Re: [HCP-Users] Question about the multi-modal parcellation brain map (Glasser et al., 2016)

[David Hofmann]

Thank you Matthew,

can you tell me, where can I download the map?

Thanks

David

2016-10-29 22:04 GMT+02:00 Glasser, Matthew :

> Matlab can read CIFTI, see option B here: https://wiki.humanconnectome.
> org/display/PublicData/HCP+Users+FAQ
>
> Peace,
>
> Matt.
>
> From:  on behalf of David Hofmann <
> davidhofma...@gmail.com>
> Date: Saturday, October 29, 2016 at 7:58 AM
> To: hcp-users 
> Subject: [HCP-Users] Question about the multi-modal parcellation brain
> map (Glasser et al., 2016)
>
> Hi all,
>
> I was wondering if this map is available for download (e.g. as a nifti
> file or some format that Matlab can handle) in order to use it to calculate
> functional correlations for my own sample?
>
> greetings
>
> David
>
> ___
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>
>
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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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Re: [HCP-Users] Question about the multi-modal parcellation brain map (Glasser et al., 2016)

[Seymour, Robert (Research Student)]

Hi David,


Here you go: https://balsa.wustl.edu/study/show/RVVG


Robert


From: hcp-users-boun...@humanconnectome.org 
 on behalf of David Hofmann 

Sent: 31 October 2016 10:23:51
To: Glasser, Matthew
Cc: hcp-users
Subject: Re: [HCP-Users] Question about the multi-modal parcellation brain map 
(Glasser et al., 2016)

Thank you Matthew,

can you tell me, where can I download the map?

Thanks

David

2016-10-29 22:04 GMT+02:00 Glasser, Matthew 
mailto:glass...@wustl.edu>>:
Matlab can read CIFTI, see option B here: 
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of David Hofmann 
mailto:davidhofma...@gmail.com>>
Date: Saturday, October 29, 2016 at 7:58 AM
To: hcp-users 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Question about the multi-modal parcellation brain map 
(Glasser et al., 2016)

Hi all,

I was wondering if this map is available for download (e.g. as a nifti file or 
some format that Matlab can handle) in order to use it to calculate functional 
correlations for my own sample?

greetings

David

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Re: [HCP-Users] Extracting time series in grayordinates from any brain parcellation

[PALLARES PICAZO, VICENTE]

Ok, but is it possible then to use another NIFTI parcellation, for
instance, a functional parcellation, with the CIFTI fMRI data? Or, since
the subcortical regions are already defined in the CIFTI file, is not
possible to re-define these ROI?

Thank you again,

Vicente

On 29 October 2016 at 22:07, Glasser, Matthew  wrote:

> The AAL parcellation is not thought of as a particularly accurate
> functional parcellation of the brain.  There is a nice parcellation
> available here:
>
> https://balsa.wustl.edu/study/show/RVVG
>
> Peace,
>
> Matt.
>
> From: "PALLARES PICAZO, VICENTE" 
> Date: Saturday, October 29, 2016 at 6:09 AM
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] Extracting time series in grayordinates from any
> brain parcellation
>
> Thank you for the prompt reply. We are interested in whole-brain
> parcellations, in particular we would like to extract the averaged time
> courses according to the AAL parcellation (Tzourio-Mazoyer et. al, 2002),
> so it would include both cortical and subcortical regions.
>
> Best,
> Vicente
>
> On 28 October 2016 at 23:22, Glasser, Matthew  wrote:
>
>> What kind of a NIFTI parcellation is this?  Subcortical?
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of "PALLARES
>> PICAZO, VICENTE" 
>> Date: Friday, October 28, 2016 at 10:12 AM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] Extracting time series in grayordinates from any
>> brain parcellation
>>
>> Dear HCP data users,
>>
>> We would like to use the fantastic resting state fMRI data set from the
>> HCP :)
>>
>> We are interested in extracting the time series from the minimal
>> preprocessing resting fMRI data to later perform our own analysis.
>>
>> After checking the available information, it seems that the most
>> appropriate way to extract the average signal in each region of interest is
>> to use the *cifti-parcellate* command.
>>
>> In the help section we have seen that the cifti-parcellate command has
>> four arguments:
>>
>> wb_command -cifti-parcellate
>>
>>  - the cifti file to parcellate
>>
>>  - a cifti label file to use for the parcellation
>>
>>  - which mapping to parcellate (integer, ROW, or COLUMN)
>>
>>  - output - output cifti file
>>
>>
>> Our questions are:
>>
>> 1) For the  argument, how can we transform our nifti
>> parcellation atlas into a cifti label file for both cortical and
>> subcortical areas?
>>
>> We have seen that there is a *wb_command -cifti-create-label* command,
>> but we are worried that for example our hippocampus label is different from
>> the hippocampus label in cifti… So, is there any way to transform our nifti
>> atlas into cifti without using the already determined CIFTI structures?
>>
>> 2)For the for  argument, we use the file  “
>> *rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii*”
>>
>> from the folder
>> *100307_3T_rfMRI_REST1_fixextended\100307\MNINonLinear\Results\rfMRI_REST1_LR*
>> . Is that correct?
>>
>> Thanks in advance for your help,
>>
>> Vicente and Ana
>>
>> ___
>> 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.
>>
>
>
> --
>
> 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
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[HCP-Users] FoV phase for fMRI

[Sebastien Hetu]

Hi,
We are trying to run a fMRI sequence on our PRISMA similar to the one used in 
the HCP–lifespan but with 1.5mm isotropic voxels and a AP phase encoding 
direction.
In the HCP sequence documents, it is mentioned that if we use AP phase encoding 
we should use a FoV phase of 100%.
We seem to be unable to set our FoV phase to 100%—we can only go to 103% (with 
our FoV of 204 mm). Do you know how to set the sequence to have 100% available?

Thank you for your help

Seb

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[HCP-Users] FreeSurferPipeline.sh with FreeSurfer dev version (-hires option)

[Antonin Skoch]

Dear experts,

I was wondering, why do you run in FreeSurferPipeline the recon-all with 
downsampled 1mm3 data?

It is due to the fact that you do not want to rely on development version of 
FreeSurfer which only enables reconstruction of high resolution data (via -cm 
or -hires option)? Isn't it a bit step backward for subcortical analysis to do 
the subcortical recon with 1mm resolution?

Since I really needed subcortical segmentation in high resolution (for 
Hippocampal subfields modelling) but wanted to capitalize on HCP pipeline added 
values, I tried to modify FreeSurferPipeline scripts to use FreeSurfer dev 
version. 

I used mris_make_surfaces from HCP verion of FreeSurfer, other binaries and 
scripts are from dev version. I had to make only several minor changes in 
FreeSurferHiResWhite and FreeSurferHiResPial: I only needed to slightly modify 
parameter format of mri_surf2surf to accomodate expectation of dev version of 
mri_surf2surf and acknowledge the fact that recon-all -white in dev version 
does not make ?h.white files, but ?h.white.preaparc and aseg.presurf instead of 
aseg. 

I ran my data by my modified "full-hires" pipeline and the results seem 
reasonable.

Do you see any potential pitfalls with this approach?

Regards,

Antonin Skoch



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Re: [HCP-Users] FreeSurferPipeline.sh with FreeSurfer dev version (-hires option)

[Harms, Michael]

Hi,
The current HCP structural pipeline was developed well before the forthcoming 
FS version that will have improved support/processing of “hires” structurals.

In fact, parts of the HCP structural pipeline are there basically so that we 
could refine the positioning of the surfaces to take full advantage of the 
acquisition resolution.  In principle, when “FS 6.0” comes out, some of this 
functionality will be incorporated into the standard ‘recon-all’ stream itself, 
so it may be possible to simplify the FS related stuff in the HCP Structural 
Pipeline.

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Antonin Skoch mailto:a...@ikem.cz>>
Date: Monday, October 31, 2016 at 11:44 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] FreeSurferPipeline.sh with FreeSurfer dev version (-hires 
option)

Dear experts,

I was wondering, why do you run in FreeSurferPipeline the recon-all with 
downsampled 1mm3 data?

It is due to the fact that you do not want to rely on development version of 
FreeSurfer which only enables reconstruction of high resolution data (via -cm 
or -hires option)? Isn't it a bit step backward for subcortical analysis to do 
the subcortical recon with 1mm resolution?

Since I really needed subcortical segmentation in high resolution (for 
Hippocampal subfields modelling) but wanted to capitalize on HCP pipeline added 
values, I tried to modify FreeSurferPipeline scripts to use FreeSurfer dev 
version.

I used mris_make_surfaces from HCP verion of FreeSurfer, other binaries and 
scripts are from dev version. I had to make only several minor changes in 
FreeSurferHiResWhite and FreeSurferHiResPial: I only needed to slightly modify 
parameter format of mri_surf2surf to accomodate expectation of dev version of 
mri_surf2surf and acknowledge the fact that recon-all -white in dev version 
does not make ?h.white files, but ?h.white.preaparc and aseg.presurf instead of 
aseg.

I ran my data by my modified "full-hires" pipeline and the results seem 
reasonable.

Do you see any potential pitfalls with this approach?

Regards,

Antonin Skoch



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Re: [HCP-Users] FoV phase for fMRI

[Harms, Michael]

Off the top of my head, no.  Three comments though:  (1) a 204 mm in-plane FOV 
is rather tight; (2) 1.5 mm voxels is going to require a longer TE and echo 
train, and/or the use of phase partial Fourier; (3) You’re going to be rather 
SNR-starved at 1.5 mm isotropic at 3T.

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Sebastien Hetu mailto:sebh...@vtc.vt.edu>>
Date: Monday, October 31, 2016 at 11:03 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] FoV phase for fMRI

Hi,
We are trying to run a fMRI sequence on our PRISMA similar to the one used in 
the HCP–lifespan but with 1.5mm isotropic voxels and a AP phase encoding 
direction.
In the HCP sequence documents, it is mentioned that if we use AP phase encoding 
we should use a FoV phase of 100%.
We seem to be unable to set our FoV phase to 100%—we can only go to 103% (with 
our FoV of 204 mm). Do you know how to set the sequence to have 100% available?

Thank you for your help

Seb

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Re: [HCP-Users] Extracting time series in grayordinates from any brain parcellation

[Timothy Coalson]

The CIFTI fMRI data does not contain subcortical information outside those
defined ROIs.  If you need to redefine them, you would need to get the data
from the volume fMRI files, and the resulting cifti files would be
challenging to compare/use with the released cifti data.

You can incorporate volume subcortical parcellation data within the
existing CIFTI subcortical ROIs into a dlabel file that also contains a
cortex parcellation, see
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-create-dense-from-template
.

Tim


On Mon, Oct 31, 2016 at 9:28 AM, PALLARES PICAZO, VICENTE <
vicente.palla...@upf.edu> wrote:

> Ok, but is it possible then to use another NIFTI parcellation, for
> instance, a functional parcellation, with the CIFTI fMRI data? Or, since
> the subcortical regions are already defined in the CIFTI file, is not
> possible to re-define these ROI?
>
> Thank you again,
>
> Vicente
>
> On 29 October 2016 at 22:07, Glasser, Matthew  wrote:
>
>> The AAL parcellation is not thought of as a particularly accurate
>> functional parcellation of the brain.  There is a nice parcellation
>> available here:
>>
>> https://balsa.wustl.edu/study/show/RVVG
>>
>> Peace,
>>
>> Matt.
>>
>> From: "PALLARES PICAZO, VICENTE" 
>> Date: Saturday, October 29, 2016 at 6:09 AM
>> To: Matt Glasser 
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] Extracting time series in grayordinates from
>> any brain parcellation
>>
>> Thank you for the prompt reply. We are interested in whole-brain
>> parcellations, in particular we would like to extract the averaged time
>> courses according to the AAL parcellation (Tzourio-Mazoyer et. al, 2002),
>> so it would include both cortical and subcortical regions.
>>
>> Best,
>> Vicente
>>
>> On 28 October 2016 at 23:22, Glasser, Matthew  wrote:
>>
>>> What kind of a NIFTI parcellation is this?  Subcortical?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From:  on behalf of "PALLARES
>>> PICAZO, VICENTE" 
>>> Date: Friday, October 28, 2016 at 10:12 AM
>>> To: "hcp-users@humanconnectome.org" 
>>> Subject: [HCP-Users] Extracting time series in grayordinates from any
>>> brain parcellation
>>>
>>> Dear HCP data users,
>>>
>>> We would like to use the fantastic resting state fMRI data set from the
>>> HCP :)
>>>
>>> We are interested in extracting the time series from the minimal
>>> preprocessing resting fMRI data to later perform our own analysis.
>>>
>>> After checking the available information, it seems that the most
>>> appropriate way to extract the average signal in each region of interest is
>>> to use the *cifti-parcellate* command.
>>>
>>> In the help section we have seen that the cifti-parcellate command has
>>> four arguments:
>>>
>>> wb_command -cifti-parcellate
>>>
>>>  - the cifti file to parcellate
>>>
>>>  - a cifti label file to use for the parcellation
>>>
>>>  - which mapping to parcellate (integer, ROW, or COLUMN)
>>>
>>>  - output - output cifti file
>>>
>>>
>>> Our questions are:
>>>
>>> 1) For the  argument, how can we transform our nifti
>>> parcellation atlas into a cifti label file for both cortical and
>>> subcortical areas?
>>>
>>> We have seen that there is a *wb_command -cifti-create-label* command,
>>> but we are worried that for example our hippocampus label is different from
>>> the hippocampus label in cifti… So, is there any way to transform our nifti
>>> atlas into cifti without using the already determined CIFTI structures?
>>>
>>> 2)For the for  argument, we use the file  “
>>> *rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii*”
>>>
>>> from the folder
>>> *100307_3T_rfMRI_REST1_fixextended\100307\MNINonLinear\Results\rfMRI_REST1_LR*
>>> . Is that correct?
>>>
>>> Thanks in advance for your help,
>>>
>>> Vicente and Ana
>>>
>>> ___
>>> 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.
>>>
>>
>>
>> --
>>
>> 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] Myelin Map Summary Statistics

[Timothy Hendrickson]

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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Re: [HCP-Users] Myelin Map Summary Statistics

[Timothy Coalson]

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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Re: [HCP-Users] HCP to FreeSurfer Resampling

[Timothy Coalson]

The instructions in part D of the pdf result in data that is already on the
fsaverage standard mesh.  If what you are trying to do with mris_preproc is
just resample to fsaverage from subject native mesh, you can skip that step
entirely.

This step looks suspicious:

wb_command -surface-sphere-project-unproject \
$dataDir/$i/MNINonLinear/Native/$i.$hemi.sphere.native.surf.gii \
$spheres_to_project_to $spheres_to_unproject_to $new_native_spheres

The instructions say to use the "MSMAll" sphere, but regardless, the input
sphere must be one that is registered to fs_LR in some way (if this is not
HCP data, so you can't run MSM on it yet, then I think you should use
"$i.$hemi.sphere.reg.reg_LR.native.surf.gii").

Tim


On Mon, Oct 31, 2016 at 3:48 PM, Timothy Hendrickson 
wrote:

> Ohh, here is the script with the .txt suffix.
>
> Once I finish this script I attempt to put my fsavg mapped gifti file:
> 41815.R.32k_TJH_fsavg.func.gii into mris_preproc in order to re-sample the
> data into the common subject fsaverage.
>
> mris_preproc --target fsaverage --hemi rh --s 41815 --is
> /home/lnpi14-raid1/bryon-data-lnpi14/142_CIFASD/HCP_3.4.0/41
> 815/MNINonLinear/fsaverage_LR32k/41815.R.32k_TJH_fsavg.func.gii --out
> 41815.32k.R.Myelin.mgh.
>
> I suppose I may have to ask the freesurfer mailing list about this.
>
> -Tim
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
>
> On Mon, Oct 31, 2016 at 3:33 PM, Timothy Coalson  wrote:
>
>> While our mailing list decided to remove your script because you didn't
>> rename it to end in .txt, I would take a guess that you may be attempting
>> to use a fsaverage data file with a native mesh surface, which won't work.
>> I'm not sure how you tell freesurfer to analyze on a particular mesh.  It
>> is also possible to resample fs_LR data onto each subject's native mesh, if
>> that is what freesurfer requires.
>>
>> Tim
>>
>>
>> On Mon, Oct 31, 2016 at 2:28 PM, Timothy Hendrickson 
>> wrote:
>>
>>> WARNING: This e-mail has been altered by MIMEDefang.  Following this
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>>> An attachment named myelinMap_FreeSurferResampling.sh was removed from
>>> this document as it
>>> constituted a security hazard.  If you require this document, please
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>>> the sender and arrange an alternate means of receiving it.
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>>>
>>> ___
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>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>>
>>> Hello HCP experts,
>>>
>>> I have been attempting to maps individual myelin maps to freesurfer
>>> using part D of the how to document provided by Coalson and colleagues:
>>> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ.
>>> 
>>> Following the conversion I was attempting to utilize the freesurfer
>>> mapped myelin maps in a group analysis by first feeding it through the
>>> freesurfer command mris_preproc and then mri_surf2surf.
>>>
>>> Once I did this I received the following error:
>>>
>>>
>>>
>>> *ERROR: dimension inconsistency in source data   Number of surface
>>> vertices = 161845   Number of value vertices = 163842*
>>> This may be more of a FreeSurfer mailing list question, but first I was
>>> hoping that a HCP expert could take a look at my script to ensure that it
>>> is accurate.
>>>
>>> Respectfully,
>>>
>>> -Tim
>>>
>>> Timothy Hendrickson
>>> Department of Psychiatry
>>> University of Minnesota
>>> Mobile: 507-259-3434 (texts okay)
>>>
>>> ___
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>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>>
>>
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Re: [HCP-Users] Extracting time series in grayordinates from any brain parcellation

[Glasser, Matthew]

The parcellation I mentioned below is CIFTI, so it will work without issue with 
CIFTI fMRI data.

Peace,

Matt.

From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Monday, October 31, 2016 at 3:17 PM
To: "PALLARES PICAZO, VICENTE" 
mailto:vicente.palla...@upf.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Extracting time series in grayordinates from any brain 
parcellation

The CIFTI fMRI data does not contain subcortical information outside those 
defined ROIs.  If you need to redefine them, you would need to get the data 
from the volume fMRI files, and the resulting cifti files would be challenging 
to compare/use with the released cifti data.

You can incorporate volume subcortical parcellation data within the existing 
CIFTI subcortical ROIs into a dlabel file that also contains a cortex 
parcellation, see 
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-create-dense-from-template
 .

Tim


On Mon, Oct 31, 2016 at 9:28 AM, PALLARES PICAZO, VICENTE 
mailto:vicente.palla...@upf.edu>> wrote:
Ok, but is it possible then to use another NIFTI parcellation, for instance, a 
functional parcellation, with the CIFTI fMRI data? Or, since the subcortical 
regions are already defined in the CIFTI file, is not possible to re-define 
these ROI?

Thank you again,

Vicente

On 29 October 2016 at 22:07, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
The AAL parcellation is not thought of as a particularly accurate functional 
parcellation of the brain.  There is a nice parcellation available here:

https://balsa.wustl.edu/study/show/RVVG

Peace,

Matt.

From: "PALLARES PICAZO, VICENTE" 
mailto:vicente.palla...@upf.edu>>
Date: Saturday, October 29, 2016 at 6:09 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Extracting time series in grayordinates from any brain 
parcellation

Thank you for the prompt reply. We are interested in whole-brain parcellations, 
in particular we would like to extract the averaged time courses according to 
the AAL parcellation (Tzourio-Mazoyer et. al, 2002), so it would include both 
cortical and subcortical regions.

Best,
Vicente

On 28 October 2016 at 23:22, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
What kind of a NIFTI parcellation is this?  Subcortical?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "PALLARES PICAZO, VICENTE" 
mailto:vicente.palla...@upf.edu>>
Date: Friday, October 28, 2016 at 10:12 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Extracting time series in grayordinates from any brain 
parcellation


Dear HCP data users,

We would like to use the fantastic resting state fMRI data set from the HCP :)

We are interested in extracting the time series from the minimal preprocessing 
resting fMRI data to later perform our own analysis.

After checking the available information, it seems that the most appropriate 
way to extract the average signal in each region of interest is to use the 
cifti-parcellate command.

In the help section we have seen that the cifti-parcellate command has four 
arguments:

wb_command -cifti-parcellate

 - the cifti file to parcellate

 - a cifti label file to use for the parcellation

 - which mapping to parcellate (integer, ROW, or COLUMN)

 - output - output cifti file


Our questions are:

1) For the  argument, how can we transform our nifti parcellation 
atlas into a cifti label file for both cortical and subcortical areas?

We have seen that there is a wb_command -cifti-create-label command, but we are 
worried that for example our hippocampus label is different from the 
hippocampus label in cifti… So, is there any way to transform our nifti atlas 
into cifti without using the already determined CIFTI structures?

2)For the for  argument, we use the file  
“rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii”

from the folder 
100307_3T_rfMRI_REST1_fixextended\100307\MNINonLinear\Results\rfMRI_REST1_LR . 
Is that correct?

Thanks in advance for your help,

Vicente and Ana

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Re: [HCP-Users] FoV phase for fMRI

[Glasser, Matthew]

Indeed, why do you wish to scan at 1.5mm?  Cortex is 1.6mm thick at the 
minimum, and you have to increase the TR substantially which isn't so good 
either for maximizing one's functional CNR.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Monday, October 31, 2016 at 2:35 PM
To: Sebastien Hetu mailto:sebh...@vtc.vt.edu>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] FoV phase for fMRI


Off the top of my head, no.  Three comments though:  (1) a 204 mm in-plane FOV 
is rather tight; (2) 1.5 mm voxels is going to require a longer TE and echo 
train, and/or the use of phase partial Fourier; (3) You're going to be rather 
SNR-starved at 1.5 mm isotropic at 3T.

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Sebastien Hetu mailto:sebh...@vtc.vt.edu>>
Date: Monday, October 31, 2016 at 11:03 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] FoV phase for fMRI

Hi,
We are trying to run a fMRI sequence on our PRISMA similar to the one used in 
the HCP-lifespan but with 1.5mm isotropic voxels and a AP phase encoding 
direction.
In the HCP sequence documents, it is mentioned that if we use AP phase encoding 
we should use a FoV phase of 100%.
We seem to be unable to set our FoV phase to 100%-we can only go to 103% (with 
our FoV of 204 mm). Do you know how to set the sequence to have 100% available?

Thank you for your help

Seb

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Re: [HCP-Users] surface label to 3D mask

[Glasser, Matthew]

It doesn¹t appear that you followed the command usage for this Connectome
Workbench command correctly.  I would have another look at that.

Peace,

Matt.

On 10/31/16, 3:10 PM, "mailman-boun...@humanconnectome.org on behalf of
Burgess, Gregory"  wrote:

>Please send this to hcp-users@humanconnectome.org (instead of the owners
>list)
>--Greg
>
>
>Greg Burgess, Ph.D.
>Staff Scientist, Human Connectome Project
>Washington University School of Medicine
>Department of Psychiatry
>Phone: 314-362-7864
>Email: gburg...@wustl.edu
>
>> On Oct 31, 2016, at 11:41 AM, Enrico Schulz 
>>wrote:
>>
>> Dear HCP community,
>>
>> I want to apply the recent brain parcellation to my DTI data. In order
>>to do tractography I need to generate 3D masks from the label file.
>> I tried the command below but received an error message:
>>
>> ERROR: Parse error while reading: error occurred while parsing element,
>>line number: 1 column number: 1
>>
>> I guess the command is not correct. Could anyone help, please?
>> I am aware that the group masks based on surface definitions are not
>>fully accurate.
>> Thank you,
>> Enrico
>>
>> wb_command -label-to-volume-mapping
>>Q1-Q6_RelatedValidation...dlabel.nii MNI152_T1_2mm_brain.nii.gz
>>test.nii.gz
>
>
>
>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] surface label to 3D mask

[Timothy Coalson]

The -label-to-volume-mapping command only works on gifti label files, and
he specified a cifti dlabel file instead.  Use -cifti-separate first.

Tim


On Mon, Oct 31, 2016 at 5:26 PM, Glasser, Matthew 
wrote:

> It doesn¹t appear that you followed the command usage for this Connectome
> Workbench command correctly.  I would have another look at that.
>
> Peace,
>
> Matt.
>
> On 10/31/16, 3:10 PM, "mailman-boun...@humanconnectome.org on behalf of
> Burgess, Gregory"  gburg...@wustl.edu> wrote:
>
> >Please send this to hcp-users@humanconnectome.org (instead of the owners
> >list)
> >--Greg
> >
> >
> >Greg Burgess, Ph.D.
> >Staff Scientist, Human Connectome Project
> >Washington University School of Medicine
> >Department of Psychiatry
> >Phone: 314-362-7864
> >Email: gburg...@wustl.edu
> >
> >> On Oct 31, 2016, at 11:41 AM, Enrico Schulz 
> >>wrote:
> >>
> >> Dear HCP community,
> >>
> >> I want to apply the recent brain parcellation to my DTI data. In order
> >>to do tractography I need to generate 3D masks from the label file.
> >> I tried the command below but received an error message:
> >>
> >> ERROR: Parse error while reading: error occurred while parsing element,
> >>line number: 1 column number: 1
> >>
> >> I guess the command is not correct. Could anyone help, please?
> >> I am aware that the group masks based on surface definitions are not
> >>fully accurate.
> >> Thank you,
> >> Enrico
> >>
> >> wb_command -label-to-volume-mapping
> >>Q1-Q6_RelatedValidation...dlabel.nii MNI152_T1_2mm_brain.nii.gz
> >>test.nii.gz
> >
> >
> >
> >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.
> >
>
>
> 
> 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] FreeSurferPipeline.sh with FreeSurfer dev version (-hires option)

[Glasser, Matthew]

We will need to update the pipelines to work with FreeSurfer 6.0 when it is 
released.  Earlier versions of FreeSurfer did required the current approach to 
get highres surface placement.  Your approach is probably fine if it is 
producing nice results for you.  If you wish, you could send us the diff so 
that we could look into incorporating it.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Antonin Skoch mailto:a...@ikem.cz>>
Date: Monday, October 31, 2016 at 11:44 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] FreeSurferPipeline.sh with FreeSurfer dev version (-hires 
option)

Dear experts,

I was wondering, why do you run in FreeSurferPipeline the recon-all with 
downsampled 1mm3 data?

It is due to the fact that you do not want to rely on development version of 
FreeSurfer which only enables reconstruction of high resolution data (via -cm 
or -hires option)? Isn't it a bit step backward for subcortical analysis to do 
the subcortical recon with 1mm resolution?

Since I really needed subcortical segmentation in high resolution (for 
Hippocampal subfields modelling) but wanted to capitalize on HCP pipeline added 
values, I tried to modify FreeSurferPipeline scripts to use FreeSurfer dev 
version.

I used mris_make_surfaces from HCP verion of FreeSurfer, other binaries and 
scripts are from dev version. I had to make only several minor changes in 
FreeSurferHiResWhite and FreeSurferHiResPial: I only needed to slightly modify 
parameter format of mri_surf2surf to accomodate expectation of dev version of 
mri_surf2surf and acknowledge the fact that recon-all -white in dev version 
does not make ?h.white files, but ?h.white.preaparc and aseg.presurf instead of 
aseg.

I ran my data by my modified "full-hires" pipeline and the results seem 
reasonable.

Do you see any potential pitfalls with this approach?

Regards,

Antonin Skoch



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Re: [HCP-Users] surface label to 3D mask

[Glasser, Matthew]

There aren’t any surfaces specified either…

Matt.

From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Monday, October 31, 2016 at 5:29 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Burgess, Gregory" mailto:gburg...@wustl.edu>>, Enrico 
Schulz mailto:enrico.sch...@gmail.com>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] surface label to 3D mask

The -label-to-volume-mapping command only works on gifti label files, and he 
specified a cifti dlabel file instead.  Use -cifti-separate first.

Tim


On Mon, Oct 31, 2016 at 5:26 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
It doesn¹t appear that you followed the command usage for this Connectome
Workbench command correctly.  I would have another look at that.

Peace,

Matt.

On 10/31/16, 3:10 PM, 
"mailman-boun...@humanconnectome.org
 on behalf of
Burgess, Gregory" 
mailto:mailman-boun...@humanconnectome.org>
 on behalf of
gburg...@wustl.edu> wrote:

>Please send this to 
>hcp-users@humanconnectome.org (instead 
>of the owners
>list)
>--Greg
>
>
>Greg Burgess, Ph.D.
>Staff Scientist, Human Connectome Project
>Washington University School of Medicine
>Department of Psychiatry
>Phone: 314-362-7864
>Email: gburg...@wustl.edu
>
>> On Oct 31, 2016, at 11:41 AM, Enrico Schulz 
>> mailto:enrico.sch...@gmail.com>>
>>wrote:
>>
>> Dear HCP community,
>>
>> I want to apply the recent brain parcellation to my DTI data. In order
>>to do tractography I need to generate 3D masks from the label file.
>> I tried the command below but received an error message:
>>
>> ERROR: Parse error while reading: error occurred while parsing element,
>>line number: 1 column number: 1
>>
>> I guess the command is not correct. Could anyone help, please?
>> I am aware that the group masks based on surface definitions are not
>>fully accurate.
>> Thank you,
>> Enrico
>>
>> wb_command -label-to-volume-mapping
>>Q1-Q6_RelatedValidation...dlabel.nii MNI152_T1_2mm_brain.nii.gz
>>test.nii.gz
>
>
>
>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] FoV phase for fMRI

[Sebastien Hetu]

We are interested in small structures of the midbrain and would therefore like 
to maximize our spatial resolution, at least go smaller than 2mm isotropic. Any 
suggestions?

cheers

seb

From: Glasser, Matthew [glass...@wustl.edu]
Sent: Monday, October 31, 2016 6:25 PM
To: Harms, Michael; Sebastien Hetu; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] FoV phase for fMRI

Indeed, why do you wish to scan at 1.5mm?  Cortex is 1.6mm thick at the 
minimum, and you have to increase the TR substantially which isn’t so good 
either for maximizing one’s functional CNR.

Peace,

Matt.

From: 
>
 on behalf of "Harms, Michael" 
>
Date: Monday, October 31, 2016 at 2:35 PM
To: Sebastien Hetu 
>,
 
"hcp-users@humanconnectome.org"
 
>
Subject: Re: [HCP-Users] FoV phase for fMRI


Off the top of my head, no.  Three comments though:  (1) a 204 mm in-plane FOV 
is rather tight; (2) 1.5 mm voxels is going to require a longer TE and echo 
train, and/or the use of phase partial Fourier; (3) You’re going to be rather 
SNR-starved at 1.5 mm isotropic at 3T.

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 Sebastien Hetu 
>
Date: Monday, October 31, 2016 at 11:03 AM
To: 
"hcp-users@humanconnectome.org"
 
>
Subject: [HCP-Users] FoV phase for fMRI

Hi,
We are trying to run a fMRI sequence on our PRISMA similar to the one used in 
the HCP–lifespan but with 1.5mm isotropic voxels and a AP phase encoding 
direction.
In the HCP sequence documents, it is mentioned that if we use AP phase encoding 
we should use a FoV phase of 100%.
We seem to be unable to set our FoV phase to 100%—we can only go to 103% (with 
our FoV of 204 mm). Do you know how to set the sequence to have 100% available?

Thank you for your help

Seb

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[HCP-Users] FNIRT for HCP diffusion data

[Shadi, Kamal]

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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