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, 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
click on links from unknown senders or unexpected emails.
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)"
<juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>>
Date: Thursday, March 29, 2018 at 12:43 PM
To: Matt Glasser <glass...@wustl.edu<mailto: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-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 <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 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 field wrong in the initial versions of the
HCP Pipeline, but the SEBASED is much better.
Peace,
Matt.
From: "Sanchez, Juan (NYSPI)"
<juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>>
Date: Thursday, March 29, 2018 at 12:36 PM
To: Matt Glasser <glass...@wustl.edu<mailto: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-Users] Intensity Normalization 3_22
Thanks Matt it does look good.
I will switch to LEGACY from SEBASED
thanks
________________________________
From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Thursday, 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 links from unknown senders or unexpected emails.
That image looks okay, what is the issue?
Peace,
Matt.
From: "Sanchez, Juan (NYSPI)"
<juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>>
Date: Thursday, March 29, 2018 at 12:29 PM
To: Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.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 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 -ing
1000 output_BiasField2 -odt float
the_sebased_bias
fslmaths Task_fMRI_emomo_1_nonlin.nii.gz -div
Task_fMRI_emomo_1_sebased_bias.nii.gz -mul Jacobian_MNI.2.nii.gz -mas
Task_fMRI_emomo_1_nonlin_mask.nii.gz -thr 0 -ing 1000 output -odt float
and replicated the original error.
________________________________
From: Keith Jamison <kjami...@umn.edu<mailto:kjami...@umn.edu>>
Sent: Thursday, March 29, 2018 12:35:38 PM
To: Glasser, Matthew
Cc: Sanchez, Juan (NYSPI);
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 links from unknown senders or unexpected emails.
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 like the bias field was incorrectly
estimated. Did you use --biascorrection=SEBASED in your call to
GenericfMRIVolumeProcessingPipeline? If you used --biascorrection=LEGACY (might
be the default?) you may also want to check if your MNINonLinear/T1w_restore
and MNINonLinear/T2w_restore look properly bias corrected.
-Keith
On Thu, Mar 29, 2018 at 11:55 AM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I think that might be an old version of the pipelines. If you run on the
latest version is it better?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Sanchez, Juan (NYSPI)"
<juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>>
Date: Thursday, March 29, 2018 at 10:23 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Intensity Normalization 3_22
Dear all
We are using the 3_22 Pipelines to process out data.
We noticed that the processed fMRI results had an unusual intensity
inhomogeneity for ALL of our runs. (first attachment)
We found that the error occurued during intensity normalization
Here:
${FSLDIR}/bin/fslmaths ${InputfMRI} $biascom $jacobiancom -mas ${BrainMask}
-mas ${InputfMRI}_mask -thr 0 -ing 10000 ${OutputfMRI} -odt float
I copied the relevant files and ran the fslmaths command localy
(InputfMRI = Task_fMRI_emomo_1)
fslmaths Task_fMRI_emomo_1_nonlin.nii.gz -div Jacobian_MNI.2.nii.gz -mul
Jacobian_MNI.2.nii.gz -mas Task_fMRI_emomo_1_nonlin_mask.nii.gz -thr 0 -ing
1000 output -odt float
The output (second attachment) looked correct.
I have tried to replicate the error and have not been able to
Can anyone suggest a possible explenation?
Thanks
J
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