[HCP-Users] Hello Matt Glasser

[A-reum Min]

hello
my name is areum.
i have some question to you.
a few days ago i was down load HCP(human connectom project) s900 data. -->
3T imaging protocol completed True ver.
but.. how can i use these HCP format.
i use a freesurfer software.
i have never seen before these format(fig.1.png) like a .gii , nii..
I want to see HCP data subjects's average cortical thickness using qdec.
how can i to do?
plz answer me

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[HCP-Users] Pial surface

[Mahmoud]

Hello All,

I've applied HCP pipeline scripts to our structural data and it looks like
everything goes well to the end of PostFreeSurferPipelline.

Opening the fs_LR.wb.spec file for the low-resolution mesh, it is obvious
that the pial surface line (the blue line) hits the dura or is at the very
outer edge of the pial surface. I was wondering which parameters and where
I should tweak to get a better result.

Thank you!
Mahmoud

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Re: [HCP-Users] (no subject)

[Donna Dierker]

I don't know the name of the package, but it might be something like 
"structural extended" -- one of them has the subject's freesurfer directory in 
it.


On Dec 27, 2015, at 7:08 PM, A-reum Min  wrote:

> hello 
> my name is areum.
> i have some question to you.
> a few days ago i was down load HCP(human connectom project) s900 data. --> 3T 
> imaging protocol completed True ver.
> but.. how can i use these HCP format.
> i use a freesurfer software.
> i have never seen before these format(fig.1.png) like a .gii , nii..
> I want to see HCP data subjects's average cortical thickness using qdec or 
> freeview.
> how can i to do? 
> plz answer me  
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
> 


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Re: [HCP-Users] (no subject)

[Donna Dierker]

Jenn wrote:
> output from the HCP pipelines that toy ate unfamiliar worth is available

Auto-complete run amok or typing while nursing? ;-)

A-reum, if you have the structural extended package, you'll find the freesurfer 
subject directory here:

> /MyDataPath/subjectID/T1w/subjectID

Qdec should be happy with the stuff in there.

I'm not sure which tools in the Freesurfer distribution can read CIFTI (e.g., 
*.dscalar.nii, *.dtseries.nii).  I know some tools can read GIFTI (*.surf.gii) 
files.  But whether all utilities do equally isn't clear to me.

If you want to do statistical analyses with these files, I'd like to point you 
to PALM:

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

There is a bit of preprocessing to be done going into PALM, but it handles 
family structure and so much more. 


On Dec 28, 2015, at 11:44 AM, Jennifer Elam  wrote:

> Yes, the preprocessed "Structural Extended" package for each subject has the 
> Freesurfer outputs that are intermediates in the HCP preprocessing pipelines.
> More info about the files output from the HCP pipelines that toy ate 
> unfamiliar worth is available in the HCP Reference Manual for the 900 
> Subjects release, on the HCP wiki,  and in various posts to the HCP-users 
> list (searchable in the archive). Links to these are all at 
> humanconnectome.org
> 
> Best, 
> Jenn
> 
> On Dec 28, 2015 10:06 AM, "Donna Dierker"  wrote:
> I don't know the name of the package, but it might be something like 
> "structural extended" -- one of them has the subject's freesurfer directory 
> in it.
> 
> 
> On Dec 27, 2015, at 7:08 PM, A-reum Min  wrote:
> 
>> hello
>> my name is areum.
>> i have some question to you.
>> a few days ago i was down load HCP(human connectom project) s900 data. --> 
>> 3T imaging protocol completed True ver.
>> but.. how can i use these HCP format.
>> i use a freesurfer software.
>> i have never seen before these format(fig.1.png) like a .gii , nii..
>> I want to see HCP data subjects's average cortical thickness using qdec or 
>> freeview.
>> how can i to do?
>> plz answer me
>> ___
>> 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


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Re: [HCP-Users] Pial surface

[Donna Dierker]

What version of Freesurfer are you using?  There was a specific one for the 
pipelines, and the version did affect results in the medial temporal 
especially, but also the insula.


On Dec 28, 2015, at 12:56 PM, Mahmoud  wrote:

> Hello Erin,
> 
> Thank you for your response. I was hoping there are some parameters to tweak 
> so I can compare the results and see which one makes more sense. Currently, 
> it looks to me that the occipital and temporal lobe surfaces are not accurate 
> enough. This made the mylin maps to show less amount of myelins, colored 
> mostly green and yellow, while I was expecting more red.
> 
> Thank you,
> Mahmoud
> 
> On Mon, Dec 28, 2015 at 1:17 PM, Erin Reid  wrote:
> Hi Mahmoud,
> The pial (blue) surface line is intended to hit the very outer edge of the 
> pial surface.  There are plenty of times that the image is not clear enough 
> for FreeSurfer to do a "perfect" job so some dura (or blood vessels) can 
> sometimes be included in the pial surface outline.  For our purposes, we 
> decided not to fix these when they were minor instances (i.e. not causing 
> significant surface errors).  
> 
> If you are wishing to tweak the results, hopefully Mike Harms can give you 
> some pointers on doing so.
> 
> Erin Reid
> 
> On 12/28/15 10:04 AM, Mahmoud wrote:
>> Hello All,
>> 
>> I've applied HCP pipeline scripts to our structural data and it looks like 
>> everything goes well to the end of PostFreeSurferPipelline.
>> 
>> Opening the fs_LR.wb.spec file for the low-resolution mesh, it is obvious 
>> that the pial surface line (the blue line) hits the dura or is at the very 
>> outer edge of the pial surface. I was wondering which parameters and where I 
>> should tweak to get a better result.
>> 
>> Thank you!
>> Mahmoud
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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Re: [HCP-Users] (no subject)

[Jennifer Elam]

Yes, the preprocessed "Structural Extended" package for each subject has
the Freesurfer outputs that are intermediates in the HCP preprocessing
pipelines.
More info about the files output from the HCP pipelines that toy ate
unfamiliar worth is available in the HCP Reference Manual for the 900
Subjects release, on the HCP wiki,  and in various posts to the HCP-users
list (searchable in the archive). Links to these are all at
humanconnectome.org

Best,
Jenn
On Dec 28, 2015 10:06 AM, "Donna Dierker"  wrote:

> I don't know the name of the package, but it might be something like
> "structural extended" -- one of them has the subject's freesurfer directory
> in it.
>
>
> On Dec 27, 2015, at 7:08 PM, A-reum Min  wrote:
>
> > hello
> > my name is areum.
> > i have some question to you.
> > a few days ago i was down load HCP(human connectom project) s900 data.
> --> 3T imaging protocol completed True ver.
> > but.. how can i use these HCP format.
> > i use a freesurfer software.
> > i have never seen before these format(fig.1.png) like a .gii , nii..
> > I want to see HCP data subjects's average cortical thickness using qdec
> or freeview.
> > how can i to do?
> > plz answer me
> > ___
> > 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
>

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Re: [HCP-Users] Pial surface

[Mahmoud]

Hello Erin,

Thank you for your response. I was hoping there are some parameters to
tweak so I can compare the results and see which one makes more sense.
Currently, it looks to me that the occipital and temporal lobe surfaces are
not accurate enough. This made the mylin maps to show less amount of
myelins, colored mostly green and yellow, while I was expecting more red.

Thank you,
Mahmoud

On Mon, Dec 28, 2015 at 1:17 PM, Erin Reid  wrote:

> Hi Mahmoud,
> The pial (blue) surface line is intended to hit the very outer edge of
> the pial surface.  There are plenty of times that the image is not clear
> enough for FreeSurfer to do a "perfect" job so some dura (or blood vessels)
> can sometimes be included in the pial surface outline.  For our purposes,
> we decided not to fix these when they were minor instances (i.e. not causing
> significant surface errors).
>
> If you are wishing to tweak the results, hopefully Mike Harms can give you
> some pointers on doing so.
>
> Erin Reid
>
> On 12/28/15 10:04 AM, Mahmoud wrote:
>
> Hello All,
>
> I've applied HCP pipeline scripts to our structural data and it looks like
> everything goes well to the end of PostFreeSurferPipelline.
>
> Opening the fs_LR.wb.spec file for the low-resolution mesh, it is obvious
> that the pial surface line (the blue line) hits the dura or is at the very
> outer edge of the pial surface. I was wondering which parameters and where
> I should tweak to get a better result.
>
> Thank you!
> Mahmoud
>
> ___
> 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
>

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Re: [HCP-Users] Pial surface

[Mahmoud]

>From the output log:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP

On Mon, Dec 28, 2015 at 2:29 PM, Donna Dierker 
wrote:

> What version of Freesurfer are you using?  There was a specific one for
> the pipelines, and the version did affect results in the medial temporal
> especially, but also the insula.
>
>
> On Dec 28, 2015, at 12:56 PM, Mahmoud  wrote:
>
> > Hello Erin,
> >
> > Thank you for your response. I was hoping there are some parameters to
> tweak so I can compare the results and see which one makes more sense.
> Currently, it looks to me that the occipital and temporal lobe surfaces are
> not accurate enough. This made the mylin maps to show less amount of
> myelins, colored mostly green and yellow, while I was expecting more red.
> >
> > Thank you,
> > Mahmoud
> >
> > On Mon, Dec 28, 2015 at 1:17 PM, Erin Reid 
> wrote:
> > Hi Mahmoud,
> > The pial (blue) surface line is intended to hit the very outer edge of
> the pial surface.  There are plenty of times that the image is not clear
> enough for FreeSurfer to do a "perfect" job so some dura (or blood vessels)
> can sometimes be included in the pial surface outline.  For our purposes,
> we decided not to fix these when they were minor instances (i.e. not
> causing significant surface errors).
> >
> > If you are wishing to tweak the results, hopefully Mike Harms can give
> you some pointers on doing so.
> >
> > Erin Reid
> >
> > On 12/28/15 10:04 AM, Mahmoud wrote:
> >> Hello All,
> >>
> >> I've applied HCP pipeline scripts to our structural data and it looks
> like everything goes well to the end of PostFreeSurferPipelline.
> >>
> >> Opening the fs_LR.wb.spec file for the low-resolution mesh, it is
> obvious that the pial surface line (the blue line) hits the dura or is at
> the very outer edge of the pial surface. I was wondering which parameters
> and where I should tweak to get a better result.
> >>
> >> Thank you!
> >> Mahmoud
> >> ___
> >> HCP-Users mailing list
> >> HCP-Users@humanconnectome.org
> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >>
> >
> > ___
> > HCP-Users mailing list
> > HCP-Users@humanconnectome.org
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
> >
> > ___
> > HCP-Users mailing list
> > HCP-Users@humanconnectome.org
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
>
>

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[HCP-Users] Downsampling to 1mm in FreesurferPipeline

[Mahmoud]

Dear HCP developers,

Could you elaborate more on this segment of Freesurferpipeline script:

It is noted because of being compatible with freesurfer we have to
downsample our submilimeter data to 1mm resolution. The scripts uses the
following commands:

flirt -interp spline -in "$T1wImage" -ref "$T1wImage" -applyisoxfm 1 -out
"$T1wImageFile"_1mm.nii.gz

applywarp --rel --interp=spline -i "$T1wImage" -r
"$T1wImageFile"_1mm.nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o
"$T1wImageFile"_1mm.nii.gz

applywarp --rel --interp=nn -i "$T1wImageBrain" -r
"$T1wImageFile"_1mm.nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o
"$T1wImageBrainFile"_1mm.nii.gz

What is the purpose of those two "applywarp" commands?

can't we use sometning like the below command to get around the 1mm
resolution issue (assuming that data size is less than 255x255x255)?
*mri_convert -i  -o  -iis 1 -ijs 1 -iks 1*


Also right after the applywarp commands, this line follows:
fslmaths "$T1wImageFile"_1mm.nii.gz -div $Mean -mul 150 -abs
"$T1wImageFile"_1mm.nii.gz

Is this for image normalization ? and from where that "150" comes ?


Thank you!
Mahmoud

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