Re: [HCP-Users] Tractography

[Glasser, Matthew]

For MNI space ROIs you use the  
--xfm=${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz and 
--invxfm=${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz 
flags in probtrackx.

Peace,

Matt.

From: hercp mailto:he...@uw.edu>>
Date: Friday, August 25, 2017 at 4:46 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] Tractography

I have another question along this line.  I want to define a ROI on the 
BestpostX files I downloaded using an existing atlas.  Do I have to convert all 
 .nii files  in that directory to MNI space using FSL-FLIRT one by one, or is 
there a more parsimonious  method?

Thanks again for all your help.

HP



From: Glasser, Matthew
Sent: Thursday, August 24, 2017 11:30 AM
To: hercp
Cc: HUMAN CONNECTOME
Subject: Re: [HCP-Users] Tractography

You need to switch from preprocessed to analysis in the package selector on 
ConnectomeDB to see it.

Peace,

Matt.

From: hercp 
Date: Thursday, August 24, 2017 at 11:40 AM
To: Matt Glasser 
Subject: Re: [HCP-Users] Tractography

Thanks, Matt.  Which files are the output of the Bedpostx process?  I am 
currently looking at subject 116524.  These are files I was able to download.


[2017-08-24_9-36-36]

Once again, thank you for your help.

Heracles Panagiotides, PhD



From: Glasser, Matthew
Sent: Thursday, August 24, 2017 6:50 AM
To: hercp ; HUMAN CONNECTOME
Subject: Re: [HCP-Users] Tractography

Also as Steve has reminded me, you can download the Bedpostx outputs 
pre-computed.

Peace,

Matt.

From:  on behalf of Matt Glasser 

Date: Thursday, August 24, 2017 at 6:53 AM
To: hercp , HUMAN CONNECTOME 
Subject: Re: [HCP-Users] Tractography

That is the price one pays for really high spatial and angular resolution 
diffusion data.  You can accelerate things quite a bit on CUDA capable GPUs.

Peace,

Matt.

From:  on behalf of hercp 
Date: Thursday, August 24, 2017 at 6:31 AM
To: HUMAN CONNECTOME 
Subject: [HCP-Users] Tractography

Hello Everyone,

I am running BEDTPOSTX Estimation on FSL using DTI data that I downloaded from 
the HCP site.  The process is taking a very long time (days) to process.  Is 
there a faster way to do tractography?

Thanks,
Heracles



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Re: [HCP-Users] Recognition memory task details

[Elam, Jennifer]

Hi Dan,

The recognition memory (REC) "task" is just remembering (subject decides 
whether they remember/know an item or if it is a new item) the items presented 
in the working memory task. The E-Prime files and picture stimuli for the REC 
task are part of the 3T E-Prime scripts 
(2.4GB)

zip archive availableas one of the HCP Task Resources in ConnectomeDB (follow 
the link -- you need to login and download via Aspera plugin).


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: Evans, Dan 
Sent: Friday, August 25, 2017 11:27:57 AM
To: Elam, Jennifer; HCP-Users@humanconnectome.org
Cc: Burgess, Gregory
Subject: RE: Recognition memory task details

I have been trying to find the E-prime download for the recognition memory 
task. I have been able to find the WM task and use it, but not the accompanying 
recognition memory task. Is it unavailable? Or have I simply missed it 
somewhere?

Best,
Dan

-
Dan Evans
Research Assistant - Clinical Neuroscience Lab
Department of Psychology
Ohio State University, Columbus, OH

From: Elam, Jennifer [e...@wustl.edu]
Sent: Thursday, August 17, 2017 10:58 AM
To: Evans, Dan; HCP-Users@humanconnectome.org
Cc: Burgess, Gregory
Subject: Re: Recognition memory task details


Hi Dan,

Some details of the recognition memory task are on p.50 of the HCP S1200 
Release Reference 
Manual.
 Greg might be able to point you to more information or analysis results.


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: hcp-users-boun...@humanconnectome.org 
 on behalf of Evans, Dan 

Sent: Thursday, August 17, 2017 9:44 AM
To: HCP-Users@humanconnectome.org
Subject: [HCP-Users] Recognition memory task details

Hi HCP Team,

I've been looking for methodological details on the recognition memory task 
that occurred after the scan, but I can't find them anywhere. The Barch et al. 
2013 paper says it reports the specifics in the supplemental materials. 
However, there is no mention of the recognition memory task in the supplemental 
materials. That paper also states that the results from the recognition memory 
task will be published in a later article but I can't seem to find one. Have 
those results been published (this question was asked by someone else back in 
2014)? If so, where can I find them as well as the detailed task methodology? 
Thanks for your help!

Best,
Dan

-
Dan Evans
Research Assistant - Clinical Neuroscience Lab
Department of Psychology
Ohio State University, Columbus, OH

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Re: [HCP-Users] Recognition memory task details

[Evans, Dan]

I have been trying to find the E-prime download for the recognition memory 
task. I have been able to find the WM task and use it, but not the accompanying 
recognition memory task. Is it unavailable? Or have I simply missed it 
somewhere?

Best,
Dan

-
Dan Evans
Research Assistant - Clinical Neuroscience Lab
Department of Psychology
Ohio State University, Columbus, OH

From: Elam, Jennifer [e...@wustl.edu]
Sent: Thursday, August 17, 2017 10:58 AM
To: Evans, Dan; HCP-Users@humanconnectome.org
Cc: Burgess, Gregory
Subject: Re: Recognition memory task details


Hi Dan,

Some details of the recognition memory task are on p.50 of the HCP S1200 
Release Reference 
Manual.
 Greg might be able to point you to more information or analysis results.


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: hcp-users-boun...@humanconnectome.org 
 on behalf of Evans, Dan 

Sent: Thursday, August 17, 2017 9:44 AM
To: HCP-Users@humanconnectome.org
Subject: [HCP-Users] Recognition memory task details

Hi HCP Team,

I've been looking for methodological details on the recognition memory task 
that occurred after the scan, but I can't find them anywhere. The Barch et al. 
2013 paper says it reports the specifics in the supplemental materials. 
However, there is no mention of the recognition memory task in the supplemental 
materials. That paper also states that the results from the recognition memory 
task will be published in a later article but I can't seem to find one. Have 
those results been published (this question was asked by someone else back in 
2014)? If so, where can I find them as well as the detailed task methodology? 
Thanks for your help!

Best,
Dan

-
Dan Evans
Research Assistant - Clinical Neuroscience Lab
Department of Psychology
Ohio State University, Columbus, OH

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Re: [HCP-Users] Merging Annotation Files into Gifti Image

[Timothy Coalson]

In workbench, we do not do things this way at all.  Putting both surfaces
into a single file is neither necessary nor recommended, even for
visualization.  wb_view will happily display both left and right surfaces
in a single tab, just load the surfaces as separate left and right gifti
files.  Maybe freeview doesn't have this capability, and that is why you
are on this track?

For having a single file that contains data for both hemispheres, the CIFTI
format is our solution (and additionally allows voxel-based structures, for
subcortical gray matter or other uses).  To get a cifti file that is
index-matched to HCP data (useful for doing comparison-type processing),
use wb_command -cifti-create-dense-from-template.  If you just want
something quick and dirty, try wb_command -cifti-create-label.

Finally, some speculation: if the "merged" surface files work in the
obvious way (copy the triangles and coordinates onto the end of the other
surface's), then you may be able to generate merged surface files by
concatenating the left and right maps into a single new map (make the array
twice as long in the vertices dimension).  I have no idea what commands
might do this, as it is not something we encourage.

Tim


On Fri, Aug 25, 2017 at 10:32 AM, Thomas DeRamus 
wrote:

> Thank you.
>
> I'll try a couple of other things and see where it takes me.
>
> On Fri, Aug 25, 2017 at 10:31 AM, Glasser, Matthew 
> wrote:
>
>> Like I said, I don’t think you could do this with surface registration
>> because you cannot easily inflate a combined surface to a sphere.   You
>> would need to project to the volume and then back to the surface.  I don’t
>> know that it really matters what volume you use.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Thomas DeRamus 
>> Date: Friday, August 25, 2017 at 10:28 AM
>> To: Matt Glasser 
>> Subject: Re: [HCP-Users] Merging Annotation Files into Gifti Image
>>
>> Its for visualization to be honest.
>>
>> I'm doing an analysis with FC and Diffusion tractography using subregions
>> of Thomas Yeo's 2011 cortical atlas and Choi's 2012 striatum atlas and I'm
>> looking at ipsilateral and contralateral connections.
>>
>> I can load the trk.gz and Brainnetviewer connectivity data pretty easily
>> in something like SurfIce but I'd like to display the Yeo's atlas in its
>> original form for the figure.
>>
>> As far as that registration goes, how would I go about doing so?
>>
>> On Fri, Aug 25, 2017 at 10:17 AM, Glasser, Matthew 
>> wrote:
>>
>>> You might actually have to remap that to the subject’s volume using the
>>> individual surfaces and then back to the merged surface.  The reason is
>>> that by merging the surfaces you change the topology, and in such a way
>>> that we cannot use surface registration to handle things.  Tim may have
>>> additional ideas…
>>>
>>> Why do you need to combine the surfaces in this way?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From:  on behalf of Thomas
>>> DeRamus 
>>> Date: Friday, August 25, 2017 at 10:05 AM
>>> To: "hcp-users@humanconnectome.org" 
>>> Subject: [HCP-Users] Merging Annotation Files into Gifti Image
>>>
>>> Hello HCP Users,
>>>
>>> New to the HCP Workbench so I apologize if this is a newbie issue but I
>>> haven't found anything in the listserv describing it.
>>>
>>> I'm tying to merge a smaller version of the Yeo2011 atlas annotation
>>> file from Freesurfer into a single gifti that I can overlay onto a gifti
>>> image with both Freesurfer hemispheres.
>>>
>>> I can merge the two hemispheres pretty easily with:
>>> mris_convert --combinesurfs lh.pial rh.pial Bothhemi.gii
>>>
>>> And I can convert the annotation files to giis pretty easily with:
>>>
>>> mris_convert --annot lh.ReducedYeo2011.annot lh.pial
>>> lh.ReducedYeo2011.gii
>>>
>>> But I can't then merge the separate annot files and project it onto the
>>> merged surface gifti. Either because it can't read the annot.gii or when it
>>> does it just projects it onto one hemisphere as a single value.
>>>
>>> Would anyone know how to do this conversion?
>>>
>>> Or alternatively, would it be easier to project a nii with the ROIs I'm
>>> interested in onto a surface with both hemispheres and then adjust
>>> accordingly? If so, how would I go about that?
>>>
>>> Annots attached.
>>>
>>> --
>>> *Thomas DeRamus*
>>> UAB Department of Psychology, Behavioral Neuroscience
>>> Graduate Research Trainee
>>> Civitan International Research Center
>>> 1719 6th Ave S, Suite 235J, Birmingham, AL 35233
>>> *Phone*: 205-934-0971 <(205)%20934-0971> *Email:* tpdera...@gmail.com,
>>> faus...@uab.edu
>>>
>>> *“If knowledge can create problems, it is not through ignorance that we
>>> can solve them.”*
>>>
>>> *—Issac Asimov*
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
>>
>> --
>> *Thomas DeRamus*
>> UAB Department of Psychology, Behavioral Neuroscience
>> Graduate Research Trainee
>> C

Re: [HCP-Users] dMRI: Error while running "eddy_postproc.sh"

[Sang-Young Kim]

Oh, I see. Yes, the —combrain-data-flag in DiffPreprocPipeline.sh was 1 since I 
did not touch it. 

I will try to use "2". 

Thank you so much. 

Sang-Young


> On Aug 25, 2017, at 12:30 PM, Harms, Michael  wrote:
> 
> 
> See the --combine-data-flag in DiffPreprocPipeline.sh
> The default value of 1 is intended for acquisitions in which you have 
> acquired the full vector table with both polarities, which isn’t how you 
> acquired your data.
> In your case, you’ll need to use a value of ‘2’ for that flag.
> 
> Cheers,
> -MH
> 
> --
> Michael Harms, Ph.D.
> 
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
> 
> On 8/25/17, 11:23 AM, "hcp-users-boun...@humanconnectome.org on behalf of 
> Sang-Young Kim"  sykim...@gmail.com> wrote:
> 
> Dear HCP users:
> 
> I have another problem for running Diffusion Preprocessing pipeline. After 
> eddy current correction, the pipeline proceeded to run eddy_postproc.sh. But 
> I got error message as follow:
> 
> **
> Traceback (most recent call last):
>  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
> line 296, in 
>overlap2)
>  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
> line 36, in main
>bvals1 = loadFile(bvals1file, 1, [-1])
>  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
> line 127, in loadFile
>raise ValueError('Wrong number of dimensions: {0}'.format(filename))
> ValueError: Wrong number of dimensions: 
> /Volumes/LaCieMac3TB/HIV_HCP_pipeline/Data/30067/Diffusion/eddy/Pos.bval
> **
> 
> Above message came up while running the command (see below) in 
> "eddy_postproc.sh".
> *
> ${globalscriptsdir}/average_bvecs.py ${eddydir}/Pos.bval 
> ${eddydir}/Pos_rotated.bvec ${eddydir}/Neg.bval ${eddydir}/Neg_rotated.bvec 
> ${datadir}/avg_data ${eddydir}/Pos_SeriesVolNum.txt 
> ${eddydir}/Neg_SeriesVolNum.txt
> *
> 
> Our dMRI data has been acquired with diffusion direction of 113 (AP 
> direction) and b0 image were acquired with opposite direction (e.g., PA) for 
> topup. So I have 1x113 bval and 3x113 bvec for DWI AP data, and 1x1 bval 
> (e.g., 0 value) and 3x1 bvec (also 0 values) for DWI PA data.
> 
> Something is wrong in bval and/or bvec file?
> 
> It will be greatly appreciated if you can help me.
> 
> Thanks in advance.
> 
> Sang-Young Kim, Ph.D.
> 
> Postdoctoral Research Fellow
> Department of Radiology, University of Pittsburgh
> 
> 
> 
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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] dMRI: Error while running "eddy_postproc.sh"

[Harms, Michael]

See the --combine-data-flag in DiffPreprocPipeline.sh
The default value of 1 is intended for acquisitions in which you have acquired 
the full vector table with both polarities, which isn’t how you acquired your 
data.
In your case, you’ll need to use a value of ‘2’ for that flag.

Cheers,
-MH

--
Michael Harms, Ph.D.

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

On 8/25/17, 11:23 AM, "hcp-users-boun...@humanconnectome.org on behalf of 
Sang-Young Kim"  wrote:

Dear HCP users:

I have another problem for running Diffusion Preprocessing pipeline. After eddy 
current correction, the pipeline proceeded to run eddy_postproc.sh. But I got 
error message as follow:

**
Traceback (most recent call last):
  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
line 296, in 
overlap2)
  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
line 36, in main
bvals1 = loadFile(bvals1file, 1, [-1])
  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
line 127, in loadFile
raise ValueError('Wrong number of dimensions: {0}'.format(filename))
ValueError: Wrong number of dimensions: 
/Volumes/LaCieMac3TB/HIV_HCP_pipeline/Data/30067/Diffusion/eddy/Pos.bval
**

Above message came up while running the command (see below) in 
"eddy_postproc.sh".
*
${globalscriptsdir}/average_bvecs.py ${eddydir}/Pos.bval 
${eddydir}/Pos_rotated.bvec ${eddydir}/Neg.bval ${eddydir}/Neg_rotated.bvec 
${datadir}/avg_data ${eddydir}/Pos_SeriesVolNum.txt 
${eddydir}/Neg_SeriesVolNum.txt
*

Our dMRI data has been acquired with diffusion direction of 113 (AP direction) 
and b0 image were acquired with opposite direction (e.g., PA) for topup. So I 
have 1x113 bval and 3x113 bvec for DWI AP data, and 1x1 bval (e.g., 0 value) 
and 3x1 bvec (also 0 values) for DWI PA data.

Something is wrong in bval and/or bvec file?

It will be greatly appreciated if you can help me.

Thanks in advance.

Sang-Young Kim, Ph.D.

Postdoctoral Research Fellow
Department of Radiology, University of Pittsburgh



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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 
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[HCP-Users] dMRI: Error while running "eddy_postproc.sh"

[Sang-Young Kim]

Dear HCP users:

I have another problem for running Diffusion Preprocessing pipeline. After eddy 
current correction, the pipeline proceeded to run eddy_postproc.sh. But I got 
error message as follow:

**
Traceback (most recent call last):
  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
line 296, in 
overlap2)
  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
line 36, in main
bvals1 = loadFile(bvals1file, 1, [-1])
  File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py", 
line 127, in loadFile
raise ValueError('Wrong number of dimensions: {0}'.format(filename))
ValueError: Wrong number of dimensions: 
/Volumes/LaCieMac3TB/HIV_HCP_pipeline/Data/30067/Diffusion/eddy/Pos.bval
**

Above message came up while running the command (see below) in 
"eddy_postproc.sh". 
*
${globalscriptsdir}/average_bvecs.py ${eddydir}/Pos.bval 
${eddydir}/Pos_rotated.bvec ${eddydir}/Neg.bval ${eddydir}/Neg_rotated.bvec 
${datadir}/avg_data ${eddydir}/Pos_SeriesVolNum.txt 
${eddydir}/Neg_SeriesVolNum.txt
*

Our dMRI data has been acquired with diffusion direction of 113 (AP direction) 
and b0 image were acquired with opposite direction (e.g., PA) for topup. So I 
have 1x113 bval and 3x113 bvec for DWI AP data, and 1x1 bval (e.g., 0 value) 
and 3x1 bvec (also 0 values) for DWI PA data.  

Something is wrong in bval and/or bvec file? 

It will be greatly appreciated if you can help me. 

Thanks in advance. 

Sang-Young Kim, Ph.D.

Postdoctoral Research Fellow
Department of Radiology, University of Pittsburgh



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Re: [HCP-Users] Merging Annotation Files into Gifti Image

[Thomas DeRamus]

Thank you.

I'll try a couple of other things and see where it takes me.

On Fri, Aug 25, 2017 at 10:31 AM, Glasser, Matthew 
wrote:

> Like I said, I don’t think you could do this with surface registration
> because you cannot easily inflate a combined surface to a sphere.   You
> would need to project to the volume and then back to the surface.  I don’t
> know that it really matters what volume you use.
>
> Peace,
>
> Matt.
>
> From: Thomas DeRamus 
> Date: Friday, August 25, 2017 at 10:28 AM
> To: Matt Glasser 
> Subject: Re: [HCP-Users] Merging Annotation Files into Gifti Image
>
> Its for visualization to be honest.
>
> I'm doing an analysis with FC and Diffusion tractography using subregions
> of Thomas Yeo's 2011 cortical atlas and Choi's 2012 striatum atlas and I'm
> looking at ipsilateral and contralateral connections.
>
> I can load the trk.gz and Brainnetviewer connectivity data pretty easily
> in something like SurfIce but I'd like to display the Yeo's atlas in its
> original form for the figure.
>
> As far as that registration goes, how would I go about doing so?
>
> On Fri, Aug 25, 2017 at 10:17 AM, Glasser, Matthew 
> wrote:
>
>> You might actually have to remap that to the subject’s volume using the
>> individual surfaces and then back to the merged surface.  The reason is
>> that by merging the surfaces you change the topology, and in such a way
>> that we cannot use surface registration to handle things.  Tim may have
>> additional ideas…
>>
>> Why do you need to combine the surfaces in this way?
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of Thomas
>> DeRamus 
>> Date: Friday, August 25, 2017 at 10:05 AM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] Merging Annotation Files into Gifti Image
>>
>> Hello HCP Users,
>>
>> New to the HCP Workbench so I apologize if this is a newbie issue but I
>> haven't found anything in the listserv describing it.
>>
>> I'm tying to merge a smaller version of the Yeo2011 atlas annotation file
>> from Freesurfer into a single gifti that I can overlay onto a gifti image
>> with both Freesurfer hemispheres.
>>
>> I can merge the two hemispheres pretty easily with:
>> mris_convert --combinesurfs lh.pial rh.pial Bothhemi.gii
>>
>> And I can convert the annotation files to giis pretty easily with:
>>
>> mris_convert --annot lh.ReducedYeo2011.annot lh.pial lh.ReducedYeo2011.gii
>>
>> But I can't then merge the separate annot files and project it onto the
>> merged surface gifti. Either because it can't read the annot.gii or when it
>> does it just projects it onto one hemisphere as a single value.
>>
>> Would anyone know how to do this conversion?
>>
>> Or alternatively, would it be easier to project a nii with the ROIs I'm
>> interested in onto a surface with both hemispheres and then adjust
>> accordingly? If so, how would I go about that?
>>
>> Annots attached.
>>
>> --
>> *Thomas DeRamus*
>> UAB Department of Psychology, Behavioral Neuroscience
>> Graduate Research Trainee
>> Civitan International Research Center
>> 1719 6th Ave S, Suite 235J, Birmingham, AL 35233
>> *Phone*: 205-934-0971 <(205)%20934-0971> *Email:* tpdera...@gmail.com,
>> faus...@uab.edu
>>
>> *“If knowledge can create problems, it is not through ignorance that we
>> can solve them.”*
>>
>> *—Issac Asimov*
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>
>
> --
> *Thomas DeRamus*
> UAB Department of Psychology, Behavioral Neuroscience
> Graduate Research Trainee
> Civitan International Research Center
> 1719 6th Ave S, Suite 235J, Birmingham, AL 35233
> *Phone*: 205-934-0971 <(205)%20934-0971> *Email:* tpdera...@gmail.com,
> faus...@uab.edu
>
> *“If knowledge can create problems, it is not through ignorance that we
> can solve them.”*
>
> *—Issac Asimov*
>



-- 
*Thomas DeRamus*
UAB Department of Psychology, Behavioral Neuroscience
Graduate Research Trainee
Civitan International Research Center
1719 6th Ave S, Suite 235J, Birmingham, AL 35233
*Phone*: 205-934-0971 *Email:* tpdera...@gmail.com, faus...@uab.edu

*“If knowledge can create problems, it is not through ignorance that we can
solve them.”*

*—Issac Asimov*

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Re: [HCP-Users] Merging Annotation Files into Gifti Image

[Glasser, Matthew]

Like I said, I don’t think you could do this with surface registration because 
you cannot easily inflate a combined surface to a sphere.   You would need to 
project to the volume and then back to the surface.  I don’t know that it 
really matters what volume you use.

Peace,

Matt.

From: Thomas DeRamus mailto:tpdera...@gmail.com>>
Date: Friday, August 25, 2017 at 10:28 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] Merging Annotation Files into Gifti Image

Its for visualization to be honest.

I'm doing an analysis with FC and Diffusion tractography using subregions of 
Thomas Yeo's 2011 cortical atlas and Choi's 2012 striatum atlas and I'm looking 
at ipsilateral and contralateral connections.

I can load the trk.gz and Brainnetviewer connectivity data pretty easily in 
something like SurfIce but I'd like to display the Yeo's atlas in its original 
form for the figure.

As far as that registration goes, how would I go about doing so?

On Fri, Aug 25, 2017 at 10:17 AM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
You might actually have to remap that to the subject’s volume using the 
individual surfaces and then back to the merged surface.  The reason is that by 
merging the surfaces you change the topology, and in such a way that we cannot 
use surface registration to handle things.  Tim may have additional ideas…

Why do you need to combine the surfaces in this way?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Thomas DeRamus mailto:tpdera...@gmail.com>>
Date: Friday, August 25, 2017 at 10:05 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Merging Annotation Files into Gifti Image

Hello HCP Users,

New to the HCP Workbench so I apologize if this is a newbie issue but I haven't 
found anything in the listserv describing it.

I'm tying to merge a smaller version of the Yeo2011 atlas annotation file from 
Freesurfer into a single gifti that I can overlay onto a gifti image with both 
Freesurfer hemispheres.

I can merge the two hemispheres pretty easily with:
mris_convert --combinesurfs lh.pial rh.pial Bothhemi.gii

And I can convert the annotation files to giis pretty easily with:

mris_convert --annot lh.ReducedYeo2011.annot lh.pial lh.ReducedYeo2011.gii

But I can't then merge the separate annot files and project it onto the merged 
surface gifti. Either because it can't read the annot.gii or when it does it 
just projects it onto one hemisphere as a single value.

Would anyone know how to do this conversion?

Or alternatively, would it be easier to project a nii with the ROIs I'm 
interested in onto a surface with both hemispheres and then adjust accordingly? 
If so, how would I go about that?

Annots attached.

--
Thomas DeRamus
UAB Department of Psychology, Behavioral Neuroscience
Graduate Research Trainee
Civitan International Research Center
1719 6th Ave S, Suite 235J, Birmingham, AL 35233
Phone: 205-934-0971 Email: 
tpdera...@gmail.com, 
faus...@uab.edu


“If knowledge can create problems, it is not through ignorance that we can 
solve them.”

—Issac Asimov

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HCP-Users@humanconnectome.org
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--
Thomas DeRamus
UAB Department of Psychology, Behavioral Neuroscience
Graduate Research Trainee
Civitan International Research Center
1719 6th Ave S, Suite 235J, Birmingham, AL 35233
Phone: 205-934-0971 Email: tpdera...@gmail.com, 
faus...@uab.edu


“If knowledge can create problems, it is not through ignorance that we can 
solve them.”

—Issac Asimov

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

Re: [HCP-Users] Merging Annotation Files into Gifti Image

[Glasser, Matthew]

You might actually have to remap that to the subject’s volume using the 
individual surfaces and then back to the merged surface.  The reason is that by 
merging the surfaces you change the topology, and in such a way that we cannot 
use surface registration to handle things.  Tim may have additional ideas…

Why do you need to combine the surfaces in this way?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Thomas DeRamus mailto:tpdera...@gmail.com>>
Date: Friday, August 25, 2017 at 10:05 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Merging Annotation Files into Gifti Image

Hello HCP Users,

New to the HCP Workbench so I apologize if this is a newbie issue but I haven't 
found anything in the listserv describing it.

I'm tying to merge a smaller version of the Yeo2011 atlas annotation file from 
Freesurfer into a single gifti that I can overlay onto a gifti image with both 
Freesurfer hemispheres.

I can merge the two hemispheres pretty easily with:
mris_convert --combinesurfs lh.pial rh.pial Bothhemi.gii

And I can convert the annotation files to giis pretty easily with:

mris_convert --annot lh.ReducedYeo2011.annot lh.pial lh.ReducedYeo2011.gii

But I can't then merge the separate annot files and project it onto the merged 
surface gifti. Either because it can't read the annot.gii or when it does it 
just projects it onto one hemisphere as a single value.

Would anyone know how to do this conversion?

Or alternatively, would it be easier to project a nii with the ROIs I'm 
interested in onto a surface with both hemispheres and then adjust accordingly? 
If so, how would I go about that?

Annots attached.

--
Thomas DeRamus
UAB Department of Psychology, Behavioral Neuroscience
Graduate Research Trainee
Civitan International Research Center
1719 6th Ave S, Suite 235J, Birmingham, AL 35233
Phone: 205-934-0971 Email: tpdera...@gmail.com, 
faus...@uab.edu


“If knowledge can create problems, it is not through ignorance that we can 
solve them.”

—Issac Asimov

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HCP-Users@humanconnectome.org
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___
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