Re: [HCP-Users] Intensity Normalization 3_22

Thanks Matt For some reason the SEBASED bias correction is not working with our data. I will try Legacy and make sure it looks ok Thanks for all of your help From: Glasser, Matthew Sent: Thursday, March 29, 2018 1:39:09 PM To: Sanchez,

Re: [HCP-Users] Intensity Normalization 3_22

The command you ran locally is using the Jacobian as the bias field, which is incorrect, and the "-div Jacobian -mul Jacobian" is just cancelling out any effect (output has same bias as input fMRI). It should instead be "-div BiasField.2 -mul Jacobian_MNI.2". That said, your original output looks

Re: [HCP-Users] Intensity Normalization 3_22

Yes I apologize for coding the bias field wrong in the initial versions of the HCP Pipeline, but the SEBASED is much better. Peace, Matt. From: "Sanchez, Juan (NYSPI)" > Date: Thursday, March 29, 2018 at 12:36 PM To: Matt

Re: [HCP-Users] Intensity Normalization 3_22

The image you showed looked fine, why don’t you think it is working? Legacy probably shouldn’t ever be used any more. Peace, Matt. From: "Sanchez, Juan (NYSPI)" > Date: Thursday, March 29, 2018 at 12:43 PM To: Matt

Re: [HCP-Users] Intensity Normalization 3_22

Thanks Keith We are uing SEBASED as we are using TOPUP dc. Thanks for catching that. I reran with: "div BiaseField2" and got the attached results fslmaths Task_fMRI_emomo_1_nonlin.nii.gz -div BiasField.2.nii.gz -mul Jacobian_MNI.2.nii.gz -mas Task_fMRI_emomo_1_nonlin_mask.nii.gz -thr 0

Re: [HCP-Users] Intensity Normalization 3_22

Thanks Matt it does look good. I will switch to LEGACY from SEBASED thanks From: Glasser, Matthew Sent: Thursday, March 29, 2018 1:35:28 PM To: Sanchez, Juan (NYSPI); Keith Jamison Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users]

Re: [HCP-Users] Intensity Normalization 3_22

The image I attached used the BiasField.2.nii.gz I recreated the original error when I used the Task_fMRI_emomo_1_sebased_bias.nii.gz sebasedBiasFieldMNI="$SubjectFolder/$AtlasSpaceFolder/Results/$NameOffMRI/${NameOffMRI}_sebased_bias.nii.gz" From: Glasser,

Re: [HCP-Users] Intensity Normalization 3_22

That image looks okay, what is the issue? Peace, Matt. From: "Sanchez, Juan (NYSPI)" > Date: Thursday, March 29, 2018 at 12:29 PM To: Keith Jamison >, Matt Glasser

Re: [HCP-Users] [HCP-CIFTI] nodes files to CIFTI files

I didn't previously realize this was on the hcp-cifti list, which is in fact intended for technical (programming, etc) questions about the cifti format. I am moving this to the hcp-users list so that others can see and respond to it. If your values result from using the Harvard-Oxford atlas

Re: [HCP-Users] Intensity Normalization 3_22

Can you please upload this folder zipped and we can take a look: ${StudyFolder}/${Subject}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased Matt. From: "Sanchez, Juan (NYSPI)" > Date: Thursday, March 29,

Re: [HCP-Users] Intensity Normalization 3_22

I don’t think you are using this function as intended. I would need to know detailed information about what you are trying to do and how you called the fMRIVolume Pipeline. Peace, Matt. From: "Sanchez, Juan (NYSPI)" >

Re: [HCP-Users] Intensity Normalization 3_22

Well, that explains a lot. Ok, we’ll try it with SBRef set to NONE. Thanks gaurav patel gauravpa...@gmail.com pateldsclab.net > On Mar 29, 2018, at 4:32 PM, Glasser, Matthew wrote: > > You would need to use a mean image SBRef then (which should

Re: [HCP-Users] Intensity Normalization 3_22

You would need to use a mean image SBRef then (which should be the default if you set the SBRef to NONE). The code relies on the differences between SE and GRE to compute the bias field, so it will not work if you are subbing in a SE scan for the SBRef. Peace, Matt. On 3/29/18, 3:29 PM,

Re: [HCP-Users] Intensity Normalization 3_22

I think that might be an old version of the pipelines. If you run on the latest version is it better? Peace, Matt. From: > on behalf of "Sanchez, Juan (NYSPI)"