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

[Timothy Coalson]

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 areas to make
averages, then a parcellated cifti file could be appropriate, and would
preserve the exact data values, rather than turning them into node sizes.
Unfortunately, it appears to be a volume-based atlas, which has some
drawbacks.  If these correlations are cortical, we would recommend that you
use surface-based analysis instead, and use a surface atlas for cortex
(such as the HCP MMP1.0).

If you want to display them as spheres anyway, the only obvious way I know
of to do this is to enter "foci" mode in wb_view, and enter them manually.
I believe you will need to have surfaces loaded for this to work.  Note
that foci may change the locations (coordinates) they display in if you use
different surfaces to display them later.

wb_command is not intended to be run by double-clicking.  It is a
command-line utility, that is, you first open a terminal window, and then
run it by typing in "wb_command" (if your $PATH is set correctly).  It does
not open a window, its only output besides writing files is putting text
into a terminal window.  You can explore its capabilities here, which are
basically webpages made by capturing this text output for wb_command's help
and information options:

https://www.humanconnectome.org/software/workbench-command

Tim


On Thu, Mar 29, 2018 at 9:57 AM, Jeena Thomas  wrote:

> Hi Tim,
>
> Thank you for this information. I currently have a Harvard Oxford atlas
> nii.gz file and I have various points of correlations, indicated by the
> .node files, determined statistically. I want to be able to map those
> points onto the Harvard Oxford Atlas. I was trying to use workbench to do
> so.
>
> Also, considering that Workbench is on my Macbook, I cannot seem to open
> the wb_command icon. When I click to open it, even if I right click and
> select 'open', it will not open. Do you have any insight into this?
>
>
> Let me know what you think!
>
> Thanks,
>
> Jeena
>
> On Mon, Mar 26, 2018 at 5:05 PM, Timothy Coalson  wrote:
>
>> Surface atlases have a different nature to volume atlases, in that
>> surface atlases are actually maps of features in spherical coordinates -
>> anatomical coordinates are optional and often not used in registration (a
>> sulcal-depth-like measure is used instead when anatomical registration is
>> desired).  I am not sure what you are trying to do, but converting a
>> volumetric atlas template to a .surf.gii (geometry) file is a very uncommon
>> task, and doesn't have a particularly clean solution that I am aware of.
>>
>> The general surface analysis pipeline is to first segment every subject's
>> structural images, make surfaces for each subject, map each subject's data
>> onto their own surfaces, register the subjects' surfaces to an atlas,
>> resample each subject's surfaces and surface data to use the atlas
>> topology, and then do cross-subject statistics.  Based on this, can you
>> tell us what you are trying to do and where it diverges from this?
>>
>> Tim
>>
>>
>> On Mon, Mar 26, 2018 at 2:51 PM, Jeena Thomas 
>> wrote:
>>
>>> Also, speaking of which, if you have any recommendations for converting
>>> an atlas that I have in nii. and nii.gz into a surf.gii, that would be
>>> really great!
>>>
>>>
>>> Thanks,
>>>
>>> Jeena
>>>
>>> On Mon, Mar 26, 2018 at 3:35 PM, Jeena Thomas 
>>> wrote:
>>>
 The columns are as follows:
 [x] [y] [z] [color] [node size: strength of correlation] [brain anatomy
 label]

 Note, though that the [brain anatomy label] is a number that currently
 does not correlate to actual anatomical regions because I do not have
 specified regions for the atlas I am using (Harvard Oxford Atlas). The
 fourth column that indicates 'color' indicates positive or negative
 correlation.


 Thank you for your time and patience,

 Jeena




 On Mon, Mar 26, 2018 at 2:10 PM, Glasser, Matthew 
 wrote:

> In that case you need to tell me what each column in the file
> represents and I can suggest what NIFTI/GIFTI/CIFTI formats you should 
> use.
>
> Peace,
>
> Matt.
>
> From: Jeena Thomas 
> Date: Monday, March 26, 2018 at 1:07 PM
>
> To: Matt Glasser 
> Cc: "hcp-ci...@humanconnectome.org" 
> Subject: Re: [HCP-CIFTI] nodes files to CIFTI files
>
> No software makes it. I just made it with a script. The node file
> essentially has 6 columns, three of which relate to coordinates that can 
> be
> mapped onto a brain.
>
> 

Re: [HCP-Users] Intensity Normalization 3_22

[Gaurav Patel]

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 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"  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 
>>> 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)" 
>>> Date: Thursday, March 29, 2018 at 3:04 PM
>>> To: Matt Glasser , Keith Jamison 
>>> Subject: Re: [HCP-Users] Intensity Normalization 3_22
>>> 
>>> there was no B0 collected and we use the SE as our Sbref
>>> 
>>> From: Glasser, Matthew 
>>> 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)" 
>>> Date: Thursday, March 29, 2018 at 2:56 PM
>>> To: Matt Glasser , Keith Jamison 
>>> Subject: Re: [HCP-Users] Intensity Normalization 3_22
>>> 
>>> here is the output file from the Volume script
>>> 
>>> From: Glasser, Matthew 
>>> 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)" 
>>> Date: Thursday, March 29, 2018 at 12:54 PM
>>> To: Matt Glasser , Keith Jamison 
>>> Cc: "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 
>>> 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)" 
>>> Date: Thursday, March 29, 2018 at 12:43 PM
>>> To: Matt Glasser , Keith Jamison 
>>> Cc: "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 
>>> Sent: Thursday, March 29, 

Re: [HCP-Users] Intensity Normalization 3_22

[Glasser, Matthew]

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"  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 
>>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)" 
>> Date: Thursday, March 29, 2018 at 3:04 PM
>> To: Matt Glasser , Keith Jamison 
>> Subject: Re: [HCP-Users] Intensity Normalization 3_22
>> 
>> there was no B0 collected and we use the SE as our Sbref
>> 
>> From: Glasser, Matthew 
>> 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)" 
>> Date: Thursday, March 29, 2018 at 2:56 PM
>> To: Matt Glasser , Keith Jamison 
>> Subject: Re: [HCP-Users] Intensity Normalization 3_22
>> 
>> here is the output file from the Volume script
>> 
>> From: Glasser, Matthew 
>> 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)" 
>> Date: Thursday, March 29, 2018 at 12:54 PM
>> To: Matt Glasser , Keith Jamison 
>> Cc: "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 
>> 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)" 
>> Date: Thursday, March 29, 2018 at 12:43 PM
>> To: Matt Glasser , Keith Jamison 
>> Cc: "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 
>> 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 

Re: [HCP-Users] Intensity Normalization 3_22

[Glasser, Matthew]

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)" 
>
Date: Thursday, March 29, 2018 at 3:04 PM
To: Matt Glasser >, Keith Jamison 
>
Subject: Re: [HCP-Users] Intensity Normalization 3_22


there was no B0 collected and we use the SE as our Sbref



From: Glasser, Matthew >
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)" 
>
Date: Thursday, March 29, 2018 at 2:56 PM
To: Matt Glasser >, Keith Jamison 
>
Subject: Re: [HCP-Users] Intensity Normalization 3_22


here is the output file from the Volume script



From: Glasser, Matthew >
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_FLIRTBBRAndFreeSurferBBRbased

Matt.

From: "Sanchez, Juan (NYSPI)" 
>
Date: Thursday, March 29, 2018 at 12:54 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:43 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:36 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "hcp-users@humanconnectome.org" 

Re: [HCP-Users] Intensity Normalization 3_22

[Glasser, Matthew]

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, 2018 at 12:54 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:43 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:36 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:29 PM
To: Keith Jamison >, Matt Glasser 
>
Cc: "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 >
Sent: Thursday, March 29, 2018 12:35:38 PM
To: Glasser, 

Re: [HCP-Users] Intensity Normalization 3_22

[Sanchez, Juan (NYSPI)]

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 
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)" 
>
Date: Thursday, March 29, 2018 at 12:43 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:36 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:29 PM
To: Keith Jamison >, Matt Glasser 
>
Cc: "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 >
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 

Re: [HCP-Users] Intensity Normalization 3_22

[Glasser, Matthew]

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 Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:36 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:29 PM
To: Keith Jamison >, Matt Glasser 
>
Cc: "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 >
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 
> 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: 
>
 on behalf of "Sanchez, Juan (NYSPI)" 

Re: [HCP-Users] Intensity Normalization 3_22

[Sanchez, Juan (NYSPI)]

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, 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)" 
>
Date: Thursday, March 29, 2018 at 12:36 PM
To: Matt Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:29 PM
To: Keith Jamison >, Matt Glasser 
>
Cc: "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 >
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 
> 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: 
>
 on behalf of "Sanchez, Juan (NYSPI)" 
>
Date: Thursday, March 29, 2018 at 10:23 AM
To: "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 1 ${OutputfMRI} -odt float



I copied 

Re: [HCP-Users] Intensity Normalization 3_22

[Glasser, Matthew]

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 Glasser >, Keith Jamison 
>
Cc: "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 >
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)" 
>
Date: Thursday, March 29, 2018 at 12:29 PM
To: Keith Jamison >, Matt Glasser 
>
Cc: "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 >
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 
> 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: 
>
 on behalf of "Sanchez, Juan (NYSPI)" 
>
Date: Thursday, March 29, 2018 at 10:23 AM
To: "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 1 ${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

___
HCP-Users mailing list

Re: [HCP-Users] Intensity Normalization 3_22

[Sanchez, Juan (NYSPI)]

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] 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)" 
>
Date: Thursday, March 29, 2018 at 12:29 PM
To: Keith Jamison >, Matt Glasser 
>
Cc: "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 >
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 
> 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: 
>
 on behalf of "Sanchez, Juan (NYSPI)" 
>
Date: Thursday, March 29, 2018 at 10:23 AM
To: "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 1 ${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

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Intensity Normalization 3_22

[Glasser, Matthew]

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 
>
Cc: "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 >
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 
> 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: 
>
 on behalf of "Sanchez, Juan (NYSPI)" 
>
Date: Thursday, March 29, 2018 at 10:23 AM
To: "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 1 ${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

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Intensity Normalization 3_22

[Sanchez, Juan (NYSPI)]

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 
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 
> 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: 
>
 on behalf of "Sanchez, Juan (NYSPI)" 
>
Date: Thursday, March 29, 2018 at 10:23 AM
To: "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 1 ${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

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Intensity Normalization 3_22

[Keith Jamison]

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 
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:  on behalf of "Sanchez, Juan
> (NYSPI)" 
> Date: Thursday, March 29, 2018 at 10:23 AM
> To: "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 1 ${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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Re: [HCP-Users] Intensity Normalization 3_22

[Glasser, Matthew]

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)" 
>
Date: Thursday, March 29, 2018 at 10:23 AM
To: "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 1 ${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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