freesurfer file (format is .w) which corresponds to a task activity surface map (group result). I have one .w file for each cerebral hemisphere. I would like to visualize these maps using wb_view, and have tried to follow the instructions you published (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?). As a first step I would need to convert the .w files into .func.gii files using mris_convert. Then I would use wb_command -metric-resample, as indicated in your instructions. This does not seem to work with my .w file: 1) mris_convert myfile.w myfile.func.gii This generates myfile.func.gii, but when I use wb_command -metric-resample I get the following error: ERROR: Parse error while reading: error occurred while parsing element, line number: 1 column number: 1 2) As an alternative approach, I opened myfile.w using Tksurfer and saved the overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then I do the following: mris_convert myfile.mgh myfile.func.gii This generates the myfile.func.gii file, but when I use wb_command -metric-resample with this file I get a different error: ERROR: All data arrays (columns) in the file must have the same number of rows. The first array (column) contains 163842 rows. Array 2 contains 327680 rows. Thank you very much for your help, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Calculate resting-state correlation (r or fisher-z) between two ROIs
Dear HCP experts, I have three subcortical ROIs (three dlabel files). I would like to obtain a correlation value (r, or fisher z) of the resting-state time course between each pair or ROIs (e.g. three r values, one for each pair: "ROI_1-ROI_2", "ROI_1-ROI_3" and "ROI_2-ROI_3"). I would like to use your group average dconn file for this calculation. I have been reading the instructions of many wb_commands but cannot figure out how to do this. I have already saved three Fisher-z maps which correspond to the resting-state correlations from each of the three ROIs (using your group dconn file). Perhaps the most simple solution would be to average the values in these maps: e.g. take the correlation map from ROI_1 and average the values of all the voxels in ROI_2 and in ROI_3 (so that I would obtain two z values, corresponding to the "ROI_1-ROI_2" and "ROI_1-ROI_3" pairs). How could I do this? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Show outline of dscalar map at a given threshold?
Thank you very much, it works! Xavier. From: Timothy Coalson [tsc...@mst.edu] Sent: Monday, November 27, 2017 7:39 PM To: Xavier Guell Paradis Cc: Glasser, Matthew; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Show outline of dscalar map at a given threshold? First, use -cifti-math to do the thresholding you want (if you have negative p-values for deactivations, you could add something like " + 2 * ((x < 0) && (x > -0.05))"): $ wb_command -cifti-math '(x > 0) && (x < 0.05)' above_thresh.dscalar.nii -var x Then, import it as a label file (this basic version will give a random color and the name "LABEL_1", read the command help for how to assign colors and names): $ wb_command -cifti-label-import above_thresh.dscalar.nii "" above_thresh.dlabel.nii Then when displaying this file on top of something (we recommend a beta map), you can click the wrench for the dlabel layer, go to the "Labels" tab, and change the drawing type from "filled" to "outline color" or "outline label color". Tim On Mon, Nov 27, 2017 at 6:24 PM, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote: Thank you very much for your reply. I have a map of surface cerebral cortical p values in a dscalar file, and would like to create a dlabel file corresponding to the values between 0 and 0.05 so that I can display this as an outline. I have not been successful when trying to create this dlabel file from my dscalar file using wb_command. Is there a succession of commands that you would recommend to achieve this? Thank you very much for your help, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Monday, November 27, 2017 4:01 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Show outline of dscalar map at a given threshold? You can create a .dlabel.nii of the above threshold vertices and then display this as an outline. There isn’t a way of doing this directly on a .dscalar.nii. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, November 27, 2017 at 2:29 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Show outline of dscalar map at a given threshold? Dear HCP experts, I was wondering if there is a way to show the outline of a dscalar map at a given threshold in workbench view. For example, I may have dscalar file with z values for the cerebral cortical surface, and may want to show only the outline of clusters corresponding to z>4 in that dscalar file. I have been exploring the options in workbench view and the mail archive and could not find a way to do this. I thought of playing with the thresholds (e.g. low threshold=4, high threshold=4.5, show data inside thresholds), but of course this only generates an ugly, uneven outline of the z>4 clusters. Thank you very much, Xavier. ___ 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<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
Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?
Dear Michael and Matt, Thank you very much for your reply. As for Michael's question - yes, I am looking for a dlabel file that includes volumes such as caudate and putamen as separate structures. Perhaps there is a workbench command that would allow to isolate these structures in a random MNINonLinear dscalar file? I have been exploring -cifti-restrict-dense-map and -cifti-create-dense-scalar but have not figured it out. I have also tried using python's nibabel and numpy tools to isolate the rows corresponding to each structure, but this seems to be a much more complicated route. Thank you very much for your help, Xavier. From: Harms, Michael [mha...@wustl.edu] Sent: Tuesday, November 21, 2017 7:29 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz? Hi, The subcortical structures are already defined in the standard CIFTI space. Are you just looking for a dlabel file that includes those subcortical labels? Cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders 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: <hcp-users-boun...@humanconnectome.org> on behalf of Xavier Guell Paradis <xavie...@mit.edu> Date: Tuesday, November 21, 2017 at 5:23 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz? Dear HCP experts, I was wondering if there is a publicly available, basic subcortical parcellation (deliniating structures such as caudate and putamen) of the standard volume structural file of HCP (such as S900_AverageT1w_restore.nii.gz). Restated, is there a parcellation that deliniates structures such as caudate and putamen in S900_AverageT1w_restore.nii.gz? Thank you very much, Xavier. ___ HCP-Users mailing list 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] Show outline of dscalar map at a given threshold?
Thank you very much for your reply. I have a map of surface cerebral cortical p values in a dscalar file, and would like to create a dlabel file corresponding to the values between 0 and 0.05 so that I can display this as an outline. I have not been successful when trying to create this dlabel file from my dscalar file using wb_command. Is there a succession of commands that you would recommend to achieve this? Thank you very much for your help, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Monday, November 27, 2017 4:01 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Show outline of dscalar map at a given threshold? You can create a .dlabel.nii of the above threshold vertices and then display this as an outline. There isn’t a way of doing this directly on a .dscalar.nii. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, November 27, 2017 at 2:29 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Show outline of dscalar map at a given threshold? Dear HCP experts, I was wondering if there is a way to show the outline of a dscalar map at a given threshold in workbench view. For example, I may have dscalar file with z values for the cerebral cortical surface, and may want to show only the outline of clusters corresponding to z>4 in that dscalar file. I have been exploring the options in workbench view and the mail archive and could not find a way to do this. I thought of playing with the thresholds (e.g. low threshold=4, high threshold=4.5, show data inside thresholds), but of course this only generates an ugly, uneven outline of the z>4 clusters. Thank you very much, Xavier. ___ 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] -cifti-separate converts from dscalar to nifti: is it possible to generate one nifti from each dscalar map?
Dear HCP experts, I have a dscalar file with 4 maps and would like to convert each map into one separate nifti file. I am not worried about the problem of surface information in a nifti file, because I am interested in subcortical data only. I have been able to transform the dscalar into a nifti file using this: wb_command -cifti-separate input.dscalar.nii COLUMN -volume-all output.nii The output.nii is a nifti file which contains 4 maps if I open it with wb_view. Is there a way to generate 4 separate nifti files (one for each map) instead of one single nifti file with all 4 maps? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it possible to generate one nifti from each dscalar map?
It works, thank you! The steps have been -cifti-separate to convert from dscalar (multiple maps) to nifti (multiple maps), and -volume-merge to divide the nifti file in separate maps. Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Tuesday, December 12, 2017 7:37 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it possible to generate one nifti from each dscalar map? wb_command -volume-merge allows you to select specific maps despite its name. It contains functionality similar to both fslmerge and bfslroi. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Tuesday, December 12, 2017 at 6:35 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it possible to generate one nifti from each dscalar map? Dear HCP experts, I have a dscalar file with 4 maps and would like to convert each map into one separate nifti file. I am not worried about the problem of surface information in a nifti file, because I am interested in subcortical data only. I have been able to transform the dscalar into a nifti file using this: wb_command -cifti-separate input.dscalar.nii COLUMN -volume-all output.nii The output.nii is a nifti file which contains 4 maps if I open it with wb_view. Is there a way to generate 4 separate nifti files (one for each map) instead of one single nifti file with all 4 maps? Thank you very much, Xavier. ___ 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] Subcortical atlas of S900_AverageT1w_restore.nii.gz?
Dear HCP experts, I was wondering if there is a publicly available, basic subcortical parcellation (deliniating structures such as caudate and putamen) of the standard volume structural file of HCP (such as S900_AverageT1w_restore.nii.gz). Restated, is there a parcellation that deliniates structures such as caudate and putamen in S900_AverageT1w_restore.nii.gz? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Is it possible to download HCP data using ascp (the command line version of aspera)?
Dear HCP experts, Is it possible to download HCP data using ascp (the command line version of aspera)? If so, is there a list of [[user@]host:]PATH for each download package of HCP data? (We would like to download the 100 unrelated resting state compact package to an online cluster, and the aspera GUI does not seem to work after installing aspera's .sh file in the cluster). Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Convert dlabel to dscalar
Dear HCP experts, I have a dlabel file that labels a particular nucleus of the left thalamus (thalamusnucleus.dlabel.nii). I would like to convert this dlabel file to a whole-brain dscalar file, so that this nucleus in the left thalamus has a value of 1 and the rest of the brain has a value of 0. I have tried the following 4 things which have not worked: 1) wb_command -cifti-create-dense-from-template template.dscalar.nii thalamusnucleus.dscalar.nii -label THALAMUS_LEFT thalamusnucleus.dlabel.nii "template.dscalar.nii" is a random dscalar file with 1 map that includes data for the whole brain. I get this error: ERROR: Parse error while reading: error occurred while parsing element, line number: 1 column number: 1 File: thalamusnucleus.dlabel.nii 2) The option -volume (instead of -label) gives the error "volume file 'thalamusnucleus.dlabel.nii' does not match volume space of template cifti file" 3) The option -cifti (instead of -label) gives the error "cifti file 'thalamusnucleus.dlabel.nii' uses a different volume space than the template file". 4) wb_command -cifti-label-to-roi thalamusnucleus.dlabel.nii thalamusnucleus.dscalar.nii -key 1 This generates a dscalar file, but when I open this file with nibabel in python I only see 111 data points (which is not the whole brain; note that what I would like to obtain is a dscalar with "1" values in my left thalamus nucleus and "0" values in the rest of the brain). Is there a better way to do this? Thank you, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Restrict dscalar to only CORTEX_LEFT+CORTEX_RIGHT
Dear HCP experts, I have a dscalar file (myfile.dscalar.nii), and I would like to restrict this file so that it only contains data for CORTEX_LEFT and CORTEX_RIGHT. If I do this right, CORTEX_LEFT and CORTEX_RIGHT should be a total number of 59412 data points. I have tried this, which has not worked: -cifti-separate myfile.dscalar.nii COLUMN -metric CORTEX_LEFT myfile_onlycortexleft.func.gii -cifti-separate myfile.dscalar.nii COLUMN -metric CORTEX_RIGHT myfile_onlycortexright.func.gii -cifti-create-dense-scalar myfile_leftandrightcortex.dscalar.nii -left-metric myfile_onlycortexleft.func.gii -right-metric myfile_onlycortexright.func.gii However, when I open the file myfile_leftandrightcortex.dscalar.nii with Python, it has 64984 data points instead of 59412 (it should have 59412 if it truly only has data points for CORTEX_LEFT and CORTEX_RIGHT). Is there another way to do this? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] AWS sync error
Hello HCP, We are a team of researchers designing some deep learning tools we have created for modality conversions, and wanting to test our library on the HCP dataset (structural T1 and T2). We are having issues copying from the s3 bucket. Currently after creating our credentials, running aws configure, and attempting to sync via: $aws configure [entering access credentials] $aws s3 sync s3://hcp-openaccess-temp . Ïnvalid Access Key ID¨AWS key does not exist in the records. We appreciate any recommendations on how to proceed. Thank you, Patrick, Xavier, TJ, Anita, Shreyas, Saige. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Is surface myelin map the same as the volume T1w/T2 map?
Thank you for your reply. I would like to obtain a bias field corrected version of S1200_AverageT1wDividedByT2w.nii. After reading the Minimal Preprocessing Pipelines 2013 paper, I thought I could average all the individual estimated residual field bias files, and subtract that from S1200_AverageT1wDividedByT2w.nii. 1 - Is this approach correct? 2 - If so, are these the files from each individual I should average: /$subject_ID/MNINonLinear/BiasField.nii.gz? 3 - Alternatively, does a S1200 average estimated residual field bias file already exist? 4 - If this method is not correct, is there a different method you would recommend? Thank you very much, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Monday, March 05, 2018 7:11 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Is surface myelin map the same as the volume T1w/T2 map? No that would be without _BC and I don’t know what the 2mmResample is. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> Date: Monday, March 5, 2018 at 4:57 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Is surface myelin map the same as the volume T1w/T2 map? Dear HCP experts, Is S1200.All.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii calculated in the same way as the S1200_AverageT1wDividedByT2w_2mmResample.nii, with the only difference that one file is surface and the other is volume? Thank you very much, Xavier. ___ 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] Downloading with Aspera: "Error: No such file or directory (Code: 4)"
Dear HCP experts, When trying to download the "structural preprocessed" data from a single subject I get the following error in Aspera: "Error: No such file or directory (Code: 4)". I have made sure that the folder I am downloading the data to exists. How could I solve this? Thank you, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Is surface myelin map the same as the volume T1w/T2 map?
Dear HCP experts, Is S1200.All.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii calculated in the same way as the S1200_AverageT1wDividedByT2w_2mmResample.nii, with the only difference that one file is surface and the other is volume? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?
Dear HCP experts, I am interested in analyzing your group-averaged subcortical volumetric data. My understanding is that your volumetric data is registered to MNI space. I was wondering if you could let me know what specific MNI template you used. I am especially interested in knowing whether it is a symmetric or an asymmetric MNI template. Thank you, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?
This means that the template is asymmetric, not symmetric, correct? Thanks, Xavier. On Fri, Apr 5, 2019 at 5:48 PM Glasser, Matthew wrote: > FSL’s MNI152. > > Matt. > > From: on behalf of Xavier Guell > Paradis > Date: Friday, April 5, 2019 at 4:46 PM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] Volumetric subcortical group-averaged data: what is > the exact MNI template you used? > > Dear HCP experts, > I am interested in analyzing your group-averaged subcortical volumetric > data. My understanding is that your volumetric data is registered to MNI > space. I was wondering if you could let me know what specific MNI template > you used. I am especially interested in knowing whether it is a symmetric > or an asymmetric MNI template. > Thank you, > Xavier. > > ___ > HCP-Users mailing list > 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
