It could be the extra long dash that my e-mail editor added. Alternatively you may need make sure you use double quotes around the expression (that is currently in single quotes).
Peace, Matt. From: peipei_xiao <[email protected]<mailto:[email protected]>> Date: Monday, November 9, 2015 at 10:42 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: Re:Re: [HCP-Users] help for lifespan data Thanks! I type the following command in MATLAB: system('wb_command -cifti-reduce rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii MEAN mean.dtseries.nii'); system('wb_command -cifti-math (x-mean) out.nii -fixnan 0 -var x rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii -var mean mean.dtseries.nii -select 1 1 –repeat '); Matlab reported the following error: "While running 'wb_command -cifti-math (x-mean) out.nii -fixnan 0 -var x rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii -var mean mean.dtseries.nii -select 1 1 –repeat': ERROR: Unexpected parameter: –repeat " In the second line of code where I have a mistake. At 2015-11-10 12:17:31, "Glasser, Matthew" <[email protected]<mailto:[email protected]>> wrote: I see, the highpass filtering in that version didn’t demean the data, but in more recent versions it does. You can demean the data like this: wb_command -cifti-reduce <input> MEAN mean.dtseries.nii wb_command -cifti-math '(x - mean)' -fixnan 0 -var x <input> -var mean mean.dtseries.nii -select 1 1 –repeat Peace, Matt. From: peipei_xiao <[email protected]<mailto:[email protected]>> Date: Monday, November 9, 2015 at 10:13 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: Re:Re: [HCP-Users] help for lifespan data version of FSL is 5.0.6 At 2015-11-10 11:19:52, "Glasser, Matthew" <[email protected]<mailto:[email protected]>> wrote: What version of FSL are you using? Peace, Matt. From: peipei_xiao <[email protected]<mailto:[email protected]>> Date: Monday, November 9, 2015 at 9:16 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: Re:Re: [HCP-Users] help for lifespan data I call the following six scripts( in Pipelines-3.10.0/Examples/Scripts/) to handle lifespan data ./PreFreeSurferPipelineBatch.sh ./FreeSurferPipelineBatch.sh ./PostFreeSurferPipelineBatch.sh ./GenericfMRIVolumeProcessingPipelineBatch.sh ./GenericfMRISurfaceProcessingPipelineBatch.sh ./IcaFixProcessingBatch.sh At 2015-11-10 11:05:15, "Glasser, Matthew" <[email protected]<mailto:[email protected]>> wrote: That sounds like a version, not a list of pipelines that you ran. Peace, Matt. From: peipei_xiao <[email protected]<mailto:[email protected]>> Date: Monday, November 9, 2015 at 9:03 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: Re:Re: [HCP-Users] help for lifespan data I used Pipelines-3.10.0 script to run all steps. At 2015-11-10 11:00:23, "Glasser, Matthew" <[email protected]<mailto:[email protected]>> wrote: No. What pipelines did you run? Peace, Matt. From: peipei_xiao <[email protected]<mailto:[email protected]>> Date: Monday, November 9, 2015 at 8:56 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: Re:Re: [HCP-Users] help for lifespan data Hi, Thanks for the reply. Sorry, there are some points in your reply that I don't understand. Does you mean I need to divide each numerical value (in the 104×420 matrix) by 10000. You point out that you are a bit surprised that the values are not demeaned if I’ve run ICA+FIX (to make the _hp2000_clean dense timeseries). Is there any error in the pipeline scripts's parameter I settings. At 2015-11-10 01:29:17, "Glasser, Matthew" <[email protected]<mailto:[email protected]>> wrote: I don’t think you need to exclude any time points. I’m a bit surprised that the values are not demeaned if you’ve run ICA+FIX (to make the _hp2000_clean dense timeseries). The original data are scaled to a grand mean of 10000, so the values are right until you demean the data (which you would want to do before concatenating across runs for example). Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of peipei_xiao <[email protected]<mailto:[email protected]>> Date: Monday, November 9, 2015 at 4:46 AM To: hcp-users <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] help for lifespan data Hi, I have some questions need help. I download the lifespan dataset from ConnectomeDB database. Then, I used Pipelines-3.10.0 script to preprocessing those data. After preprocessing, I used workbench-command [wb_command -cifti-parcellate rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii *.LR.dlabel.nii COLUMN cortical.ptseries.nii] to get subjects' time-course data(rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii). Each time-course data is a matrix, such as a 104×420 matrix. 104 represents there are 104 labels, and 420 represents 420 time points. Now, I have two question? First, In the SPM pipeline of fMRI preprocessing, we need to exclude the first 10 time points of the time-course data. Should I exclude the first 10 time points of the lifespan data? Second, I found that the numerical value in 104×420 time-course matrix almostly 10^5, following is a one label,420 time points time-course data. Does the numerical value of time course data is correct. Does there need any transform, such as use the function of log10 to process those data. 11669 1173011805118451179811791116921164711687117291176711788117741174711755117471178611816118031178511817117491174211809117851174311826118421183311886117991180011747117811174911787117801181411774118101178211841118631178311779118581184011892118681189911865118611186011826117731176911696116941175711758117191179311724117731172411802118311181311794117971174111792117471172711817117911178311813117981177011783117541177211741117791180611740117731173811729117521179611816117541178111789118101182411830118351177111810117371179511772117731190811819117391173311758117501173111781117251176011758117441175311728116821174311736117791180911823118831178411807118401188611856118001174211731116931171111721117361180011805116561168611754117791175311726117341176811810118411173711759118491185711776117461176411758117771178611850117411173411761117861171311782117591171611733117301179011709117341178611784118131176211788117131173811758117931177111816117921180611836118221187211892118871187111898118701183411882118171180811785118021181911781117631176411715117411178011746117551169811679117311174911782117691175511709116191170711707117441174311739117611172711688117131172011781117871179411744117601177111715117591168611676117411175911709117721177611792117881175711700117071170611718117471176611787117871170011803117591180311808117611173711717117471172511780117711180011806118301179911746117241169911767117731185111810119011188411902119591185811855118491185711838117321176311747117231172211746116811168511692117351181411773117831177711848118221177111763117931185611820118361188411858117541174911738117601179111827117511172011751117481179511794118441188411856118331191311792117961177111737117081174111736118061181011809117971184911882119061186311816117791182311843118071182011722117351177011730116911174011689117531174511776118411179911855118261175411799118001180311859118851179511790116941162811706117951179711797117951178911807117601169911734117181170711663116921175411801117241179111764117921182811798118081185811820118051178411860118121188211861119401189511820118381179711691116701169611676116691172411741117081171611757 _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
