Is this a question about the main HCP pipelines or the MEG pipelines? Matt.
On 8/5/16, 12:24 PM, "[email protected] on behalf of Demiral, Sukru (NIH/NIAAA) [F]" <[email protected] on behalf of [email protected]> wrote: > >Hi all, > >I have two questions related to anatomy pipeline. There are a number of >wmparc and aseg files in the output of the anatomy pipeline. Is there a >description of which processes these wmparc files went through? I >understand that some are normalized to the standard brain and some are >intensity normalized, I am a bit confused. I just need to use original >anatomical space wmparc. Same thing for the aseg results. If anyone can >drop a line or point a documentation that would be great. Thanks, > >Baris >-----Original Message----- >From: [email protected] >[mailto:[email protected]] >Sent: Friday, August 05, 2016 1:00 PM >To: [email protected] >Subject: HCP-Users Digest, Vol 45, Issue 5 > >Send HCP-Users mailing list submissions to >[email protected] > >To subscribe or unsubscribe via the World Wide Web, visit >http://lists.humanconnectome.org/mailman/listinfo/hcp-users >or, via email, send a message with subject or body 'help' to >[email protected] > >You can reach the person managing the list at >[email protected] > >When replying, please edit your Subject line so it is more specific than >"Re: Contents of HCP-Users digest..." > > >Today's Topics: > > 1. Re: Movement Confounds and Censoring (Michael F.W. Dreyfuss) > 2. Re: Extracting Power parcellations from > RSN-networks.32k_fs_LR (Timothy Coalson) > 3. Re: Movement Confounds and Censoring (Glasser, Matthew) > 4. Re: Movement Confounds and Censoring (Glasser, Matthew) > 5. Re: Extracting Power parcellations from > RSN-networks.32k_fs_LR (Salim Arslan) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 4 Aug 2016 23:15:30 +0000 >From: "Michael F.W. Dreyfuss" <[email protected]> >Subject: Re: [HCP-Users] Movement Confounds and Censoring >To: "Burgess, Gregory" <[email protected]> >Cc: "[email protected]" <[email protected]> >Message-ID: ><dm5pr06mb2713c8694ae7bc2c4b283d34fc...@dm5pr06mb2713.namprd06.prod.outlo >ok.com> > >Content-Type: text/plain; charset="windows-1252" > >Thank you. On a practical note, if I want to include both motion >regressors and time points censoring with a censor file I produce for >each run how can I do that? I am refering specifically to the following >chunk of code: > > >#Create design files, model confounds if desired > >DIR=`pwd` > >cd ${FEATDir} > >if [ $Confound = "NONE" ] ; then > > feat_model ${FEATDir}/design > >else > > feat_model ${FEATDir}/design >${ResultsFolder}/${LevelOnefMRIName}/${Confound} > >fi > >cd $DIR > > >When I change that to the code below including another argument for >thecensor file, the result is the same as if I added no confound (it >ignores both arguments): > > >feat_model ${FEATDir}/design >${ResultsFolder}/${LevelOnefMRIName}/${Confound} >${ResultsFolder}/${LevelOnefMRIName}/censor.txt > > >How can I include both motion regression and censoring files in the >design files using feat_model or another command? > > >Thank you, > >Michael > >________________________________ >From: Burgess, Gregory <[email protected]> >Sent: Thursday, August 4, 2016 10:35:33 AM >To: Michael F.W. Dreyfuss >Cc: [email protected] >Subject: Re: [HCP-Users] Movement Confounds and Censoring > >> On Aug 4, 2016, at 8:52 AM, Michael F.W. Dreyfuss >><[email protected]> wrote: >> >> Thank you, >> >> Is it recommended to use the motion regressors with or without >>detrending on data that has been processed with the HCP preprocessing >>scripts? > >You should perform the same filtering on your confound regressors (and >task model) that you are performing on your data. So, I?d start with the >original Movement_Regressors.txt. > > >> Is there a recommended cutoff for censoring time points or a >>recommended threshold of mean relative displacement for excluding a >>subject or run? > >One of the interesting difficulties with HCP data (and occasionally other >MB fMRI data from other groups) is that motion parameters from MB data >pick up on some source of variability that is not typically visible in >motion parameters estimated from fMRI data with lower spatial and >temporal resolution. So, censoring thresholds that are typical in lower >resolution fMRI might result in censoring a considerable proportion of >your data. You might want to look at DVARS to see if it can detect >apparent motion artifact more cleanly. > >Either way, the best strategy is to look at your data to set your own >threshold. (Look at strategies from Power, J. D., Mitra, A., Laumann, T. >O., Snyder, A. Z., Schlaggar, B. L., & Petersen, S. E. (2014). Methods to >detect, characterize, and remove motion artifact in resting state fMRI. >NeuroImage, 84, 320?341. >https://urldefense.proofpoint.com/v2/url?u=http-3A__doi.org_10.1016_j.neur >oimage.2013.08.048&d=DQIF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s& >r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=rA5E466xAGA4eFveDcDcOazqcX >IKVYINMcieo_qUh1o&s=W83s5PHORheYaI8ov_xC8VSiKFk3nw9qHj8Q2IvgnNg&e= ) > > >> I installed FIX and can implement it on my data, but I can only have it >>trained to data from your scanners at Wash U since I do not have enough >>additional data from our scanner here to train it on, so I do not feel >>comfortable using it on my data. > >You could consider hand categorizing the ICA components, if you feel >comfortable making those judgments and you don?t have tons of data. There >are also some other automated approaches such as AROMA that have become >popular with folks. I have no experience with AROMA yet, but I?d imagine >that it would rate spike-like ICA components as noise. > > >--Greg > >____________________________________________________________________ >Greg Burgess, Ph.D. >Staff Scientist, Human Connectome Project Washington University School of >Medicine Department of Psychiatry >Phone: 314-362-7864 >Email: [email protected] > >> >> Thank you, >> Michael >> From: Burgess, Gregory <[email protected]> >> Sent: Tuesday, August 2, 2016 2:30:10 PM >> To: Michael F.W. Dreyfuss >> Cc: [email protected] >> Subject: Re: [HCP-Users] Movement Confounds and Censoring >> >> > On Aug 2, 2016, at 10:17 AM, Michael F.W. Dreyfuss >><[email protected]> wrote: >> >> > >> >> > Hi, I have some basic questions about the movement parameters that >>are put out by the HCP preprocessing scripts. >> >> > >> >> > 1) What is the difference between Movement_Regressors_dt.txt and >>Movement_Regressors.txt? I would like to use one as a confound. >> >> >> >> The Movement_Regressors.txt are the parameters computed from the motion >>correction algorithm. The Movement_Regressors_dt.txt is the same file >>put through a detrend command to remove the linear trend and mean. >> >> >> >> > >> >> > 2) What does each column in these represent? I'm assuming 6 >>directions of displacement, and 3 for rotation? >> >> >> >> The 12 columns represent Displacement {x, y, z}, Rotation {x, y, z}, >> Backward Derivative of Displacement {x, y, z}, and Backward Derivative >> of Rotation {x, y, z} >> >> >> >> > >> >> > 3) What are the units in these and the other movement files in the >>output? mm? voxels? >> >> >> >> The units are mm for displacements and degrees for rotations. >> >> >> >> > >> >> > 4) I would like to censor time points with too much motion in >>Movement_AbsoluteRMS.txt. Is there a specific movement cutoff you >>recommend? I have made a script that produces a censor file in the fsl >>format (i.e. columns of all 0s with a 1 at the time point that is >>censored). Is there a simple way to add that censor file into the >>existing analysis scripts along with the motion as a confound? >> >> >> >> First, I would suggest using the Movement_RelativeRMS.txt file for >>censoring instead. The AbsoluteRMS reflects the total movement from the >>motion correlation registration target, which is the SBRef volume >>collected at the beginning of the scan. In contrast, the RelativeRMS >>reflects the amount of motion from the previous time point, which should >>be considered a more direct measurement of movement on that specific >>time point. >> >> >> >> I?m not sure to which existing analysis scripts you are referring. We >>don?t release analyses of individual scans. So, you should probably >>include these censoring confounds as covariates in whatever >>preprocessing you?re doing for the individual scans. >> >> >> >> After saying all of that, it is worth mentioning that FIX denoising: >> >> - Regresses a set of 24 motion parameters (six rigid body parameters, >> their backward derivatives, and the squares of those 12 columns) >> >> - Regresses noise component variance (orthogonal to signal components) >>from the scan-level ICA. >> >> >> >> In practice, the behavior of FIX is similar to regressing movement >>paremeters and voxel-specific censoring (plus other artifact cleanup). >>If you utilize FIX preprocessed data, you don?t need to regress motion >>parameters, and you might feel comfortable skipping censoring as well. >> >> >> >> --Greg >> >> >> >> ____________________________________________________________________ >> >> Greg Burgess, Ph.D. >> >> Staff Scientist, Human Connectome Project >> >> Washington University School of Medicine >> >> Department of Psychiatry >> >> Phone: 314-362-7864 >> >> Email: [email protected] >> >> >> >> >> >> > >> >> > Thank you, >> >> > Michael >> >> > _______________________________________________ >> >> > HCP-Users mailing list >> >> > [email protected] >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconne >> > ctome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb62iw4YL4RFalcE2h >> > QUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYF >> > Swg&m=FMg6DAhRQHwDPdwDze2CIg4j1-kMkVc9h-XJ0PXmDWQ&s=ck-KAIP80cxbdHtG >> > 0fMXtiT8T_-4QzuQ-lNVQlPrDs8&e= >> >> >> >> >> >> >> >> >> >> ________________________________ >> >> 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. >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160804/ >032a7110/attachment-0001.html > >------------------------------ > >Message: 2 >Date: Thu, 4 Aug 2016 18:46:14 -0500 >From: Timothy Coalson <[email protected]> >Subject: Re: [HCP-Users] Extracting Power parcellations from >RSN-networks.32k_fs_LR >To: Salim Arslan <[email protected]> >Cc: "[email protected]" <[email protected]> >Message-ID: ><CAK_=taz7ftv6uk3_59io7ugbdlzzmu_c_f1x+ngbprc_ty6...@mail.gmail.com> >Content-Type: text/plain; charset="utf-8" > >Using -cifti-separate on the original cifti file and viewing in wb_view >looks identical to the original. However, I think I see what is going >on, after getting a hint from the way you reset the color scheme - the >file has >2 labels named "a3_Default_mode", and similar for other labels, and >turning one of them off reveals these holes. > >What has happened is that someone has set the names and colors of two >label values to be identical (except for a space on the end of one, to >slip past the uniqueness tests on the label names), but they are actually >different integers in those patches. I don't know how this happened, as >map 4 doesn't have this difference in values. We should probably fix >this in the data file. > >Tim > > >On Thu, Aug 4, 2016 at 3:44 AM, Salim Arslan <[email protected]> >wrote: > >> Hi Tim, >> >> Thanks for your attention. >> >> After your message, I also thought the problem was about the order of >> the hemisphere in the cifti file. However, after running wb_command >> -file-information -no-map-info I can confirm that the order is correct. >> Here is the output: >> >> Name: RSN-networks.32k_fs_LR.dlabel.nii >> Type: Connectivity - Dense Label >> Structure: CortexLeft CortexRight >> Data Size: 1.04 Megabytes >> Maps to Surface: true >> Maps to Volume: false >> Maps with LabelTable: true >> Maps with Palette: false >> Number of Rows: 64984 >> Number of Columns: 4 >> Volume Dim[0]: 0 >> Volume Dim[1]: 0 >> Volume Dim[2]: 0 >> Palette Type: None >> CIFTI Dim[0]: 4 >> CIFTI Dim[1]: 64984 >> ALONG_ROW map type: LABELS >> ALONG_COLUMN map type: BRAIN_MODELS >> Has Volume Data: false >> CortexLeft: 32492 out of 32492 vertices >> CortexRight: 32492 out of 32492 vertices >> >> >> I do not think anotherCii has also nothing to do with this, as it is >> just a cii file with the same row dimensionality (64984x1). >> >> Following the suggestion in your other message, I have extracted the >> hemisphere-specific full-surface label files using wb_command >> -cifti-separate with the -label repeatable option and saved the output >> in a gii file. The result was the same. >> >> One thing I forgot to mention and might be important is that, among 4 >> parcellations stored in RSN-networks.32k_fs_LR.dlbal.nii, only the >> holes-filled power labels (3rd column) has this problem. The others >> are just fine. This also makes me think that dlabel file, at least >> partly, was generated in an unusual way. Perhaps someone involved in >> the generation of the tutorial data package or the aforementioned >> BALSA study can shed light on this. >> >> Salim >> >> >> >> ------------------------------ >> *From:* Timothy Coalson <[email protected]> >> *To:* Salim Arslan <[email protected]> >> *Cc:* "[email protected]" <[email protected]> >> *Sent:* Wednesday, August 3, 2016 9:36 PM >> *Subject:* Re: [HCP-Users] Extracting Power parcellations from >> RSN-networks.32k_fs_LR >> >> First, the size of 64984 shows that the cifti file in question did not >> have the medial wall masked out internally, which is likely the >> starting point for these problems. I don't know how medialMask is >> defined, but if it isn't 32492 elements long (in this case), then that >> will cause another problem, as the break between left and right data >> will be in the wrong place. >> >> If you really didn't do any steps between defining labelsL and >> labelsR, and anotherCii was made as a copy of that same cii variable, >> then I don't know how it managed to mess things up, though, unless >> this cifti file also managed to have right hemisphere before left >> hemisphere (the format supports this, but we have tried to be >> consistent with the order - the lack of a medial wall mask indicates >> this dlabel file was generated in an unusual way, though). You can >> use "wb_command -file-information -no-map-info" to see the order of >>structures in the cifti file. >> >> Tim >> >> >> On Wed, Aug 3, 2016 at 11:22 AM, Salim Arslan <[email protected]> >> wrote: >> >> Hello, >> >> I am trying to get Power parcellations out of >> RSN-networks.32k_fs_LR.dlabel.nii, that comes with the "Brain Analysis >> Library of Spatial maps and Atlases (BALSA) database study" ( >> https://balsa.wustl.edu/study/show/WG33). It is also part of the >> tutorial dataset. >> >> I did what I have been always doing for extracting data from CIFTI >> files in Matlab. Using ciftiopen, I obtained the cii object, which in >> this case, contains the cdata matrix of size 64984x4. The 3rd column >> here corresponds to the holes-filled Power parcellations. To extract >> those for both hemispheres, I simply split up the 64984 vector and >> masked out the medial wall vertices and then saved the labels back to >>CIFTI. >> >> cii = ciftiopen('RSN-networks.32k_fs_LR.dlabel.nii', wb_command); >> cdata = cii.cdata; parcellation = cdata(:,3); labelsL = >> cifti(1:length(medialMask)); labelsR = >> cifti(length(medialMask)+1:end); anotherCii.cdata = [labelsL;labelsR]; >> ciftisave(anotherCii,'power.dlabel.nii',wb_command) >> >> However when I visualized the labels on workbench, I noticed some >> holes (with random labels) in many parcels. Please see the attached >> figure for clarification. >> >> I assume this is something to do with the medial masking, but cannot >> figure out what is wrong. Any help is appreciated. >> >> Thanks for your attention. >> >> Best regards, >> Salim >> >> -- >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> >> >> >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160804/ >fe163ca6/attachment-0001.html > >------------------------------ > >Message: 3 >Date: Fri, 5 Aug 2016 00:21:22 +0000 >From: "Glasser, Matthew" <[email protected]> >Subject: Re: [HCP-Users] Movement Confounds and Censoring >To: "Burgess, Gregory" <[email protected]>, "Michael F.W. Dreyfuss" ><[email protected]> >Cc: "[email protected]" <[email protected]> >Message-ID: <d3c945f8.1224c3%[email protected]> >Content-Type: text/plain; charset="iso-8859-1" > >If you are acquiring HCP-style data, it would probably be fine to use >ICA+FIX based on HCP training. > >Matt. > >On 8/4/16, 9:35 AM, "[email protected] on behalf of >Burgess, Gregory" <[email protected] on behalf of >[email protected]> wrote: > >>> On Aug 4, 2016, at 8:52 AM, Michael F.W. Dreyfuss >>><[email protected]> wrote: >>> >>> Thank you, >>> >>> Is it recommended to use the motion regressors with or without >>>detrending on data that has been processed with the HCP preprocessing >>>scripts? >> >>You should perform the same filtering on your confound regressors (and >>task model) that you are performing on your data. So, I?d start with >>the original Movement_Regressors.txt. >> >> >>> Is there a recommended cutoff for censoring time points or a >>>recommended threshold of mean relative displacement for excluding a >>>subject or run? >> >>One of the interesting difficulties with HCP data (and occasionally >>other MB fMRI data from other groups) is that motion parameters from MB >>data pick up on some source of variability that is not typically >>visible in motion parameters estimated from fMRI data with lower >>spatial and temporal resolution. So, censoring thresholds that are >>typical in lower resolution fMRI might result in censoring a >>considerable proportion of your data. You might want to look at DVARS >>to see if it can detect apparent motion artifact more cleanly. >> >>Either way, the best strategy is to look at your data to set your own >>threshold. (Look at strategies from Power, J. D., Mitra, A., Laumann, T. >>O., Snyder, A. Z., Schlaggar, B. L., & Petersen, S. E. (2014). Methods >>to detect, characterize, and remove motion artifact in resting state >>fMRI. >>NeuroImage, 84, 320?341. >>http://doi.org/10.1016/j.neuroimage.2013.08.048) >> >> >>> I installed FIX and can implement it on my data, but I can only have >>>it trained to data from your scanners at Wash U since I do not have >>>enough additional data from our scanner here to train it on, so I do >>>not feel comfortable using it on my data. >> >>You could consider hand categorizing the ICA components, if you feel >>comfortable making those judgments and you don?t have tons of data. >>There are also some other automated approaches such as AROMA that have >>become popular with folks. I have no experience with AROMA yet, but I?d >>imagine that it would rate spike-like ICA components as noise. >> >> >>--Greg >> >>____________________________________________________________________ >>Greg Burgess, Ph.D. >>Staff Scientist, Human Connectome Project Washington University School >>of Medicine Department of Psychiatry >>Phone: 314-362-7864 >>Email: [email protected] >> >>> >>> Thank you, >>> Michael >>> From: Burgess, Gregory <[email protected]> >>> Sent: Tuesday, August 2, 2016 2:30:10 PM >>> To: Michael F.W. Dreyfuss >>> Cc: [email protected] >>> Subject: Re: [HCP-Users] Movement Confounds and Censoring >>> >>> > On Aug 2, 2016, at 10:17 AM, Michael F.W. Dreyfuss >>><[email protected]> wrote: >>> >>> > >>> >>> > Hi, I have some basic questions about the movement parameters that >>>are put out by the HCP preprocessing scripts. >>> >>> > >>> >>> > 1) What is the difference between Movement_Regressors_dt.txt and >>>Movement_Regressors.txt? I would like to use one as a confound. >>> >>> >>> >>> The Movement_Regressors.txt are the parameters computed from the >>>motion correction algorithm. The Movement_Regressors_dt.txt is the >>>same file put through a detrend command to remove the linear trend and >>>mean. >>> >>> >>> >>> > >>> >>> > 2) What does each column in these represent? I'm assuming 6 >>>directions of displacement, and 3 for rotation? >>> >>> >>> >>> The 12 columns represent Displacement {x, y, z}, Rotation {x, y, z}, >>>Backward Derivative of Displacement {x, y, z}, and Backward Derivative >>>of Rotation {x, y, z} >>> >>> >>> >>> > >>> >>> > 3) What are the units in these and the other movement files in the >>>output? mm? voxels? >>> >>> >>> >>> The units are mm for displacements and degrees for rotations. >>> >>> >>> >>> > >>> >>> > 4) I would like to censor time points with too much motion in >>>Movement_AbsoluteRMS.txt. Is there a specific movement cutoff you >>>recommend? I have made a script that produces a censor file in the fsl >>>format (i.e. columns of all 0s with a 1 at the time point that is >>>censored). Is there a simple way to add that censor file into the >>>existing analysis scripts along with the motion as a confound? >>> >>> >>> >>> First, I would suggest using the Movement_RelativeRMS.txt file for >>>censoring instead. The AbsoluteRMS reflects the total movement from >>>the motion correlation registration target, which is the SBRef volume >>>collected at the beginning of the scan. In contrast, the RelativeRMS >>>reflects the amount of motion from the previous time point, which >>>should be considered a more direct measurement of movement on that >>>specific time point. >>> >>> >>> >>> I?m not sure to which existing analysis scripts you are referring. We >>>don?t release analyses of individual scans. So, you should probably >>>include these censoring confounds as covariates in whatever >>>preprocessing you?re doing for the individual scans. >>> >>> >>> >>> After saying all of that, it is worth mentioning that FIX denoising: >>> >>> - Regresses a set of 24 motion parameters (six rigid body parameters, >>>their backward derivatives, and the squares of those 12 columns) >>> >>> - Regresses noise component variance (orthogonal to signal >>>components) from the scan-level ICA. >>> >>> >>> >>> In practice, the behavior of FIX is similar to regressing movement >>>paremeters and voxel-specific censoring (plus other artifact cleanup). >>>If you utilize FIX preprocessed data, you don?t need to regress motion >>>parameters, and you might feel comfortable skipping censoring as well. >>> >>> >>> >>> --Greg >>> >>> >>> >>> ____________________________________________________________________ >>> >>> Greg Burgess, Ph.D. >>> >>> Staff Scientist, Human Connectome Project >>> >>> Washington University School of Medicine >>> >>> Department of Psychiatry >>> >>> Phone: 314-362-7864 >>> >>> Email: [email protected] >>> >>> >>> >>> >>> >>> > >>> >>> > Thank you, >>> >>> > Michael >>> >>> > _______________________________________________ >>> >>> > HCP-Users mailing list >>> >>> > [email protected] >>> >>> > >>>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnect >>>ome >>>.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT >>>9-R >>>Xrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=FMg6DA >>>hRQ >>>HwDPdwDze2CIg4j1-kMkVc9h-XJ0PXmDWQ&s=ck-KAIP80cxbdHtG0fMXtiT8T_-4QzuQ- >>>lNV >>>QlPrDs8&e= >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ________________________________ >>> >>> 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 >>[email protected] >>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. > > > >------------------------------ > >Message: 4 >Date: Fri, 5 Aug 2016 00:24:19 +0000 >From: "Glasser, Matthew" <[email protected]> >Subject: Re: [HCP-Users] Movement Confounds and Censoring >To: "Michael F.W. Dreyfuss" <[email protected]>, "Burgess, >Gregory"<[email protected]> >Cc: "[email protected]" <[email protected]> >Message-ID: <d3c946cf.1224cc%[email protected]> >Content-Type: text/plain; charset="windows-1252" > >You probably need to merge the files using something like paste. > >Peace, > >Matt. > >From: ><[email protected]<mailto:hcp-users-bounces@humanconne >ctome.org>> on behalf of "Michael F.W. Dreyfuss" ><[email protected]<mailto:[email protected]>> >Date: Thursday, August 4, 2016 at 6:15 PM >To: "Burgess, Gregory" <[email protected]<mailto:[email protected]>> >Cc: "[email protected]<mailto:[email protected]>" ><[email protected]<mailto:[email protected]>> >Subject: Re: [HCP-Users] Movement Confounds and Censoring > > >Thank you. On a practical note, if I want to include both motion >regressors and time points censoring with a censor file I produce for >each run how can I do that? I am refering specifically to the following >chunk of code: > > >#Create design files, model confounds if desired > >DIR=`pwd` > >cd ${FEATDir} > >if [ $Confound= "NONE"] ;then > > feat_model ${FEATDir}/design > >else > > feat_model ${FEATDir}/design >${ResultsFolder}/${LevelOnefMRIName}/${Confound} > >fi > >cd $DIR > > >When I change that to the code below including another argument for >thecensor file, the result is the same as if I added no confound (it >ignores both arguments): > > >feat_model ${FEATDir}/design >${ResultsFolder}/${LevelOnefMRIName}/${Confound} >${ResultsFolder}/${LevelOnefMRIName}/censor.txt > > >How can I include both motion regression and censoring files in the >design files using feat_model or another command? > > >Thank you, > >Michael > >________________________________ >From: Burgess, Gregory <[email protected]<mailto:[email protected]>> >Sent: Thursday, August 4, 2016 10:35:33 AM >To: Michael F.W. Dreyfuss >Cc: [email protected]<mailto:[email protected]> >Subject: Re: [HCP-Users] Movement Confounds and Censoring > >> On Aug 4, 2016, at 8:52 AM, Michael F.W. Dreyfuss >><[email protected]<mailto:[email protected]>> wrote: >> >> Thank you, >> >> Is it recommended to use the motion regressors with or without >>detrending on data that has been processed with the HCP preprocessing >>scripts? > >You should perform the same filtering on your confound regressors (and >task model) that you are performing on your data. So, I?d start with the >original Movement_Regressors.txt. > > >> Is there a recommended cutoff for censoring time points or a >>recommended threshold of mean relative displacement for excluding a >>subject or run? > >One of the interesting difficulties with HCP data (and occasionally other >MB fMRI data from other groups) is that motion parameters from MB data >pick up on some source of variability that is not typically visible in >motion parameters estimated from fMRI data with lower spatial and >temporal resolution. So, censoring thresholds that are typical in lower >resolution fMRI might result in censoring a considerable proportion of >your data. You might want to look at DVARS to see if it can detect >apparent motion artifact more cleanly. > >Either way, the best strategy is to look at your data to set your own >threshold. (Look at strategies from Power, J. D., Mitra, A., Laumann, T. >O., Snyder, A. Z., Schlaggar, B. L., & Petersen, S. E. (2014). Methods to >detect, characterize, and remove motion artifact in resting state fMRI. >NeuroImage, 84, 320?341. >https://urldefense.proofpoint.com/v2/url?u=http-3A__doi.org_10.1016_j.neur >oimage.2013.08.048&d=DQIF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s& >r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=rA5E466xAGA4eFveDcDcOazqcX >IKVYINMcieo_qUh1o&s=W83s5PHORheYaI8ov_xC8VSiKFk3nw9qHj8Q2IvgnNg&e= ) > > >> I installed FIX and can implement it on my data, but I can only have it >>trained to data from your scanners at Wash U since I do not have enough >>additional data from our scanner here to train it on, so I do not feel >>comfortable using it on my data. > >You could consider hand categorizing the ICA components, if you feel >comfortable making those judgments and you don?t have tons of data. There >are also some other automated approaches such as AROMA that have become >popular with folks. I have no experience with AROMA yet, but I?d imagine >that it would rate spike-like ICA components as noise. > > >--Greg > >____________________________________________________________________ >Greg Burgess, Ph.D. >Staff Scientist, Human Connectome Project Washington University School of >Medicine Department of Psychiatry >Phone: 314-362-7864 >Email: [email protected]<mailto:[email protected]> > >> >> Thank you, >> Michael >> From: Burgess, Gregory <[email protected]<mailto:[email protected]>> >> Sent: Tuesday, August 2, 2016 2:30:10 PM >> To: Michael F.W. Dreyfuss >> Cc: >> [email protected]<mailto:[email protected]> >> Subject: Re: [HCP-Users] Movement Confounds and Censoring >> >> > On Aug 2, 2016, at 10:17 AM, Michael F.W. Dreyfuss >><[email protected]<mailto:[email protected]>> wrote: >> >> > >> >> > Hi, I have some basic questions about the movement parameters that >>are put out by the HCP preprocessing scripts. >> >> > >> >> > 1) What is the difference between Movement_Regressors_dt.txt and >>Movement_Regressors.txt? I would like to use one as a confound. >> >> >> >> The Movement_Regressors.txt are the parameters computed from the motion >>correction algorithm. The Movement_Regressors_dt.txt is the same file >>put through a detrend command to remove the linear trend and mean. >> >> >> >> > >> >> > 2) What does each column in these represent? I'm assuming 6 >>directions of displacement, and 3 for rotation? >> >> >> >> The 12 columns represent Displacement {x, y, z}, Rotation {x, y, z}, >> Backward Derivative of Displacement {x, y, z}, and Backward Derivative >> of Rotation {x, y, z} >> >> >> >> > >> >> > 3) What are the units in these and the other movement files in the >>output? mm? voxels? >> >> >> >> The units are mm for displacements and degrees for rotations. >> >> >> >> > >> >> > 4) I would like to censor time points with too much motion in >>Movement_AbsoluteRMS.txt. Is there a specific movement cutoff you >>recommend? I have made a script that produces a censor file in the fsl >>format (i.e. columns of all 0s with a 1 at the time point that is >>censored). Is there a simple way to add that censor file into the >>existing analysis scripts along with the motion as a confound? >> >> >> >> First, I would suggest using the Movement_RelativeRMS.txt file for >>censoring instead. The AbsoluteRMS reflects the total movement from the >>motion correlation registration target, which is the SBRef volume >>collected at the beginning of the scan. In contrast, the RelativeRMS >>reflects the amount of motion from the previous time point, which should >>be considered a more direct measurement of movement on that specific >>time point. >> >> >> >> I?m not sure to which existing analysis scripts you are referring. We >>don?t release analyses of individual scans. So, you should probably >>include these censoring confounds as covariates in whatever >>preprocessing you?re doing for the individual scans. >> >> >> >> After saying all of that, it is worth mentioning that FIX denoising: >> >> - Regresses a set of 24 motion parameters (six rigid body parameters, >> their backward derivatives, and the squares of those 12 columns) >> >> - Regresses noise component variance (orthogonal to signal components) >>from the scan-level ICA. >> >> >> >> In practice, the behavior of FIX is similar to regressing movement >>paremeters and voxel-specific censoring (plus other artifact cleanup). >>If you utilize FIX preprocessed data, you don?t need to regress motion >>parameters, and you might feel comfortable skipping censoring as well. >> >> >> >> --Greg >> >> >> >> ____________________________________________________________________ >> >> Greg Burgess, Ph.D. >> >> Staff Scientist, Human Connectome Project >> >> Washington University School of Medicine >> >> Department of Psychiatry >> >> Phone: 314-362-7864 >> >> Email: [email protected]<mailto:[email protected]> >> >> >> >> >> >> > >> >> > Thank you, >> >> > Michael >> >> > _______________________________________________ >> >> > HCP-Users mailing list >> >> > [email protected]<mailto:[email protected]> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconne >> > ctome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb62iw4YL4RFalcE2h >> > QUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYF >> > Swg&m=FMg6DAhRQHwDPdwDze2CIg4j1-kMkVc9h-XJ0PXmDWQ&s=ck-KAIP80cxbdHtG >> > 0fMXtiT8T_-4QzuQ-lNVQlPrDs8&e= >> >> >> >> >> >> >> >> >> >> ________________________________ >> >> 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 >[email protected]<mailto:[email protected]> >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. >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160805/ >68f705d7/attachment-0001.html > >------------------------------ > >Message: 5 >Date: Fri, 5 Aug 2016 08:27:38 +0000 (UTC) >From: Salim Arslan <[email protected]> >Subject: Re: [HCP-Users] Extracting Power parcellations from >RSN-networks.32k_fs_LR >To: Timothy Coalson <[email protected]> >Cc: "[email protected]" <[email protected]> >Message-ID: ><[email protected]> >Content-Type: text/plain; charset="utf-8" > >Dear Tim, >Thanks for the follow-up. Could you suggest a quick solution for this >that can do the work until the release of the fixed data file? I am not >much familiar with most of the wb_command,- as you can see in my original >post, I am more of a Matlab person- so perhaps, if you could give me a >hint about how to change those label files, I would really appreciate. A >command that can be used for filling the holes in the 4th map in order to >regenerate the 3rd map would also help. >Best regards,Salim? > > From: Timothy Coalson <[email protected]> > To: Salim Arslan <[email protected]> >Cc: "[email protected]" <[email protected]> > Sent: Friday, August 5, 2016 12:46 AM > Subject: Re: [HCP-Users] Extracting Power parcellations from >RSN-networks.32k_fs_LR > >Using -cifti-separate on the original cifti file and viewing in wb_view >looks identical to the original.? However, I think I see what is going >on, after getting a hint from the way you reset the color scheme - the >file has 2 labels named "a3_Default_mode", and similar for other labels, >and turning one of them off reveals these holes. >What has happened is that someone has set the names and colors of two >label values to be identical (except for a space on the end of one, to >slip past the uniqueness tests on the label names), but they are actually >different integers in those patches.? I don't know how this happened, as >map 4 doesn't have this difference in values.? We should probably fix >this in the data file. >Tim > >On Thu, Aug 4, 2016 at 3:44 AM, Salim Arslan <[email protected]> >wrote: > >Hi Tim, >Thanks for your attention. >After your message, I also thought the problem was about the order of the >hemisphere in the cifti file. However, after running?wb_command >-file-information -no-map-info I can confirm that the order is correct. >Here is the output: >Name: ? ? ? ? ? ? ? ? ? ?RSN-networks.32k_fs_LR. dlabel.niiType: ? ? ? ? >? ? ? ? ? ?Connectivity - Dense LabelStructure: ? ? ? ? ? ? ? CortexLeft >CortexRight?Data Size: ? ? ? ? ? ? ? 1.04 MegabytesMaps to Surface: ? ? ? >? trueMaps to Volume: ? ? ? ? ?falseMaps with LabelTable: ? ?trueMaps >with Palette: ? ? ? falseNumber of Rows: ? ? ? ? ?64984Number of Columns: >? ? ? 4Volume Dim[0]: ? ? ? ? ? 0Volume Dim[1]: ? ? ? ? ? 0Volume Dim[2]: >? ? ? ? ? 0Palette Type: ? ? ? ? ? ?NoneCIFTI Dim[0]: ? ? ? ? ? ?4CIFTI >Dim[1]: ? ? ? ? ? ?64984ALONG_ROW map type: ? ? ?LABELSALONG_COLUMN map >type: ? BRAIN_MODELS? ? Has Volume Data: ? ? false? ? CortexLeft: ? ? ? ? >?32492 out of 32492 vertices? ? CortexRight: ? ? ? ? 32492 out of 32492 >vertices > >I do not think anotherCii has also nothing to do with this, as it is just >a cii file with the same row dimensionality (64984x1).? >Following the suggestion in your other message, I have extracted the >hemisphere-specific full-surface label files using wb_command >-cifti-separate with the -label repeatable option and saved the output in >a gii file. The result was the same.? >One thing I forgot to mention and might be important is that, among 4 >parcellations stored in RSN-networks.32k_fs_LR.dlbal. nii, only the >holes-filled power labels (3rd column) has this problem. The others are >just fine. This also makes me think that dlabel file, at least ?partly, >was generated in an unusual way. Perhaps someone involved in the >generation of the tutorial data package or the aforementioned BALSA study >can shed light on this. >Salim? > > > From: Timothy Coalson <[email protected]> > To: Salim Arslan <[email protected]> >Cc: "[email protected] " <[email protected] > > Sent: Wednesday, August 3, 2016 9:36 PM > Subject: Re: [HCP-Users] Extracting Power parcellations from >RSN-networks.32k_fs_LR > >First, the size of 64984 shows that the cifti file in question did not >have the medial wall masked out internally, which is likely the starting >point for these problems.? I don't know how medialMask is defined, but if >it isn't 32492 elements long (in this case), then that will cause another >problem, as the break between left and right data will be in the wrong >place. >If you really didn't do any steps between defining labelsL and labelsR, >and anotherCii was made as a copy of that same cii variable, then I don't >know how it managed to mess things up, though, unless this cifti file >also managed to have right hemisphere before left hemisphere (the format >supports this, but we have tried to be consistent with the order - the >lack of a medial wall mask indicates this dlabel file was generated in an >unusual way, though).? You can use "wb_command -file-information >-no-map-info" to see the order of structures in the cifti file. >Tim > >On Wed, Aug 3, 2016 at 11:22 AM, Salim Arslan <[email protected]> >wrote: > >Hello, > >I am trying to get Power parcellations out of >RSN-networks.32k_fs_LR.dlabel. nii, that comes with the "Brain Analysis >Library of Spatial maps and Atlases (BALSA) database study" >(https://balsa.wustl.edu/ study/show/WG33). It is also part of the >tutorial dataset. > >I did what I have been always doing for extracting data from CIFTI files >in Matlab. Using ciftiopen, I obtained the cii object, which in this >case, contains the cdata matrix of size 64984x4. The 3rd column here >corresponds to the holes-filled Power parcellations. To extract those for >both hemispheres, I simply split up the 64984 vector and masked out the >medial wall vertices and then saved the labels back to CIFTI. > >cii = ciftiopen('RSN-networks.32k_ fs_LR.dlabel.nii', wb_command);? >cdata = cii.cdata; >parcellation = cdata(:,3); >labelsL = cifti(1:length(medialMask)); >labelsR = cifti(length(medialMask)+1: end); anotherCii.cdata = >[labelsL;labelsR]; ciftisave(anotherCii,'power. dlabel.nii',wb_command) > >However when I visualized the labels on workbench, I noticed some holes >(with random labels) in many parcels. Please see the attached figure for >clarification. > >I assume this is something to do with the medial masking, but cannot >figure out what is wrong. Any help is appreciated. > >Thanks for your attention.? >Best regards,Salim > >-- >______________________________ _________________ HCP-Users mailing list >[email protected] http://lists.humanconnectome. >org/mailman/listinfo/hcp-users > > > > > > > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20160805/ >22a4d1b9/attachment-0001.html > >------------------------------ > >_______________________________________________ >HCP-Users mailing list >[email protected] >http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > >End of HCP-Users Digest, Vol 45, Issue 5 >**************************************** > >_______________________________________________ >HCP-Users mailing list >[email protected] >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. 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