Re: [HCP-Users] (no subject) -> amygdala atlas

[David Van Essen]

Hi Heracles,

There’s a very nice parcellated amygdala atlas based on HCP data published by 
Tyszka and Pauli (https://www.ncbi.nlm.nih.gov/pubmed/27354150).  The atlas 
dataset is accessible via http://evendim.caltech.edu/amygdala-atlas/ in various 
spaces (MNI152 1mm and 700um and CIT168 700um) in both Nifti-1 format and Cifti 
dlabels.

David

> On Sep 12, 2017, at 4:55 PM, hercp  wrote:
> 
> Does anyone know if there any atlases of amygdala subdivisions?
>  
> Heracles Panagiotides, PhD
> 
> 
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[HCP-Users] (no subject)

[hercp]

Does anyone know if there any atlases of amygdala subdivisions?

Heracles Panagiotides, PhD



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Re: [HCP-Users] Resampling freesurfer-HCP

[Glasser, Matthew]

I would ask on the FreeSurfer mailing list how to convert those file types to 
GIFTI as we are not familiar with them.

Peace,

Matt.

From: 
>
 on behalf of Timothy Coalson >
Date: Tuesday, September 12, 2017 at 1:43 PM
To: Xavier Guell Paradis >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Resampling freesurfer-HCP

I am not familiar with the .w format, but it sounds like mris_convert is not 
actually converting it to gifti format.  The second error from the .mgh method 
sounds like it has the surface geometry in the file, which must be removed - 
workbench requires geometry files (.surf.gii) and data files (.func.gii) to be 
separate.

You could also start from the unthresholded file instead, which would not have 
this apparently unusual .w format.  We generally don't recommend thresholding, 
but instead making outlines of what is significant, and showing that on top of 
the unthresholded beta.

Tim


On Tue, Sep 12, 2017 at 1:21 PM, Xavier Guell Paradis 
> wrote:
I thought it might be useful to add that the initial .w file is thresholded and 
does not contain values for all cerebral cortical regions.
Thank you very much,
Xavier.

From: 
hcp-users-boun...@humanconnectome.org
 
[hcp-users-boun...@humanconnectome.org]
 on behalf of Xavier Guell Paradis [xavie...@mit.edu]
Sent: Tuesday, September 12, 2017 2:05 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Resampling freesurfer-HCP

Dear HCP experts,
I have an overlay freesurfer file (format is .w) which corresponds to a task 
activity surface map (group result). I have one .w file for each cerebral 
hemisphere. I would like to visualize these maps using wb_view, and have tried 
to follow the instructions you published 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?).
As a first step I would need to convert the .w files into .func.gii files using 
mris_convert. Then I would use wb_command -metric-resample, as indicated in 
your instructions. This does not seem to work with my .w file:

1) mris_convert myfile.w myfile.func.gii
This generates myfile.func.gii, but when I use wb_command -metric-resample I 
get the following error:
ERROR: Parse error while reading: error occurred while parsing element, line 
number: 1 column number: 1

2) As an alternative approach, I opened myfile.w using Tksurfer and saved the 
overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then 
I do the following:
mris_convert myfile.mgh myfile.func.gii
This generates the myfile.func.gii file, but when I use wb_command 
-metric-resample with this file I get a different error:
ERROR: All data arrays (columns) in the file must have the same number of rows. 
 The first array (column) contains 163842 rows.  Array 2 contains 327680 rows.

Thank you very much for your help,
Xavier.

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Re: [HCP-Users] Resampling freesurfer-HCP

[Timothy Coalson]

I am not familiar with the .w format, but it sounds like mris_convert is
not actually converting it to gifti format.  The second error from the .mgh
method sounds like it has the surface geometry in the file, which must be
removed - workbench requires geometry files (.surf.gii) and data files
(.func.gii) to be separate.

You could also start from the unthresholded file instead, which would not
have this apparently unusual .w format.  We generally don't recommend
thresholding, but instead making outlines of what is significant, and
showing that on top of the unthresholded beta.

Tim


On Tue, Sep 12, 2017 at 1:21 PM, Xavier Guell Paradis 
wrote:

> I thought it might be useful to add that the initial .w file is
> thresholded and does not contain values for all cerebral cortical regions.
> Thank you very much,
> Xavier.
> 
> From: hcp-users-boun...@humanconnectome.org [hcp-users-bounces@
> humanconnectome.org] on behalf of Xavier Guell Paradis [xavie...@mit.edu]
> Sent: Tuesday, September 12, 2017 2:05 PM
> To: hcp-users@humanconnectome.org
> Subject: [HCP-Users] Resampling freesurfer-HCP
>
> Dear HCP experts,
> I have an overlay freesurfer file (format is .w) which corresponds to a
> task activity surface map (group result). I have one .w file for each
> cerebral hemisphere. I would like to visualize these maps using wb_view,
> and have tried to follow the instructions you published (
> https://wiki.humanconnectome.org/display/PublicData/HCP+
> Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?).
> As a first step I would need to convert the .w files into .func.gii files
> using mris_convert. Then I would use wb_command -metric-resample, as
> indicated in your instructions. This does not seem to work with my .w file:
>
> 1) mris_convert myfile.w myfile.func.gii
> This generates myfile.func.gii, but when I use wb_command -metric-resample
> I get the following error:
> ERROR: Parse error while reading: error occurred while parsing element,
> line number: 1 column number: 1
>
> 2) As an alternative approach, I opened myfile.w using Tksurfer and saved
> the overlay (myfile.w) with .mgh format (generating a new file:
> "myfile.mgh"). Then I do the following:
> mris_convert myfile.mgh myfile.func.gii
> This generates the myfile.func.gii file, but when I use wb_command
> -metric-resample with this file I get a different error:
> ERROR: All data arrays (columns) in the file must have the same number of
> rows.  The first array (column) contains 163842 rows.  Array 2 contains
> 327680 rows.
>
> Thank you very much for your help,
> Xavier.
>
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>
>
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>

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Re: [HCP-Users] Resampling freesurfer-HCP

[Xavier Guell Paradis]

I thought it might be useful to add that the initial .w file is thresholded and 
does not contain values for all cerebral cortical regions.
Thank you very much,
Xavier.

From: hcp-users-boun...@humanconnectome.org 
[hcp-users-boun...@humanconnectome.org] on behalf of Xavier Guell Paradis 
[xavie...@mit.edu]
Sent: Tuesday, September 12, 2017 2:05 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Resampling freesurfer-HCP

Dear HCP experts,
I have an overlay freesurfer file (format is .w) which corresponds to a task 
activity surface map (group result). I have one .w file for each cerebral 
hemisphere. I would like to visualize these maps using wb_view, and have tried 
to follow the instructions you published 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?).
As a first step I would need to convert the .w files into .func.gii files using 
mris_convert. Then I would use wb_command -metric-resample, as indicated in 
your instructions. This does not seem to work with my .w file:

1) mris_convert myfile.w myfile.func.gii
This generates myfile.func.gii, but when I use wb_command -metric-resample I 
get the following error:
ERROR: Parse error while reading: error occurred while parsing element, line 
number: 1 column number: 1

2) As an alternative approach, I opened myfile.w using Tksurfer and saved the 
overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then 
I do the following:
mris_convert myfile.mgh myfile.func.gii
This generates the myfile.func.gii file, but when I use wb_command 
-metric-resample with this file I get a different error:
ERROR: All data arrays (columns) in the file must have the same number of rows. 
 The first array (column) contains 163842 rows.  Array 2 contains 327680 rows.

Thank you very much for your help,
Xavier.

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[HCP-Users] Resampling freesurfer-HCP

[Xavier Guell Paradis]

Dear HCP experts,
I have an overlay freesurfer file (format is .w) which corresponds to a task 
activity surface map (group result). I have one .w file for each cerebral 
hemisphere. I would like to visualize these maps using wb_view, and have tried 
to follow the instructions you published 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?).
As a first step I would need to convert the .w files into .func.gii files using 
mris_convert. Then I would use wb_command -metric-resample, as indicated in 
your instructions. This does not seem to work with my .w file:

1) mris_convert myfile.w myfile.func.gii
This generates myfile.func.gii, but when I use wb_command -metric-resample I 
get the following error:
ERROR: Parse error while reading: error occurred while parsing element, line 
number: 1 column number: 1

2) As an alternative approach, I opened myfile.w using Tksurfer and saved the 
overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then 
I do the following:
mris_convert myfile.mgh myfile.func.gii
This generates the myfile.func.gii file, but when I use wb_command 
-metric-resample with this file I get a different error:
ERROR: All data arrays (columns) in the file must have the same number of rows. 
 The first array (column) contains 163842 rows.  Array 2 contains 327680 rows.

Thank you very much for your help,
Xavier.

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Re: [HCP-Users] FIX error in fix_3_clean.m

[Glasser, Matthew]

Thanks for letting us know that it worked.

Peace,

Matt.

From: Sang-Young Kim >
Date: Tuesday, September 12, 2017 at 10:00 AM
To: Keith Jamison >
Cc: Matt Glasser >, 
"HCP-Users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] FIX error in fix_3_clean.m

Hello, Keith:

After making change in the script of call_matlab.sh in FIX installation folder, 
the FIX is working without the error.
I hope someone who have the same issue with me see this post.

I really appreciate your help.

Best,

Sang-Young


On Sep 11, 2017, at 6:51 PM, Keith Jamison 
> wrote:

In your FSL FIX installation, you can try making the same change in line #307 
of call_matlab.sh

-Keith

On Mon, Sep 11, 2017 at 6:34 PM, Sang-Young Kim 
> wrote:
I am running the script ${HOME}/projects/Pipelines/ICAFIX/hcp_fix.

Is there a point to modify the script in order for working FIX?

Thanks.

Sang-Young


On Sep 11, 2017, at 6:28 PM, Keith Jamison 
> wrote:

Try changing line #381 in ReApplyFix/ReApplyFixPipeline.sh from:

ML_PATHS="addpath('${FSL_MATLAB_PATH}'); addpath('${FSL_FIX_CIFTIRW}');"

to

ML_PATHS="restoredefaultpath; addpath('${FSL_MATLAB_PATH}'); 
addpath('${FSL_FIX_CIFTIRW}');"

-Keith

On Mon, Sep 11, 2017 at 5:54 PM, Sang-Young Kim 
> wrote:
Yes, I’m using CIFTI data. This is the interpreted version.

Sang-Young


On Sep 11, 2017, at 5:59 PM, Glasser, Matthew 
> wrote:

Are you using CIFTI data?  Is this the compiled version of matlab or the
interpreted version?

Peace,

Matt.

On 9/11/17, 4:19 PM, 
"hcp-users-boun...@humanconnectome.org
 on behalf of
Sang-Young Kim" 

 on behalf of
sykim...@gmail.com> wrote:

Dear HCP experts:

I¹m struggling with FIX for many days. The problem is that FIX does not
generate cleaned data.
So I found error message in .fix.log file as shown below.

TR =

  1

Elapsed time is 2.053048 seconds.
{?Error using file_array/permute (line 10)
file_array objects can not be permuted.

Error in read_gifti_file>gifti_Data (line 191)
 d = permute(reshape(d,fliplr(s.Dim)),length(s.Dim):-1:1);

Error in read_gifti_file>gifti_DataArray (line 122)
 s(1).data = gifti_Data(t,c(i),s(1).attributes);

Error in read_gifti_file (line 45)
 this.data{end+1} = gifti_DataArray(t,uid(i),filename);

Error in gifti (line 74)
 this = read_gifti_file(varargin{1},giftistruct);

Error in ciftiopen (line 16)
cifti = gifti([tmpname '.gii']);

Error in fix_3_clean (line 48)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
}?
**

Actually I saw many posts with the same error. But no clear solution is
provided. I believe I set the path correctly and use last version of
GIFTI toolbox. And I have tested "ciftiopen" function directly on the
matlab. It worked in matlab.
But I have no idea why above error came up while running FIX.

Any insights would be greatly appreciated.

Thanks.

Sang-Young Kim, Ph.D.

Postdoctoral Fellow
Department of Radiology, University of Pittsburgh
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Re: [HCP-Users] FIX error in fix_3_clean.m

[Sang-Young Kim]

Hello, Keith:

After making change in the script of call_matlab.sh in FIX installation folder, 
the FIX is working without the error. 
I hope someone who have the same issue with me see this post. 

I really appreciate your help. 

Best, 

Sang-Young


> On Sep 11, 2017, at 6:51 PM, Keith Jamison  wrote:
> 
> In your FSL FIX installation, you can try making the same change in line #307 
> of call_matlab.sh
> 
> -Keith
> 
> On Mon, Sep 11, 2017 at 6:34 PM, Sang-Young Kim  > wrote:
> I am running the script ${HOME}/projects/Pipelines/ICAFIX/hcp_fix. 
> 
> Is there a point to modify the script in order for working FIX?
> 
> Thanks. 
> 
> Sang-Young
> 
> 
>> On Sep 11, 2017, at 6:28 PM, Keith Jamison > > wrote:
>> 
>> Try changing line #381 in ReApplyFix/ReApplyFixPipeline.sh from:
>> 
>> ML_PATHS="addpath('${FSL_MATLAB_PATH}'); addpath('${FSL_FIX_CIFTIRW}');"
>> 
>> to 
>> 
>> ML_PATHS="restoredefaultpath; addpath('${FSL_MATLAB_PATH}'); 
>> addpath('${FSL_FIX_CIFTIRW}');"
>> 
>> -Keith
>> 
>> On Mon, Sep 11, 2017 at 5:54 PM, Sang-Young Kim > > wrote:
>> Yes, I’m using CIFTI data. This is the interpreted version. 
>> 
>> Sang-Young
>> 
>> 
>>> On Sep 11, 2017, at 5:59 PM, Glasser, Matthew >> > wrote:
>>> 
>>> Are you using CIFTI data?  Is this the compiled version of matlab or the
>>> interpreted version?
>>> 
>>> Peace,
>>> 
>>> Matt.
>>> 
>>> On 9/11/17, 4:19 PM, "hcp-users-boun...@humanconnectome.org 
>>>  on behalf of
>>> Sang-Young Kim" >>  on behalf of
>>> sykim...@gmail.com > wrote:
>>> 
 Dear HCP experts:
 
 I¹m struggling with FIX for many days. The problem is that FIX does not
 generate cleaned data.
 So I found error message in .fix.log file as shown below.
 
 TR =
 
   1
 
 Elapsed time is 2.053048 seconds.
 {?Error using file_array/permute (line 10)
 file_array objects can not be permuted.
 
 Error in read_gifti_file>gifti_Data (line 191)
  d = permute(reshape(d,fliplr(s.Dim)),length(s.Dim):-1:1);
 
 Error in read_gifti_file>gifti_DataArray (line 122)
  s(1).data = gifti_Data(t,c(i),s(1).attributes);
 
 Error in read_gifti_file (line 45)
  this.data{end+1} = gifti_DataArray(t,uid(i),filename);
 
 Error in gifti (line 74)
  this = read_gifti_file(varargin{1},giftistruct);
 
 Error in ciftiopen (line 16)
 cifti = gifti([tmpname '.gii']);
 
 Error in fix_3_clean (line 48)
 BO=ciftiopen('Atlas.dtseries.nii',WBC);
 }? 
 **
 
 Actually I saw many posts with the same error. But no clear solution is
 provided. I believe I set the path correctly and use last version of
 GIFTI toolbox. And I have tested "ciftiopen" function directly on the
 matlab. It worked in matlab.
 But I have no idea why above error came up while running FIX.
 
 Any insights would be greatly appreciated.
 
 Thanks. 
 
 Sang-Young Kim, Ph.D.
 
 Postdoctoral Fellow
 Department of Radiology, University of Pittsburgh
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 HCP-Users@humanconnectome.org 
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> 
> 


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