Re: [HCP-Users] -probtrackx-dot-convert volume label problem

[Timothy Coalson]

As a guess, did you use "-crop" when you used -cifti-separate to get the
amygdala ROI?  If so, that changes the volume space (specifically the FOV),
so indices don't correspond with the normal 2mm volume space.  This would
mean that you now need to make a label volume in this new FOV space.
Alternatively, you could get the ROI without using -crop, rerun probtrackx,
and then the standard Atlas_ROIs file will work.

The  must have the same dimensions and origin/spacing as the roi
file you used in probtrackx, otherwise the indices won't match.  I would
not call an amygdala-only volume "Atlas_ROIs", that would be misleading,
and you should double check your amygdala ROI file for its value, as it
probably uses 1 rather than 18, and fix the labels text file based on that,
but the -volume-label-import command otherwise looks like it would produce
something that should work for your current probtrackx results.

Tim


On Wed, Nov 2, 2016 at 7:20 AM, Maarten Vaessen  wrote:

> Hello,
>
> I'm trying to convert a .dot from probtrackx2 with -matrix3 option to a
> dconn.nii. The -lrtarget was a list containing all volumes and surfaces
> conforming to the HCP grayordinate file. The -target3 is the L (or R)
> amygdala from Atlas_ROI.2.nii.gz. The output from probtrackx2 looks
> sensible.
>
> I use the following command and get this error:
> wb_command -probtrackx-dot-convert fdt_matrix3.dot fdt_matrix3.dconn.nii
> -col-cifti 91282_Greyordinates.dscalar.nii COLUMN -row-voxels
> coords_for_fdt_matrix3 amyL_label_from_Atlas.nii.gz
>
> ERROR: voxel index in list file did not match a structure: 0, 1, 56
>
>
> Now, I am not sure what to use as input for -probtrackx-dot-convert
> -row-voxels:
>
> [-row-voxels] - the output mapping along a row will be voxels
>
>  - a text file containing IJK indices for the voxels
>  used
> --> this should be the coords_for_fdt_matrix3 right?
>
>  - a label volume with the dimensions and sform used, with
> structure labels
> --> here I am a bit lost. I tried several options, the probably most
> sensible being:
> wb_command -volume-label-import subj/MNINonLinear/ROIs/Atlas_ROIs.2.nii
> amyL_label.txt amyL_label_from_Atlas.nii.gz -discard-others
>
> amyL_label.txt =
> AMYGDALA_LEFT
> 18 103 255 255 255
>
> What would be the correct input to get this to work?
>
> Thx,
>
> -Maarten
>
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Re: [HCP-Users] Myelin Map Summary Statistics

[Timothy Coalson]

Use -cifti-weighted-stats, it reports the measures separately per
hemisphere (and can integrate over surface area instead of a naive mean),
and use the -roi option to report within an ROI.  If you want to use a lot
of ROIs that don't overlap, look at -cifti-parcellate.

Tim


On Wed, Nov 2, 2016 at 3:20 PM, Timothy Hendrickson 
wrote:

> Thanks Matt.
>
> Hmm I am still confused. So here is my command to extract myelin for the
> entire cortex: wb_command -cifti-stats 43387.MyelinMap.32k_fs_LR.dscalar.nii
> -reduce MEAN.
> Since -cifti-stats requires the -reduce flag the data I receive is only
> one number. What I am hoping to accomplish is to extract the average
> surface myelin for the left and right hemisphere and all surface ROIs.
> For example with freesurfer I can rather easily generate a stats file
> which informs me a measurement (of my choosing) at each particular
> location. For example see attached: lh.allSite.aparc.thickness.csv.
>
> I apologize for the continued questions. I am fairly new to HCP data and
> am still learning the in and outs :)
>
> -Tim
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
>
> On Wed, Nov 2, 2016 at 1:20 PM, Glasser, Matthew 
> wrote:
>
>> You should be able to do that with the commands Tim mentioned with the
>> -roi sub option.
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of Timothy
>> Hendrickson 
>> Date: Wednesday, November 2, 2016 at 11:42 AM
>> To: Timothy Coalson 
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] Myelin Map Summary Statistics
>>
>> Hmm, I have a follow up question. I can extract average myelin for the
>> entire cortex rather easily however I am having more trouble extracting
>> hemispheric and ROI information.
>> Suggestions?
>>
>> Timothy Hendrickson
>> Department of Psychiatry
>> University of Minnesota
>> Mobile: 507-259-3434 (texts okay)
>>
>> On Mon, Oct 31, 2016 at 3:45 PM, Timothy Coalson  wrote:
>>
>>> Take a look at http://www.humanconnectome.org/software/workbench-command
>>> .php?function=-cifti-weighted-stats and/or http://www.humanconnect
>>> ome.org/software/workbench-command.php?function=-cifti-stats .
>>>
>>> Tim
>>>
>>>
>>> On Mon, Oct 31, 2016 at 3:32 PM, Timothy Hendrickson 
>>> wrote:
>>>
 HCP experts,

 Is there a way to extract myelin values from individual dscalar CIFTI
 files?
 What I am looking for is an average myelin value at the hemispheric and
 ROI level.

 -Tim

 Timothy Hendrickson
 Department of Psychiatry
 University of Minnesota
 Mobile: 507-259-3434 (texts okay)

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 HCP-Users@humanconnectome.org
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>>>
>>>
>> ___
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>> 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.
>>
>
>

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Re: [HCP-Users] Myelin Map Summary Statistics

[Timothy Hendrickson]

Thanks Matt.

Hmm I am still confused. So here is my command to extract myelin for the
entire cortex: wb_command -cifti-stats
43387.MyelinMap.32k_fs_LR.dscalar.nii -reduce MEAN.
Since -cifti-stats requires the -reduce flag the data I receive is only one
number. What I am hoping to accomplish is to extract the average surface
myelin for the left and right hemisphere and all surface ROIs.
For example with freesurfer I can rather easily generate a stats file which
informs me a measurement (of my choosing) at each particular location. For
example see attached: lh.allSite.aparc.thickness.csv.

I apologize for the continued questions. I am fairly new to HCP data and am
still learning the in and outs :)

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)

On Wed, Nov 2, 2016 at 1:20 PM, Glasser, Matthew  wrote:

> You should be able to do that with the commands Tim mentioned with the
> -roi sub option.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Timothy
> Hendrickson 
> Date: Wednesday, November 2, 2016 at 11:42 AM
> To: Timothy Coalson 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Myelin Map Summary Statistics
>
> Hmm, I have a follow up question. I can extract average myelin for the
> entire cortex rather easily however I am having more trouble extracting
> hemispheric and ROI information.
> Suggestions?
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
>
> On Mon, Oct 31, 2016 at 3:45 PM, Timothy Coalson  wrote:
>
>> Take a look at http://www.humanconnectome.org/software/workbench-command
>> .php?function=-cifti-weighted-stats and/or http://www.humanconnect
>> ome.org/software/workbench-command.php?function=-cifti-stats .
>>
>> Tim
>>
>>
>> On Mon, Oct 31, 2016 at 3:32 PM, Timothy Hendrickson 
>> wrote:
>>
>>> HCP experts,
>>>
>>> Is there a way to extract myelin values from individual dscalar CIFTI
>>> files?
>>> What I am looking for is an average myelin value at the hemispheric and
>>> ROI level.
>>>
>>> -Tim
>>>
>>> Timothy Hendrickson
>>> Department of Psychiatry
>>> University of Minnesota
>>> Mobile: 507-259-3434 (texts okay)
>>>
>>> ___
>>> 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
>
>
> --
>
> 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.
>

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Subject Number,lh_bankssts_thickness,lh_caudalanteriorcingulate_thickness,lh_caudalmiddlefrontal_thickness,lh_cuneus_thickness,lh_entorhinal_thickness,lh_fusiform_thickness,lh_inferiorparietal_thickness,lh_inferiortemporal_thickness,lh_isthmuscingulate_thickness,lh_lateraloccipital_thickness,lh_lateralorbitofrontal_thickness,lh_lingual_thickness,lh_medialorbitofrontal_thickness,lh_middletemporal_thickness,lh_parahippocampal_thickness,lh_paracentral_thickness,lh_parsopercularis_thickness,lh_parsorbitalis_thickness,lh_parstriangularis_thickness,lh_pericalcarine_thickness,lh_postcentral_thickness,lh_posteriorcingulate_thickness,lh_precentral_thickness,lh_precuneus_thickness,lh_rostralanteriorcingulate_thickness,lh_rostralmiddlefrontal_thickness,lh_superiorfrontal_thickness,lh_superiorparietal_thickness,lh_superiortemporal_thickness,lh_supramarginal_thickness,lh_frontalpole_thickness,lh_temporalpole_thickness,lh_transversetemporal_thickness,lh_insula_thickness,lh_MeanThickness_thickness
CCA239,2.843,2.729,2.975,2.033,3.502,2.811,2.855,3.035,2.547,2.296,2.899,2.159,2.73,3.223,2.958,2.901,3.203,3.37,3.032,1.77,2.6,2.977,2.984,2.685,3.344,2.865,3.216,2.522,3.345,2.979,3.527,4.191,2.822,3.57,2.86983
CCA240,2.335,2.761,2.671,1.864,2.384,2.494,2.447,2.662,2.382,1.966,2.545,1.942,2.571,2.806,2.552,2.445,2.678,2.537,2.498,1.608,1.965,2.48,2.697,2.331,3.117,2.45,2.848,2.222,2.747,2.723,2.361,3.593,2.122,3.168,2.48027

[HCP-Users] redefining the trial

[mehdy dousty]

Hello,
I am using the preprocessed data of resting state MEG signal, in the
Matlab matrix the data is divided into  2 seconds, then for the work I am
dealing with right now we need around 10 seconds of the data, 5 trials ,
thus the data is redefined to 10 seconds, and as we expect there is no
discontinuity on electrode level , BUT when I compute the  inverse problem
by sLoretta the time series of each source has that exact 5 times
discontinuity, so I checked the result for different number of trials and
this happened again? so as it is so odd to me, I would like to know
your opinion about it and how can I solve it?
Thanks

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Re: [HCP-Users] correlation

[nailin yao]

Thank you Matt!

Best,
Nailin

2016-11-02 14:53 GMT-04:00 Glasser, Matthew :

> The fMRI data are already in standard CIFTI space.
>
> Peace,
>
> Matt.
>
> From: nailin yao 
> Date: Wednesday, November 2, 2016 at 1:52 PM
> To: Matt Glasser 
> Cc: Timothy Coalson , "hcp-users-request@
> humanconnectome.org" , "
> hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] correlation
>
> Thank you Tim and Matt,
>
> So when I extract hippocampus from Atlas_ROIs.2.nii.gz, and use it as roi
> to do -cifti-average-roi-correlation on one of the subject, does the ROI
> automatically overlay on the native subcortical space of that subject, or
> normalized space which is the same for everyone? Thank you!
>
> Best,
> Nailin
>
> 2016-11-01 19:15 GMT-04:00 Glasser, Matthew :
>
>> I think he wants to do a correlation of an ROI of the hippocampus.  There
>> you would benefit from doing as Tim suggests, but then using
>> wb_command -cifti-average-roi-correlation
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of Timothy
>> Coalson 
>> Date: Tuesday, November 1, 2016 at 5:06 PM
>> To: nailin yao 
>> Cc: "hcp-users-requ...@humanconnectome.org" <
>> hcp-users-requ...@humanconnectome.org>, "hcp-users@humanconnectome.org" <
>> hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] correlation
>>
>> One way to do this is to use -cifti-separate on a small 91k grayordinates
>> cifti with "-volume HIPPOCAMPUS_LEFT  -roi "
>> and similar for right hippocampus, then combine the left and right ROIs
>> with -volume-math.  You could also extract the labels from the
>> Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz file
>> with -volume-label-to-roi.
>>
>> Tim
>>
>>
>> On Tue, Nov 1, 2016 at 4:49 PM, nailin yao  wrote:
>>
>>> Hi,
>>>
>>> I'm trying to do an overall correlation from hippocampus on cifti file (
>>>
>>> rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii), and I run the command:
>>>
>>>
>>>  ./wb_command -cifti-correlation /Users/ny87/temp/S0009QPW/MNIN
>>> onLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii
>>> /Users/ny87/temp/S0009QPW/MNINonLinear/try_hipp_corr.dscalar.nii
>>> -roi-override -vol-roi /Users/ny87/temp/S0009QPW/MNIN
>>> onLinear/try_output_hipp.nii
>>>
>>>
>>> which result is ERROR: roi volume space doesn't match cifti volume space.
>>>
>>>
>>> May I know which atlas file is the right one to extract hippocampus ROI
>>> ?
>>>
>>>
>>> Thank you very much!
>>>
>>>
>>> Best,
>>>
>>> Nailin
>>>
>>> --
>>> Nailin Yao,  PhD
>>>
>>> Postdoctoral Associate
>>> Department of Psychiatry, Yale University
>>>
>>> ___
>>> 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
>>
>>
>> --
>>
>> 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.
>>
>
>
>
> --
> Nailin Yao,  PhD
>
> Postdoctoral Associate
> Department of Psychiatry, Yale University
>
>
> --
>
> 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.
>



-- 
Nailin Yao,  PhD

Postdoctoral Associate
Department of Psychiatry, Yale University

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Re: [HCP-Users] FNIRT for HCP diffusion data

[Glasser, Matthew]

You can use the nodif_brain_mask for this.  As for questions about the FDT GUI, 
you will have to ask those on the FSL list as I am only familiar with the 
probtrackx command line.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Wednesday, November 2, 2016 at 1:58 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

Many thanks Matt.
I ran probtrackx with no XFM then.
It seemed that probtrackx completed successfully, although I got this error at 
the very end:

[cid:ADA2B284-976C-43DC-A8A3-0F49A79CD654]

Any idea?

From: "Glasser, Matthew" >
Date: Wednesday, November 2, 2016 at 2:30 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

No need for XFMs.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Wednesday, November 2, 2016 at 1:19 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

So just to see if I understood your point, If I use surfaces in 
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k for probtrackx, then there is no 
need to provide –xfm and —inxfm transform arguments? Or do I still need to run 
FNIRT between diffusion space and T1w and use the results in —xfm and —xfm 
arguments of probtrackx?

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:41 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

The MMP1.0 ROIs are not registered to a 3D average brain.  They exist on a 2D 
standard surface mesh.  I mention below the individual subject versions of this 
surface mesh that you could use for tractography.  In that case, you would use 
the white matter surface as your waypoint and the pial surface as your stop.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Tuesday, November 1, 2016 at 6:39 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

My plan is indeed to run probtrackx using surface ROIs. But since HCP diffusion 
data is not registered to the average brain template of the MMP1.0 ROIs, my 
question is what is the recommended way of running FNIRT for doing so? What is 
the appropriate template file(T1w)? And is there any config file HCP releases 
to be used by FNIRT?

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:29 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

You can map the parcellation from the surface to the volume using the white and 
pial surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k and the 
ribbon-based option.  Also, some tractography tools like probtrackx allow you 
to track directly to surface ROIs (which is better).

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Tuesday, November 1, 2016 at 6:27 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

Hi Matt.,

Yes, It is an HCP subject.

Thanks,
Kamal

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:25 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

Is this an HCP subject or another subject?

Peace,

Matt.

From: 

Re: [HCP-Users] FNIRT for HCP diffusion data

[Shadi, Kamal]

Many thanks Matt.
I ran probtrackx with no XFM then.
It seemed that probtrackx completed successfully, although I got this error at 
the very end:

[cid:ADA2B284-976C-43DC-A8A3-0F49A79CD654]

Any idea?

From: "Glasser, Matthew" >
Date: Wednesday, November 2, 2016 at 2:30 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

No need for XFMs.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Wednesday, November 2, 2016 at 1:19 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

So just to see if I understood your point, If I use surfaces in 
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k for probtrackx, then there is no 
need to provide –xfm and —inxfm transform arguments? Or do I still need to run 
FNIRT between diffusion space and T1w and use the results in —xfm and —xfm 
arguments of probtrackx?

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:41 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

The MMP1.0 ROIs are not registered to a 3D average brain.  They exist on a 2D 
standard surface mesh.  I mention below the individual subject versions of this 
surface mesh that you could use for tractography.  In that case, you would use 
the white matter surface as your waypoint and the pial surface as your stop.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Tuesday, November 1, 2016 at 6:39 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

My plan is indeed to run probtrackx using surface ROIs. But since HCP diffusion 
data is not registered to the average brain template of the MMP1.0 ROIs, my 
question is what is the recommended way of running FNIRT for doing so? What is 
the appropriate template file(T1w)? And is there any config file HCP releases 
to be used by FNIRT?

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:29 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

You can map the parcellation from the surface to the volume using the white and 
pial surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k and the 
ribbon-based option.  Also, some tractography tools like probtrackx allow you 
to track directly to surface ROIs (which is better).

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Tuesday, November 1, 2016 at 6:27 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

Hi Matt.,

Yes, It is an HCP subject.

Thanks,
Kamal

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:25 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

Is this an HCP subject or another subject?

Peace,

Matt.

From: 
>
 on behalf of "Shadi, Kamal" 
>
Date: Tuesday, November 1, 2016 at 12:18 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] FNIRT for HCP diffusion data

Hi all,

I am trying to run probtrackx using HCP preprocessed diffusion data and MMP1.0 
ROIs.
To my understanding the corresponding T1w image of MMP1.0 ROIs is:
HCP_PhaseTwo / 

Re: [HCP-Users] correlation

[nailin yao]

Thank you Tim and Matt,

So when I extract hippocampus from Atlas_ROIs.2.nii.gz, and use it as roi
to do -cifti-average-roi-correlation on one of the subject, does the ROI
automatically overlay on the native subcortical space of that subject, or
normalized space which is the same for everyone? Thank you!

Best,
Nailin

2016-11-01 19:15 GMT-04:00 Glasser, Matthew :

> I think he wants to do a correlation of an ROI of the hippocampus.  There
> you would benefit from doing as Tim suggests, but then using
> wb_command -cifti-average-roi-correlation
>
> Peace,
>
> Matt.
>
> From:  on behalf of Timothy
> Coalson 
> Date: Tuesday, November 1, 2016 at 5:06 PM
> To: nailin yao 
> Cc: "hcp-users-requ...@humanconnectome.org"  humanconnectome.org>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] correlation
>
> One way to do this is to use -cifti-separate on a small 91k grayordinates
> cifti with "-volume HIPPOCAMPUS_LEFT  -roi "
> and similar for right hippocampus, then combine the left and right ROIs
> with -volume-math.  You could also extract the labels from the
> Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz file
> with -volume-label-to-roi.
>
> Tim
>
>
> On Tue, Nov 1, 2016 at 4:49 PM, nailin yao  wrote:
>
>> Hi,
>>
>> I'm trying to do an overall correlation from hippocampus on cifti file (
>>
>> rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii), and I run the command:
>>
>>
>>  ./wb_command -cifti-correlation /Users/ny87/temp/S0009QPW/MNIN
>> onLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii
>> /Users/ny87/temp/S0009QPW/MNINonLinear/try_hipp_corr.dscalar.nii
>> -roi-override -vol-roi /Users/ny87/temp/S0009QPW/MNIN
>> onLinear/try_output_hipp.nii
>>
>>
>> which result is ERROR: roi volume space doesn't match cifti volume space.
>>
>>
>> May I know which atlas file is the right one to extract hippocampus ROI ?
>>
>>
>> Thank you very much!
>>
>>
>> Best,
>>
>> Nailin
>>
>> --
>> Nailin Yao,  PhD
>>
>> Postdoctoral Associate
>> Department of Psychiatry, Yale University
>>
>> ___
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>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
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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 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.
>



-- 
Nailin Yao,  PhD

Postdoctoral Associate
Department of Psychiatry, Yale University

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Re: [HCP-Users] FNIRT for HCP diffusion data

[Glasser, Matthew]

No need for XFMs.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Wednesday, November 2, 2016 at 1:19 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

So just to see if I understood your point, If I use surfaces in 
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k for probtrackx, then there is no 
need to provide -xfm and -inxfm transform arguments? Or do I still need to run 
FNIRT between diffusion space and T1w and use the results in -xfm and -xfm 
arguments of probtrackx?

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:41 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

The MMP1.0 ROIs are not registered to a 3D average brain.  They exist on a 2D 
standard surface mesh.  I mention below the individual subject versions of this 
surface mesh that you could use for tractography.  In that case, you would use 
the white matter surface as your waypoint and the pial surface as your stop.

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Tuesday, November 1, 2016 at 6:39 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

My plan is indeed to run probtrackx using surface ROIs. But since HCP diffusion 
data is not registered to the average brain template of the MMP1.0 ROIs, my 
question is what is the recommended way of running FNIRT for doing so? What is 
the appropriate template file(T1w)? And is there any config file HCP releases 
to be used by FNIRT?

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:29 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

You can map the parcellation from the surface to the volume using the white and 
pial surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k and the 
ribbon-based option.  Also, some tractography tools like probtrackx allow you 
to track directly to surface ROIs (which is better).

Peace,

Matt.

From: "Shadi, Kamal" >
Date: Tuesday, November 1, 2016 at 6:27 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

Hi Matt.,

Yes, It is an HCP subject.

Thanks,
Kamal

From: "Glasser, Matthew" >
Date: Tuesday, November 1, 2016 at 7:25 PM
To: "Shadi, Kamal" >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FNIRT for HCP diffusion data

Is this an HCP subject or another subject?

Peace,

Matt.

From: 
>
 on behalf of "Shadi, Kamal" 
>
Date: Tuesday, November 1, 2016 at 12:18 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] FNIRT for HCP diffusion data

Hi all,

I am trying to run probtrackx using HCP preprocessed diffusion data and MMP1.0 
ROIs.
To my understanding the corresponding T1w image of MMP1.0 ROIs is:
HCP_PhaseTwo / Q1-Q6_RelatedParcellation210 / MNINonLinear / 
Q1-Q6_RelatedParcellation210_AverageT1w_restore.nii.gz

Is this a right choice?


Now I want to register a subject diffusion.bedpostx directory to the MMP1.0 ROI 
space using FNIRT.

Is there an HCP config file for the FNIRT registration? If not any recommended 
settings?


Any pointer is much appreciated.

Thanks,

Kamal Shadi

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Re: [HCP-Users] Myelin Map Summary Statistics

[Glasser, Matthew]

You should be able to do that with the commands Tim mentioned with the -roi sub 
option.

Peace,

Matt.

From: 
>
 on behalf of Timothy Hendrickson >
Date: Wednesday, November 2, 2016 at 11:42 AM
To: Timothy Coalson >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Myelin Map Summary Statistics

Hmm, I have a follow up question. I can extract average myelin for the entire 
cortex rather easily however I am having more trouble extracting hemispheric 
and ROI information.
Suggestions?

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)

On Mon, Oct 31, 2016 at 3:45 PM, Timothy Coalson 
> wrote:
Take a look at 
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-weighted-stats
 and/or 
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-stats
 .

Tim


On Mon, Oct 31, 2016 at 3:32 PM, Timothy Hendrickson 
> wrote:
HCP experts,

Is there a way to extract myelin values from individual dscalar CIFTI files?
What I am looking for is an average myelin value at the hemispheric and ROI 
level.

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)

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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 
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.

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[HCP-Users] -probtrackx-dot-convert volume label problem

[Maarten Vaessen]

Hello,

I'm trying to convert a .dot from probtrackx2 with -matrix3 option to a
dconn.nii. The -lrtarget was a list containing all volumes and surfaces
conforming to the HCP grayordinate file. The -target3 is the L (or R)
amygdala from Atlas_ROI.2.nii.gz. The output from probtrackx2 looks
sensible.

I use the following command and get this error:
wb_command -probtrackx-dot-convert fdt_matrix3.dot fdt_matrix3.dconn.nii
-col-cifti 91282_Greyordinates.dscalar.nii COLUMN -row-voxels
coords_for_fdt_matrix3 amyL_label_from_Atlas.nii.gz

ERROR: voxel index in list file did not match a structure: 0, 1, 56


Now, I am not sure what to use as input for -probtrackx-dot-convert
-row-voxels:

[-row-voxels] - the output mapping along a row will be voxels

 - a text file containing IJK indices for the voxels used
--> this should be the coords_for_fdt_matrix3 right?

 - a label volume with the dimensions and sform used, with
structure labels
--> here I am a bit lost. I tried several options, the probably most
sensible being:
wb_command -volume-label-import subj/MNINonLinear/ROIs/Atlas_ROIs.2.nii
amyL_label.txt amyL_label_from_Atlas.nii.gz -discard-others

amyL_label.txt =
AMYGDALA_LEFT
18 103 255 255 255

What would be the correct input to get this to work?

Thx,

-Maarten

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