Re: [HCP-Users] Gradient power amplifier error

2016-12-01 Thread Harms, Michael 

BTW, Re (2): We are Excite/Refocus Pulse durations of 3840/7680 in our 1.5 mm 
protocol currently.

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of Michael Harms >
Date: Thursday, December 1, 2016 at 2:53 PM
To: neuroimage analyst 
>, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Gradient power amplifier error


Hi,
Re (1): I believe you need a license to run in FREE mode.  Do you have it?
Re (2): By how much was it clipped?  You could try reducing the flip angles — 
78/160 is what we’ve been using for HCP.  Or, increase the duration of the 
relevant pulse on the Sequence:Special tab.
Re (3): I see that your b_max is 2500 (not 1500).  Do you have multiple high 
b-value frames in a row?  If so, try interspersing them with the b=1000 frames. 
 It is a bit of a trial and error process.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of neuroimage analyst 
>
Date: Thursday, December 1, 2016 at 2:40 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Gradient power amplifier error


Hi,

We just installed the CMRR sequence on 3T Skyra (IDEA: VE11C). This was our 
first attempt to run the sequence on the scanner. Our desired resolution was 
1.5mm3 with 64 diffusion directions and 2 b-values (1K, 1,5K) and one b0. I 
have attached the sequence and the snapshot of the error. MB = 3, GRAPPA = 2; 
monopolar gradients; and MDDW diffusion mode.

  1.  We were unable to set the diffusion mode to FREE. It was greyed out. How 
do we change that?
  2.  Before the sequence ran, it gave an error of 1RF pulse clipped. Is there 
something that we can change so that we dont get this warning?
  3.  How can we resolve the power amplifier error?

We will appreciate any response that can help us to run the sequence on the 
scanner.

Thanks

Regards

VM.

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


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 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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


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 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

Re: [HCP-Users] Gradient power amplifier error

2016-12-01 Thread Harms, Michael 

Hi,
Re (1): I believe you need a license to run in FREE mode.  Do you have it?
Re (2): By how much was it clipped?  You could try reducing the flip angles — 
78/160 is what we’ve been using for HCP.  Or, increase the duration of the 
relevant pulse on the Sequence:Special tab.
Re (3): I see that your b_max is 2500 (not 1500).  Do you have multiple high 
b-value frames in a row?  If so, try interspersing them with the b=1000 frames. 
 It is a bit of a trial and error process.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: 
>
 on behalf of neuroimage analyst 
>
Date: Thursday, December 1, 2016 at 2:40 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Gradient power amplifier error


Hi,

We just installed the CMRR sequence on 3T Skyra (IDEA: VE11C). This was our 
first attempt to run the sequence on the scanner. Our desired resolution was 
1.5mm3 with 64 diffusion directions and 2 b-values (1K, 1,5K) and one b0. I 
have attached the sequence and the snapshot of the error. MB = 3, GRAPPA = 2; 
monopolar gradients; and MDDW diffusion mode.

  1.  We were unable to set the diffusion mode to FREE. It was greyed out. How 
do we change that?
  2.  Before the sequence ran, it gave an error of 1RF pulse clipped. Is there 
something that we can change so that we dont get this warning?
  3.  How can we resolve the power amplifier error?

We will appreciate any response that can help us to run the sequence on the 
scanner.

Thanks

Regards

VM.

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


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 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

Re: [HCP-Users] Distorted MNI space result (T?w_restore) -- maybe due to "bad" initial brain mask?

2016-12-01 Thread Harms, Michael 

Note that the scenes we’ve assembled for “StructuralQC” include a check of
the FNIRT registration.
You can find the scripts necessary to generate those scenes here:

https://github.com/Washington-University/StructuralQC

cheers,
-MH


--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 12/1/16, 1:04 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Gaurav Patel"  wrote:

We've been noticing similar masking issues with our non-HCP data acquired
on a GE MR750, and have found that fat sat in our sequence was turned off,
so we will attempt to do the same and report whether that changes things.

__
  gaurav patel
  gauravpa...@gmail.com
  www.neurofreak.net




On Dec 1, 2016, at 2:01 PM, Julien Dubois wrote:

> It looks like the Freesurfer pipeline does not make use of the MNI space
>registration from the last Prefreesurfer step.
> Hence, to correct for the suboptimal MNI registration due to the fat sat
>discrepancy, my plan of action is to:
> 1) generate a "no fat sat" T1w template
> 2) re-run AtlasRegistrationToMNI152_FLIRTandFNIRT.sh (last step of the
>PreFreesurfer pipeline)
> 3) re-run the PostFreesurfer pipeline
> Does that sound reasonable?
>
> If 2) doesn't work well, I'll look into using the T2w image for MNI
>space registration instead.
>
> - Julien
>
>
> Julien Dubois, PhD
> Postdoctoral Scientist
> Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles
> Department of the Humanities and Social Sciences, California Institute
>of Technology, Pasadena
> Tel: +1 (310)423-8377
> Web: http://nigiri.caltech.edu/~jdubois
>
>
> On Thu, Dec 1, 2016 at 10:24 AM, Glasser, Matthew 
>wrote:
> If you have a decent number of subjects that go through the pipelines
>okay, you can just generate another average template after MNI
>registration.  Else, there isn’t any particular reason why a T1w-based
>MNI registration is better than a T2w-based registration.  We probably
>should make a flag that automatically allows you to base the brain mask
>and atlas registration on the T2w image.
>
> Peace,
>
> Matt.
>
> From: Julien Dubois 
> Date: Thursday, December 1, 2016 at 11:49 AM
>
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Distorted MNI space result (T?w_restore) --
>maybe due to "bad" initial brain mask?
>
> Thank you Matt.
>
> I actually don't think the brain extraction is the culprit, after
>spending more time with the intermediate outputs. Indeed,
>T1w/T1w_acpc_dc_restore_brain.nii.gz actually looks quite good.
>
> The issue mostly arises at the fnirt step in
>AtlasRegistrationToMNI152_FLIRTandFNIRT.sh. And indeed, it is clear that
>the template from the HCP pipelines (MNI152_T1_2mm.nii.gz) is very dark
>between the brain and the skull, while my input image
>(T1w/T1w_acpc_dc_restore.nii.gz) is not. The best solution will thus
>consist in using a template with fat sat off.
>
> Any idea where I might find such a template? I'll look around, but if
>you have suggestions, let me know.
>
> - Julien
>
> Julien Dubois, PhD
> Postdoctoral Scientist
> Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles
> Department of the Humanities and Social Sciences, California Institute
>of Technology, Pasadena
> Tel: +1 (310)423-8377
> Web: http://nigiri.caltech.edu/~jdubois
>
>
> On Wed, Nov 30, 2016 at 5:41 PM, Glasser, Matthew 
>wrote:
> If you had a volume template in MNI space that had fat sat off, it might
>register better.  Alternatively you might modify the pipelines to use the
>brain mask from the T2w scan and to do the atlas registration from the
>T2w scan.
>
> Peace,
>
> Matt.
>
> From: Julien Dubois 
> Date: Wednesday, November 30, 2016 at 5:51 PM
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Distorted MNI space result (T?w_restore) --
>maybe due to "bad" initial brain mask?
>
> I am not sure -- I am checking with the people who acquired that data.
> I have had similar issues before with in-house data which does not have
>fat sat turned on.
> Do you recommend a tweak to the PreFreeSurfer pipeline if fat sat is not
>turned on?
>
> I now see that you recommmend fat sat in the HCP T1 protocol [“Fat
>suppr. = Water excit. Fast”] to reduce signal from bone marrow and scalp
>fat
>
> - Julien
>
> Julien Dubois, PhD
> Postdoctoral Scientist
> Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles
> Department of the Humanities and Social Sciences, California Institute
>of

Re: [HCP-Users] Exporting the dense connectome matrix

2016-12-01 Thread Glasser, Matthew 
The file you are requesting would exceed 200GB in size and as a result we don't 
support this (the equivalent CIFTI file is 32.5GB).

If you are having specific issues with analyzing CIFTI files, let us know what 
those are and we can help.

Peace,

Matt.

From: 
>
 on behalf of "Dayan, Eran" 
>
Date: Thursday, December 1, 2016 at 11:00 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Exporting the dense connectome matrix

Hi all,

I was wondering if there is an easy way to export the dense functional 
connectome matrix into a txt file? I am specifically interested in the voxel by 
voxel matrix, rather than the grayordinate matrix. Tried to download the 
relevant cifti file from DB and open it in MATLAB (using a dedicated toolbox) 
but failed. Is there a way to do this using Workbench? And if so, what would be 
the way to register the voxels of the matrix into MNI space?

Thanks!

Eran





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


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 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

[HCP-Users] Exporting the dense connectome matrix

2016-12-01 Thread Dayan, Eran 
Hi all,

I was wondering if there is an easy way to export the dense functional 
connectome matrix into a txt file? I am specifically interested in the voxel by 
voxel matrix, rather than the grayordinate matrix. Tried to download the 
relevant cifti file from DB and open it in MATLAB (using a dedicated toolbox) 
but failed. Is there a way to do this using Workbench? And if so, what would be 
the way to register the voxels of the matrix into MNI space?

Thanks!

Eran





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

Re: [HCP-Users] How to do cluster-level correction on the raw T statistical cifti data

2016-12-01 Thread Glasser, Matthew 
We recommend the PALM software package in FSL for this sort of thing:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM

Peace,

Matt.

From: 
>
 on behalf of Cai Yue >
Date: Thursday, December 1, 2016 at 6:55 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] How to do cluster-level correction on the raw T 
statistical cifti data

Dear HCP developers,

I have a problem with the cluster-level correction  on the cifti data. I have 
searched a lot on the internet about this issue, but haven't got solutions. I 
got the p and T cifti data from the GLM analysis. I am wonderting if there is a 
cluster-level method (like alphasim) to apply on the raw T or p statistical 
data.

Thanks,
Yue





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


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 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

[HCP-Users] How to do cluster-level correction on the raw T statistical cifti data

2016-12-01 Thread Cai Yue 
Dear HCP developers,


I have a problem with the cluster-level correction  on the cifti data. I have 
searched a lot on the internet about this issue, but haven't got solutions. I 
got the p and T cifti data from the GLM analysis. I am wonderting if there is a 
cluster-level method (like alphasim) to apply on the raw T or p statistical 
data. 


Thanks,
Yue 
 





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