Re: [HCP-Users] A Question about tfMRI_X_RL_Atlas.dtseries.nii preprocessing steps

[Glasser, Matthew]

If you want the tfMRI .dtseries.nii you need to download the appropriate fMRI minimally preprocessed packages (not the tfMRI analysis packages). Peace, Matt. From: Mahshid <mhs...@gmail.com> Date: Friday, May 2, 2014 at 3:36 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] A Question about tfMRI_X_RL_Atlas.dtseries.nii preprocessing steps I want to use the time series, not the contrasts for now. So I am not sure if the timeseries are provided in level 2? Because I could only find SubjID_tfMRI_WM_level2_hp200_s4.dscalar.nii which seems to be the contrasts between the conditions. and also would you please let me know which preprocessing steps have been applied to the tfMRI_WM_RL_Atlas.dtseries.nii? Thanks again, Mahshid  On Fri, May 2, 2014 at 4:10 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Is there a reason you need the level1 results or can you just use the level2 results?  If the problem is the smoothing that was already applied, the new release will not have that.   Peace, Matt. From: <Harms>, Michael <mha...@wustl.edu> Date: Friday, May 2, 2014 at 3:00 PM To: Mahshid Najafi <mhs...@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] A Question about tfMRI_X_RL_Atlas.dtseries.nii preprocessing steps Hi Mahshid, We are not releasing the run-level (Level1) task processed data -- only the Level2 data, which effectively "averages" the two runs for each task and subject.  To use the level1.fsf to generate the Level1 results on the grayordinate/CIFTI data involves transforming the CIFTI into NIFTI, merging files, running flameo, and then converting back to CIFTI (both conversions use -cifti-convert in wb_command).  Conceptually it is straightforward, although there is some book-keeping involved.  We hope to be able to release the HCP pipeline scripts sometime not too long after forthcoming "500 Subjects" release, if you are willing to wait until that time. 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: Mahshid Najafi <mhs...@gmail.com> Date: Friday, May 2, 2014 1:39 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] A Question about tfMRI_X_RL_Atlas.dtseries.nii preprocessing steps Dear HCPs, Hi, I want to use the grayordinate timeseries in tfMRI which are preprocessed with level 1, (which includes smoothing and temporal filtering). So, is tfMRI_WM_RL_Atlas.dtseries.nii in SubjectsID/MNINonLinear/Results/tfMRI_WM_RL/ both minimally preprocessed and level 1 preprocessed? If not, can we use tfMRI_WM_RL_hp200_s4_level1.fsf (with modification of the inputs) for the grayordinates data too? Thanks,  Mahshid    _______________________________________________ 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   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