[HCP-Users] -volume-label-import

[Sanchez, Juan (NYSPI)]

Dear HCP community

I am trying to create a labeled volume that will work with 
-cifti-create-dense-from-template

The volume data has over 100 ROI's and the cifti create function only imports 
specified labels


 CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT 
ALL_GREY_MATTER ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM 
CAUDATE_LEFT CAUDATE_RIGHT CEREBELLAR_WHITE_MATTER_LEFT 
CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT CEREBELLUM_RIGHT 
CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX 
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT 
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER 
PALLIDUM_LEFT PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT 
THALAMUS_RIGHT


I need to import all of the labeled ROI's values from the nii into the 
subortical cifti. I tried labeling all of the ROI's with OTHER and name 
collision in the input names did not allow that to work.


Does anyone know how to solve this or a work around

Thanks so much

J


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Re: [HCP-Users] FreeSurfer6 subcortical segmentation

[Sanchez, Juan (NYSPI)]

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We are  implementing the segmentHA_T1.sh and the segmentThalamicNuclei.sh 
scripts that are int he bin directory of FreeSurfer 6 (dev)


We are currently working on generating these from the Freesurfer output of the 
HCP Pipelines and then transforming them into the subject MNI Surface Space.


J






From: Glasser, Matthew 
Sent: Wednesday, February 6, 2019 6:29:21 PM
To: Sanchez, Juan (NYSPI); hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] FreeSurfer6 subcortical segmentation


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


I don’t see these being generated in our current test FreeSurfer 6.0 runs.  How 
are they generated?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Date: Wednesday, February 6, 2019 at 12:56 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] FreeSurfer6 subcortical segmentation


Hey HCP community

When Freesurfer 6.0  is implemented into the HCP Pipeline, are there plans to 
use the subcortical segmentation script outputs (amygdala and thalamus mgz 
files) into cifti space (column 3)?

If so will they be an addition to the current ROI atlas or will they be 
separate?


Thanks so much

Juan



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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
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immediately notify the sender via telephone or return mail.

[HCP-Users] FreeSurfer6 subcortical segmentation

[Sanchez, Juan (NYSPI)]

Hey HCP community

When Freesurfer 6.0  is implemented into the HCP Pipeline, are there plans to 
use the subcortical segmentation script outputs (amygdala and thalamus mgz 
files) into cifti space (column 3)?

If so will they be an addition to the current ROI atlas or will they be 
separate?


Thanks so much

Juan



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[HCP-Users] stable version with freesurfer 6

[Sanchez, Juan (NYSPI)]

Dear HCP community

We have just upgraded our magnet and have had success implementing a modified 
version of the 3_22 Pipelines. I wanted to inquire if there was a stable 
version with FreeSurfer 6.0 and if there has been any progress made on the NHP 
pipelines?

Thanks so much

Juan Sanchez

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Re: [HCP-Users] stable pipeline version

[Sanchez, Juan (NYSPI)]

Thank you Matt.

Will there be an announcement re: the FreeSurfer?

Best

Juan


From: Glasser, Matthew 
Sent: Tuesday, October 9, 2018 10:10:29 PM
To: Sanchez, Juan (NYSPI); hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] stable pipeline version


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


If you can wait a week or two we will have some useful updates out.  Also there 
is the impending switch to FreeSurfer 6.0 that would be good to have.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Date: Tuesday, October 9, 2018 at 9:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] stable pipeline version


We have been using the 3.4 version of the pipelines to process data acquired 
locally.   Our lab wants to switch over to the latest versions as we upgrade 
our magnet. Is there a stable release of the pipelines? I was going to clone 
the 3.27 version from github and proceed from there. However,  the last time we 
tried this with 3.22, we had to download and implement a number of fixes that 
were not a part of the 3.22 download.  Could you suggest the best way to 
implement the most current and stable versions?  Thanks

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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
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[HCP-Users] stable pipeline version

[Sanchez, Juan (NYSPI)]

We have been using the 3.4 version of the pipelines to process data acquired 
locally.   Our lab wants to switch over to the latest versions as we upgrade 
our magnet. Is there a stable release of the pipelines? I was going to clone 
the 3.27 version from github and proceed from there. However,  the last time we 
tried this with 3.22, we had to download and implement a number of fixes that 
were not a part of the 3.22 download.  Could you suggest the best way to 
implement the most current and stable versions?  Thanks

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[HCP-Users] border to rois

[Sanchez, Juan (NYSPI)]

Dear HCP community

When creating dlabel ROIs from border files in workbench we are having trouble 
including the border perimeter on the surface.

Does anyone have any suggestions?

Best

Juan Sanchez-Pena

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Re: [HCP-Users] HCP-Users Digest, Vol 68, Issue 11

[Sanchez, Juan (NYSPI)]

Dear HCP community

Could you please attach the FreeSurferNHP.sh as a zip or tar file.

Our email system scrubbed the attachment


Best

Juan Sanchez-Pena


From: hcp-users-boun...@humanconnectome.org 
 on behalf of 
hcp-users-requ...@humanconnectome.org 
Sent: Wednesday, July 11, 2018 5:57:47 PM
To: hcp-users@humanconnectome.org
Subject: HCP-Users Digest, Vol 68, Issue 11

ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


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When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. FreeSurferNHP.sh (Sanchez, Juan (NYSPI))
   2. Re: A few specific questions about the HCP data | MNI space
  dedrifting & file structure (Bajada, Claude Julien)
   3. Re: access to hcp-openaccess-temp (Timothy Coalson)
   4. Re: A few specific questions about the HCP data | MNI space
  dedrifting & file structure (Timothy Coalson)
   5. PreFreeSurferPipeline debugging (Jayasekera, Dinal)


--

Message: 1
Date: Wed, 11 Jul 2018 17:47:32 +0000
From: "Sanchez, Juan (NYSPI)" 
Subject: [HCP-Users] FreeSurferNHP.sh
To: "hcp-users@humanconnectome.org" 
Message-ID:



Content-Type: text/plain; charset="iso-8859-1"

Dear HCP community,

We would like to acquire the latest NHP Pipelines for the HCP Pipelines

Thanks so much

Juan Sanchez-Pena

NYSPI

Columbia University
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Message: 2
Date: Wed, 11 Jul 2018 17:50:37 +
From: "Bajada, Claude Julien" 
Subject: Re: [HCP-Users] A few specific questions about the HCP data |
MNI space dedrifting & file structure
To: Timothy Coalson , "Glasser, Matthew"

Cc: "hcp-users@humanconnectome.org" 
Message-ID:
<99176650acf65a45b95648a7300357f61175f...@mbx2010-e01.ad.fz-juelich.de>

Content-Type: text/plain; charset="us-ascii"

Hi Tim,

I am trying to follow the drifting procedure below. Can I clarify a few points?

You state:
"Once you have this average, you can invert it (like any other warpfield), and 
then concatenate it after the acpc to MNI warp for each subject, giving you a 
new dedrifted (for the chosen population) template space."

>From this I understand that the multiplication and inversion gives us a warp 
>field that warps the MNI registered subject to the new "drifted" space, 
>correct?

By "concatenate it after the acpc to MNI warp" do you mean multiply the 
acpc2mni warp by the new mni2dedrift? Thus generating an acpc2dedrift?

Second, you state: "By carefully finding the volume of brain masks in acpc 
space and after resampling to this new dedrifted space, you can check for this 
effect"

What exactly am I meant to be checking? I should compare the volume of the mask 
in acpc (native) space and in the drifted space. Should they be roughly the 
same volume? Also you say that I should "carefully find the volume" what 
exactly do you mean by "carefully"

Thanks in advance,

Claude


From: Timothy Coalson [tsc...@mst.edu]
Sent: 02 July 2018 19:28
To: Glasser, Matthew
Cc: Harms, Michael; Bajada, Claude Julien; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A few specific questions about the HCP data | MNI 
space dedrifting & file structure

We previously looked at the MNI drift, and found that it is almost entirely an 
affine, even for the nonlinear template.  We have a suspicion that this means 
that it was originally caused by the early MNI linear template, and that the 
issue was known by the time MNI nonlinear templates were released, as it 
implies that the nonlinear template was dedrifted, but then an affine was 
deliberately added in order to match the previous MNI linear template.  
However, we have not investigated whether this was the case.

Since all of our anatomical size and shape measurements are computed using a 
rigid acpc space (after gradient distortion correction), this drift in MNI 
space is largely unimportant to many steps of analysis of things like fMRI.  Be 
aware that even with proper dedrifting, any non-rigid volume regi

[HCP-Users] FreeSurferNHP.sh

[Sanchez, Juan (NYSPI)]

Dear HCP community,

We would like to acquire the latest NHP Pipelines for the HCP Pipelines

Thanks so much

Juan Sanchez-Pena

NYSPI

Columbia University

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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 <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

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 <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<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

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 <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<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 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

[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 <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<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 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] HCP-Users Digest, Vol 64, Issue 2

[Sanchez, Juan (NYSPI)]

They do!

From: Glasser, Matthew <glass...@wustl.edu>
Sent: Friday, March 2, 2018 2:25:47 PM
To: Sanchez, Juan (NYSPI); hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


So you are saying that the Pipelines work fine on the Mac for you aside from 
this cp issue?

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: Friday, March 2, 2018 at 1:24 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2


Dear Kwan-Jin Jung

I had rthe same problems when I installed the 3_22 HCP Pipleines

Here is what we did:


  1.  syntax in scripts: Just remove the "--preserve=timestamps" from all of 
the Pipeline scripts

2. workbench: Get the "dev_latest" zip file that says "mac64" from here:

http://brainvis.wustl.edu/workbench/



From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of 
hcp-users-requ...@humanconnectome.org<mailto:hcp-users-requ...@humanconnectome.org>
 
<hcp-users-requ...@humanconnectome.org<mailto:hcp-users-requ...@humanconnectome.org>>
Sent: Friday, March 2, 2018 1:00:01 PM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: HCP-Users Digest, Vol 64, Issue 2

ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


Send HCP-Users mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to

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You can reach the person managing the list at

hcp-users-ow...@humanconnectome.org<mailto:hcp-users-ow...@humanconnectome.org>

When replying, please edit your Subject line so it is more specific
than "Re: Contents of HCP-Users digest..."


Today's Topics:

   1. Re: Best Approach for using old volumetric data to pick
  parcels-of-interest (Stevens, Michael)
   2. Movement regressor missing (Linnman, Clas,Ph.D.)
   3. Re: Movement regressor missing (Glasser, Matthew)
   4. Error in FreeSurfer processing "recon-all.v6.hires: command
  not found" (Pubuditha Abeyasinghe)
   5. Re: Error in FreeSurfer processing "recon-all.v6.hires:
  command not found" (Glasser, Matthew)
   6. Re: Error in FreeSurfer processing "recon-all.v6.hires:
  command not found" (Timothy B. Brown)
   7. Re: Best Approach for using old volumetric data to pick
  parcels-of-interest (Timothy Coalson)
   8. Re: ROI cluster centers to surface grayordinates (Timothy Coalson)
   9. Re: Best Approach for using old volumetric data to pick
  parcels-of-interest (Erin W. E. Dickie)
  10. Re: Correct interpretation of NIH battery test
  'Words-in-Noise' in HCP subjects (Robert Becker)
  11. Split dtseries (A R)
  12. Re: Split dtseries (Glasser, Matthew)
  13. Change of FreeSurferHiresPial.sh for MacBook IOS (Kwan-Jin Jung)
  14. Re: Change of FreeSurferHiresPial.sh for MacBook IOS
  (Glasser, Matthew)


--

Message: 1
Date: Thu, 1 Mar 2018 19:22:32 +
From: "Stevens, Michael" 
<michael.stev...@hhchealth.org<mailto:michael.stev...@hhchealth.org>>
Subject: Re: [HCP-Users] Best Approach for using old volumetric data
to pick parcels-of-interest
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, "Glasser, Matthew"
<glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Erin W. E. Dickie" 
<erin.w.dic...@gmail.com<mailto:erin.w.dic...@gmail.com>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Message-ID:

<1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org<mailto:1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org>>
Content-Type: text/plain; charset="utf-8

Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2

[Sanchez, Juan (NYSPI)]

Dear Kwan-Jin Jung

I had rthe same problems when I installed the 3_22 HCP Pipleines

Here is what we did:


  1.  syntax in scripts: Just remove the "--preserve=timestamps" from all of 
the Pipeline scripts

2. workbench: Get the "dev_latest" zip file that says "mac64" from here:

http://brainvis.wustl.edu/workbench/



From: hcp-users-boun...@humanconnectome.org 
 on behalf of 
hcp-users-requ...@humanconnectome.org 
Sent: Friday, March 2, 2018 1:00:01 PM
To: hcp-users@humanconnectome.org
Subject: HCP-Users Digest, Vol 64, Issue 2

ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


Send HCP-Users mailing list submissions to
hcp-users@humanconnectome.org

To subscribe or unsubscribe via the World Wide Web, visit
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
or, via email, send a message with subject or body 'help' to
hcp-users-requ...@humanconnectome.org

You can reach the person managing the list at
hcp-users-ow...@humanconnectome.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of HCP-Users digest..."


Today's Topics:

   1. Re: Best Approach for using old volumetric data to pick
  parcels-of-interest (Stevens, Michael)
   2. Movement regressor missing (Linnman, Clas,Ph.D.)
   3. Re: Movement regressor missing (Glasser, Matthew)
   4. Error in FreeSurfer processing "recon-all.v6.hires: command
  not found" (Pubuditha Abeyasinghe)
   5. Re: Error in FreeSurfer processing "recon-all.v6.hires:
  command not found" (Glasser, Matthew)
   6. Re: Error in FreeSurfer processing "recon-all.v6.hires:
  command not found" (Timothy B. Brown)
   7. Re: Best Approach for using old volumetric data to pick
  parcels-of-interest (Timothy Coalson)
   8. Re: ROI cluster centers to surface grayordinates (Timothy Coalson)
   9. Re: Best Approach for using old volumetric data to pick
  parcels-of-interest (Erin W. E. Dickie)
  10. Re: Correct interpretation of NIH battery test
  'Words-in-Noise' in HCP subjects (Robert Becker)
  11. Split dtseries (A R)
  12. Re: Split dtseries (Glasser, Matthew)
  13. Change of FreeSurferHiresPial.sh for MacBook IOS (Kwan-Jin Jung)
  14. Re: Change of FreeSurferHiresPial.sh for MacBook IOS
  (Glasser, Matthew)


--

Message: 1
Date: Thu, 1 Mar 2018 19:22:32 +
From: "Stevens, Michael" 
Subject: Re: [HCP-Users] Best Approach for using old volumetric data
to pick parcels-of-interest
To: Timothy Coalson , "Glasser, Matthew"

Cc: "Erin W. E. Dickie" ,
"hcp-users@humanconnectome.org" 
Message-ID:
<1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org>
Content-Type: text/plain; charset="utf-8"

Hi Tim,

Thanks.  That?s clear and sounds like a really reasonable approach.

Can you point me towards the exact files I?d need to reference and maybe 
suggest which function calls I?ll need to use to do the volume-to-surface 
mapping you describe?  I?ll whip up a quick script to loop through about 120 
datasets from this R01 project and let you know how well it works.

Mike


From: Timothy Coalson [mailto:tsc...@mst.edu]
Sent: Friday, February 23, 2018 6:49 PM
To: Glasser, Matthew
Cc: Stevens, Michael; Erin W. E. Dickie; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Best Approach for using old volumetric data to pick 
parcels-of-interest

This is an email from Outside HHC. USE CAUTION opening attachments or links 
from unknown senders.

Surface-based methods may boost your statistical power enough (by better 
alignment, exclusion of irrelevant tissue, and smoothing that doesn't cross 
sulcal banks, if you decide you need smoothing) that you may not need to rely 
as much on existing ROIs.  Parcel-based statistics have a lot of power, because 
the multiple comparisons are orders of magnitude smaller, spatially independent 
noise averages out, and the signal averages together.  We believe that a lot of 
old data would benefit from reanalysis using surfaces.

However, our paper is mainly focused on specificity and continuous data.  If 
you have a binary volume ROI and you only need a rough guess of it on the 
surface, you can get approximate answers, in a way that should reduce false 
negatives (and give more false positives) from the surface/volume transition 
problems.  You can map the ROI to the anatomical MNI surfaces of a group of 
subjects, and take the max across subjects.  Each individual may miss the 
expected group ribbon location in any given location, but it is very likely 
that every point in the expected group ribbon location will 

[HCP-Users] version updates and FreeSurferNHP.sh

[Sanchez, Juan (NYSPI)]

Dear hcp community


We were able to successfully run the 3_22 pipelines (with the updated 
PostFreeSurfer scripts) on our GE magnet using the development workbench 
software.

I wanted to ask the community if there were any fsl and freesurfer version 
requirements for these pipelines or if we could just use the latest verisons of 
each


I also wanted to inquire about any recent pipeline developments for the Non 
Human Primate pipelines

Thanks

J

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Re: [HCP-Users] workbench command error from 3_22 Pipelines

[Sanchez, Juan (NYSPI)]

Thank you David I truncated the paste

Here it is:

While running:

/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
 -surface-distortion 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.sphere.native.surf.gii
 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.sphere.reg.reg_LR.native.surf.gii
 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.Strain_FS.native.shape.gii
 -local-affine-method


ERROR: Unexpected parameter: -local-affine-method



From: Sanchez, Juan (NYSPI)
Sent: Friday, January 12, 2018 10:29:52 AM
To: hcp-users@humanconnectome.org
Subject: workbench command error from 3_22 Pipelines

Dear HCP community,
We are using the  latest Pipeline 3_22 with updated scripts from:  
(https://github.com/Washington-University/Pipelines)
While running PostFreeSurferPipelineBatch.sh I am getting the following 
workbench error

While running:

/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
 -surface-distortion 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.sphere.native.surf.gii
 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.sphere.reg.reg_LR.native.surf.gii
 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.Strain_FS.native.shape.gii
 -local-affine-method

We are using version 1.2.3



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[HCP-Users] workbench command error from 3_22 Pipelines

[Sanchez, Juan (NYSPI)]

Dear HCP community,
We are using the  latest Pipeline 3_22 with updated scripts from:  
(https://github.com/Washington-University/Pipelines)
While running PostFreeSurferPipelineBatch.sh I am getting the following 
workbench error

While running:

/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
 -surface-distortion 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.sphere.native.surf.gii
 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.sphere.reg.reg_LR.native.surf.gii
 
/data/data7/ABCD_beta/ABCD_3_22/ABCD_01/MNINonLinear/Native/ABCD_01.L.Strain_FS.native.shape.gii
 -local-affine-method

We are using version 1.2.3



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Re: [HCP-Users] Resting State processing

[Sanchez, Juan (NYSPI)]

I was having the same problem with the 3_22  
FreeSurfer2CaretConvertAndRegisterNonlinear.sh
and was able to download the msm binaried and the params file from 
https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v1/

however I am runinng into a problem with the script at

${MSMBin}/msm --levels=4 --conf=${MSMBin}/allparameterssulcDRconf 
--inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
 
--trans="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
 
--refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
 
--indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii
 
--refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii
 --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose

cd $DIR

cp 
"$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii
 
"$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii

The HIGHRES file does not exist.

From: hcp-users-boun...@humanconnectome.org 
 on behalf of Timothy Hendrickson 

Sent: Tuesday, January 9, 2018 12:11:20 PM
To: Glasser, Matthew
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Resting State processing


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


Hi Matthew,

The file does not exist. I see now that the PostFreeSurfer pipeline I have 
locally is different than the latest version found on github (specifically 
FreeSurfer2CaretConvertAndRegisterNonlinear.sh). I see that the line 
referencing allparameterssulcDRconf has been commented out in favor of 
MSMSulcStrainFinalconf, however, this file does not appear to exist either. 
Which version of MSM HOCR is the most recent that should be used? I am using 
version 2)

On a completely other note why aren't these configuration files already 
included in the HCP pipelines? It seems very burdensome to require each user to 
mimic the exact version of the MSM binaries that 
FreeSurfer2CaretConvertAndRegisterNonlinear.sh expects.

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew 
> wrote:
Does the file exist?  That might be the old config file it is looking for 
suggesting that you don’t have the latest master.

Peace,

Matt.

From: Timothy Hendrickson >
Date: Monday, January 8, 2018 at 9:15 AM
To: "hcp-users@humanconnectome.org" 
>
Cc: Matt Glasser >
Subject: Re: [HCP-Users] Resting State processing

Hello all,

Despite having the most recent version of the hcp pipeline (3.22) and 
downloading the MSM configuration binaries, however, I am still receiving an 
error when I attempt to run the PreFreeSurfer pipeline with RegName="MSMSulc". 
This is the error message I receive: 
/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
 Couldn't open the file!

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)


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