Re: [HCP-Users] Downsampling from fs_LR_32k to fsaverage5

2016-04-18 Thread Timothy Coalson 
The -surface-sphere-project-unproject command is used for concatenating
registrations, and since you want to go from fs_LR to fsaverage, which is a
registration that we compute, concatenating registrations isn't the way to
get there.

However, I don't know if we release the fsaverage registrations per-subject
(to us, they are an intermediate registration).  We appear to have
atlas-to-atlas registrations available in the pipeline repository, under
global/templates/standard_mesh_atlases, the fs_L and fs_R directories
contain the fsaverage spheres registered to fs_LR as I understand it.

Do you specifically need to be in fsaverage, or is just a simple
downsampling okay?  We have lower resolutions of fs_LR, for instance 20k,
and you can also create near-arbitrary resolution spheres if you want more
control over downsampling.  For some analyses, parcellation could be more
appropriate than downsampling.

It should be noted that using the individual subjects fsaverage
registration would discard the registration improvements made by MSM (for
MSMsulc, mainly less distortion).  If an atlas-to-atlas registration is
used, then the registration improvements may be retained (alignment
improvements will be retained, distortion will depend on the method used
for atlas to atlas registration), but of course will give a different
result than actually using freesurfer's registration.

Tim


On Mon, Apr 18, 2016 at 9:44 AM, Donna Dierker 
wrote:

> Hi Estrid,
>
> Help from others is likely to be needed, but I can help a little.
>
> The HCP surfaces get to 32k_fs_LR mesh via the Freesurfer registration
> (?h.sphere.reg); however, the fs_LR mesh is not the same as the fsaverage
> mesh, even though it is based on it.  The fsaverage left and right
> hemispheres are not in registration with one another.  Vertex i in the left
> hem could be in the occipital lobe, while it could be in the frontal lobe
> in the right hem.  The fs_LR mesh is in register across hemispheres --
> vertices in left and right hems are in as close to the same place as
> registration could get them to be.  This facilitates cross-hem analyses.
>
> There is a relevant script here:
>
>
> https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh
>
> Specifically this line i sthe one to be studied:
>
> > #Concatenate FS registration to FS --> FS_LR registration
> > ${CARET7DIR}/wb_command -surface-sphere-project-unproject
> "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii
> "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
> "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
> "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii
>
> If you're like me, it will take a few days for you to get your head around
> it.
>
> But I think something like this -- projecting to one standard surface and
> unprojecting from another -- will be the answer.  It might take multiple
> hops to get there, but probably only until you get the magic spheres you
> need to make this work.
>
> I still struggle with understanding the distinction between meshes whose
> vertices are in correspondence, and ones that have differing numbers of
> vertices, but a spatially aligned with one another.
>
> Donna
>
>
> On Apr 18, 2016, at 8:47 AM, Estrid Jakobsen  wrote:
>
> > Dear experts,
> >
> > I'm trying to use wb_command -metric-resample to downsample a vector of
> data points from fs_LR_32k (32492x1) to fsaverage5 (10242x1) space.
> >
> > If I'm not mistaken, this should be possible without prior registration,
> because the HCP fs_LR_32k surfaces and the fsaverage5 surface should
> already be in register. I've saved my data vector as a metric gifti file
> (data.func.gii) in matlab by loading a pre-existing .gii file using the
> gifti toolbox and replacing gifti.cdata with my own data vector. I'm then
> running the following command:
> >
> > wb_command -metric-resample data.func.gii
> 100307.L.sphere.32k_fs_LR.surf.gii fsa5.lh.sphere.surf.gii ADAP_BARY_AREA
> data_fsa5.func.gii -area-surfs 100307.L.inflated.32k_fs_LR.surf.gii
> fsa5_lh.inflated.surf.gii -current-roi mask.func.gii -valid-roi-out
> roi_out.func.gii
> >
> > The command runs without errors, but the output looks strange (see
> attachment). It seems as though the neighborhood information is preserved
> but the coordinates are not, especially obvious by the medial wall mask
> being shifted anterior. I've tried running the command with and without the
> -area-surfs and -current-roi (to mask out the medial wall) options, neither
> of which seem to make any difference.
> >
> > Any suggestions as to what might be going wrong here would be very much
> appreciated.
> > Thanks!
> >
> > Estrid
> >
> > 
> > Estrid Jakobsen

Re: [HCP-Users] structrual extended package for HCP_900 subjects on aws

2016-04-18 Thread Denis-Alexander Engemann 
Hi Jenn,

I checked it once more after having waited for a few days. The numbers
remain incomplete. Essentially the data are not there for a good amount of
subjects, it seems at least all MEG subjects from the 900 release. Can you
confirm this? Or am I missing something?

Cheers,
Denis

On Sat, Apr 16, 2016 at 11:51 AM Denis-Alexander Engemann <
denis.engem...@gmail.com> wrote:

> Great, thanks for the update! Something seems to have moved indeed, but
> not too much apparently. I just checked some 90 MEG subjects, and still the
> structural preprocessing is not fully complete. I'm not sure though if this
> may now have different reasons.
>
> Consider this script where I go through the MEG subjects to see what is
> available.
> https://gist.github.com/dengemann/e6a76197fb07c543120f8cc35ca495e1
>
> For the HCP500 subjects I find "mri", "surf" and "label" subfoldes, the
> others only seem to have "stats". Is this expected?
>
> Denis
>
> On Fri, Apr 15, 2016 at 8:55 PM Jennifer Elam  wrote:
>
>> Hi Denis and all HCP-Users,
>>
>> We now have all Structural Extended Preprocessed data packages available
>> for ALL 900 Subjects Release (S900) subjects with structural MRI data (897
>> subjects) in ConnectomeDB. Yay!
>>
>>
>>
>> The structural extended packages includes outputs from Freesurfer that
>> are not in the main Structural Preprocessed packages. The structural
>> extended packages are included in the S900 Connectome in a Box, which is
>> available for order now.
>>
>>
>>
>> Best,
>>
>> Jenn
>>
>>
>>
>> Jennifer Elam, Ph.D.
>> Scientific Outreach, Human Connectome Project
>>
>>
>> Washington University School of Medicine
>>
>> Department of Neuroscience, Box 8108
>>
>>
>> 660 South Euclid Avenue
>> St. Louis, MO 63110
>> 314-362-9387
>>
>> e...@wustl.edu
>> www.humanconnectome.org
>>
>>
>>
>> *From:* Denis-Alexander Engemann [mailto:denis.engem...@gmail.com]
>> *Sent:* Monday, April 04, 2016 3:30 AM
>> *To:* Jennifer Elam; hcp-users@humanconnectome.org
>>
>>
>> *Subject:* Re: [HCP-Users] structrual extended package for HCP_900
>> subjects on aws
>>
>>
>>
>> Dear Jenn,
>>
>>
>>
>> thanks for letting me know and for looking into it!
>>
>>
>>
>> Cheers,
>>
>> Denis
>>
>> On Fri, Apr 1, 2016 at 9:59 PM Jennifer Elam  wrote:
>>
>> Hi Denis,
>>
>> We’ve looked into the problem and have found that the structural extended
>> data for 178 newly added subjects for S900 was inadvertently unpackaged and
>> therefore not available for download in ConnectomeDB. We are working on
>> fixing this and we’ll send out another message when its available.
>>
>>
>>
>> Best,
>>
>> Jenn
>>
>>
>>
>> Jennifer Elam, Ph.D.
>> Outreach Coordinator, Human Connectome Project
>> Washington University School of Medicine
>> Department of Anatomy and Neurobiology, Box 8108
>> 660 South Euclid Avenue
>> St. Louis, MO 63110
>> 314-362-9387
>> el...@pcg.wustl.edu
>> www.humanconnectome.org
>>
>>
>>
>> *From:* hcp-users-boun...@humanconnectome.org [mailto:
>> hcp-users-boun...@humanconnectome.org] *On Behalf Of *Denis-Alexander
>> Engemann
>> *Sent:* Thursday, March 31, 2016 3:24 AM
>> *To:* hcp-users@humanconnectome.org
>> *Subject:* Re: [HCP-Users] structrual extended package for HCP_900
>> subjects on aws
>>
>>
>>
>> It turns out that the structural extended preprocessing package is not
>> available for the new subjects.
>>
>>
>>
>> Is there any fix planned for this or is there a way to at least get some
>> of the outputs from 'surf' and 'mri'?
>>
>>
>>
>> Denis
>>
>>
>>
>> On Tue, Mar 29, 2016 at 10:35 AM Denis-Alexander Engemann <
>> denis.engem...@gmail.com> wrote:
>>
>> Dear HCPers,
>>
>>
>>
>> it seems that the freesurfer files included in the structural extended
>> subjects are not available on aws for the HCP_900 subjects, at least not
>> for the MEG subjects. I am referring to the following outputs:
>>
>>
>>
>> ${subject}/T1w/${subject}/mri
>>
>> ${subject}/T1w/${subject}/surf
>>
>> ${subject}/T1w/${subject}/label
>>
>>
>>
>> Can anyone confirm?
>>
>>
>>
>> Cheers,
>>
>> Denis
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>

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Re: [HCP-Users] continuous stimuli for story math data

2016-04-18 Thread Georgios Michalareas 

Hi Denis,
I have contacted the appropriate people in HCP in order to arrange to 
put them in ConnectomeDB so that users can download them from there.

I ll post an update on the issue as soon as I get news.

Best
Giorgos


On 4/18/2016 4:31 PM, Denis-Alexander Engemann wrote:

Dear HCPers,

we're wondering if the audio data used in the story math task are 
available somewhere. This would be quite important for a wide range of 
pycholinguistic analyses. Any hint would be appreciated.


Denis

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Re: [HCP-Users] continuous stimuli for story math data

2016-04-18 Thread Greg Burgess 
You can download all of the HCP E-Prime scripts and task stimuli at:
https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=Scripts=HCP_TFMRI_scripts.zip

You will need to have a ConnectomeDB account, agree to the Open Access 
agreement, and will need to install the Aspera client to do this download.
--Greg


Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience
Phone: 314-362-7864
Email: gburg...@wustl.edu

> On Apr 18, 2016, at 9:31 AM, Denis-Alexander Engemann 
>  wrote:
> 
> Dear HCPers,
> 
> we're wondering if the audio data used in the story math task are available 
> somewhere. This would be quite important for a wide range of pycholinguistic 
> analyses. Any hint would be appreciated.
> 
> Denis
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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