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, "Gaurav Patel" <gaurav.pa...@gmail.com on behalf of
gauravpa...@gmail.com> wrote:
>Hi mattŠi think we discussed this a few years ago‹we use our spin echo
>images as our sbrefs because of some glitch with collecting our
>single-band ref images. this has generally worked fine with pipelines
>3.4; is this messing with something in the new pipeline versions? I¹m
>not sure where the GRE image comes from in the new pipelines; we stopped
>collecting b0 fieldmaps in this new protocol, chossing to rely only on
>topup for distortion correction. Juan will send you a copy of the
>fmrivolume batch script if that helps.
>________________________
> gaurav patel
> gauravpa...@gmail.com
> pateldsclab.net
>
>> On Mar 29, 2018, at 4:07 PM, Glasser, Matthew <glass...@wustl.edu>
>>wrote:
>>
>> I don¹t 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)" <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>
>> Subject: Re: [HCP-Users] Intensity Normalization 3_22
>>
>> there was no B0 collected and we use the SE as our Sbref
>>
>> From: Glasser, Matthew <glass...@wustl.edu>
>> Sent: Thursday, March 29, 2018 4:03:09 PM
>> To: Sanchez, Juan (NYSPI); Keith Jamison
>> 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.
>> How did you call the pipeline? The GRE and SE images look the same.
>>
>> Peace,
>>
>> Matt.
>>
>> From: "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu>
>> Date: Thursday, March 29, 2018 at 2:56 PM
>> To: Matt Glasser <glass...@wustl.edu>, Keith Jamison <kjami...@umn.edu>
>> Subject: Re: [HCP-Users] Intensity Normalization 3_22
>>
>> here is the output file from the Volume script
>>
>> From: Glasser, Matthew <glass...@wustl.edu>
>> Sent: Thursday, March 29, 2018 3:02:53 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.
>> Can you please upload this folder zipped and we can take a look:
>>
>>
>>${StudyFolder}/${Subject}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndF
>>reeSurferBBRbased
>>
>> Matt.
>>
>> From: "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu>
>> Date: Thursday, March 29, 2018 at 12:54 PM
>> To: Matt Glasser <glass...@wustl.edu>, Keith Jamison <kjami...@umn.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: 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, 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 don¹t you think it is working?
>>
>> Legacy probably shouldn¹t ever be used any more.
>>
>> Peace,
>>
>> Matt.
>>
>> From: "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu>
>> Date: Thursday, March 29, 2018 at 12:43 PM
>> To: Matt Glasser <glass...@wustl.edu>, Keith Jamison <kjami...@umn.edu>
>> Cc: "hcp-users@humanconnectome.org" <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>
>> Sent: Thursday, March 29, 2018 1:39:09 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.
>> 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>
>> Date: Thursday, March 29, 2018 at 12:36 PM
>> To: Matt Glasser <glass...@wustl.edu>, Keith Jamison <kjami...@umn.edu>
>> Cc: "hcp-users@humanconnectome.org" <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>
>> Sent: Thursday, March 29, 2018 1:35:28 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.
>> That image looks okay, what is the issue?
>>
>> Peace,
>>
>> Matt.
>>
>> From: "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu>
>> Date: Thursday, March 29, 2018 at 12:29 PM
>> To: Keith Jamison <kjami...@umn.edu>, Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <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>
>> 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 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>
>>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> on behalf of "Sanchez,
>>>Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu>
>>> Date: Thursday, March 29, 2018 at 10:23 AM
>>> To: "hcp-users@humanconnectome.org" <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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>>
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