Re: [HCP-Users] Intensity Normalization 3_22

; >>> Matt. >>> >>> From: "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu> >>> Date: Thursday, March 29, 2018 at 3:04 PM >>> To: Matt Glasser <glass...@wustl.edu>, Keith Jamison <kjami...@umn.edu> >>> Subje

Re: [HCP-Users] Intensity Normalization 3_22

.edu> >> Date: Thursday, March 29, 2018 at 3:04 PM >> To: Matt Glasser <glass...@wustl.edu>, Keith Jamison <kjami...@umn.edu> >> Subject: Re: [HCP-Users] Intensity Normalization 3_22 >> >> there was no B0 collected and we use the SE as our Sbref >&

Re: [HCP-Users] Intensity Normalization 3_22

spi.columbia.edu>> Date: Thursday, March 29, 2018 at 3:04 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.edu>> Subject: Re: [HCP-Users] Intensity Normalization 3_22 there was

Re: [HCP-Users] Intensity Normalization 3_22

lto:glass...@wustl.edu>>, Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-U

Re: [HCP-Users] Intensity Normalization 3_22

m: Glasser, Matthew <glass...@wustl.edu> Sent: Thursday, March 29, 2018 1:48:56 PM To: Sanchez, Juan (NYSPI); Keith Jamison Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Intensity Normalization 3_22 ATTENTION: This email came from an external source. Do not open attachments or cli

Re: [HCP-Users] Intensity Normalization 3_22

thew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Thursday, March 29, 2018 1:39:09 PM To: Sanchez, Juan (NYSPI); Keith Jamison Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Intensity Normalization 3_22 ATTENTION: This

Re: [HCP-Users] Intensity Normalization 3_22

anchez, Juan (NYSPI); Keith Jamison Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Intensity Normalization 3_22 ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails. Yes I apologize for coding the bias

Re: [HCP-Users] Intensity Normalization 3_22

sday, March 29, 2018 1:35:28 PM To: Sanchez, Juan (NYSPI); Keith Jamison Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Intensity Normalization 3_22 ATTENTION: This email came from an external source. Do not open attachments or click on

Re: [HCP-Users] Intensity Normalization 3_22

me.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: 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

Re: [HCP-Users] Intensity Normalization 3_22

.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] Intensity Normal

Re: [HCP-Users] Intensity Normalization 3_22

inal error. From: Keith Jamison <kjami...@umn.edu> Sent: Thursday, March 29, 2018 12:35:38 PM To: Glasser, Matthew Cc: Sanchez, Juan (NYSPI); hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Intensity Normalization 3_22 ATTENTION: This email came from an ext

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

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)"