Re: [HCP-Users] CIFTI to Matlab

2019-01-17 Thread Anita Sinha 
Tim,

I just used three dots “...” to delete my complete folder path in the email I 
sent for privacy reasons. I’ll try the suggestion you mentioned.

Thanks for your help!

Regards,

Anita

On Jan 17, 2019, at 5:10 PM, Timothy Coalson 
mailto:tsc...@mst.edu>> wrote:

Try doing:

system('/wb_command');

Except using the exact string you are providing to ciftiopen's second argument. 
 You should get the usage information for wb_command if the path is correct and 
things are working.

Tim


On Thu, Jan 17, 2019 at 4:38 PM Anita Sinha 
mailto:amsi...@wisc.edu>> wrote:

Matt/Michael,


When I run g = gifti, I get g = gifti object 1-by-1. I have confirmed that I 
have the correct file paths to the wb_command, however, it seems to duplicate 
part of a file path string, which is why it cannot find the file. Is this a 
known issue?


This is what I'm running:


y = '/.../.../CM.dtseries.nii';
ciftiFile = ciftiopen(y,'Z:/.../workbench/bin_windows64/wb_command');
CM = ciftiFile.cdata;

and receive the same error:

Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file 
C:\Users\AMS217\AppData\Local\Temp\tp366ef3da_4687_4d6e_9b4a_bb7f0ce6fd8e.gii 
failed.

Error in gifti (line 100)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 34)
cifti = gifti([tmpfile '.gii']);


Do I need to convert it to char or something so it is read in correctly?


Regards,


Anita Sinha

Biomedical Engineering Graduate Student

University of Wisconsin-Madison

amsi...@wisc.edu<mailto:amsi...@wisc.edu>


From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Thursday, January 17, 2019 4:27:17 PM
To: Harms, Michael; Anita Sinha; 
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] CIFTI to Matlab

That could also be due to it not finding the file or not finding wb_command.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Thursday, January 17, 2019 at 4:05 PM
To: Anita Sinha mailto:amsi...@wisc.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] CIFTI to Matlab




Hi,

It sounds like you don’t have the gifti library properly installed.



Within matlab, what happens when you type

g = gifti



Do you get a gifti structure?



Cheers,

-MH





--

Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

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<mailto:mha...@wustl.edu>



From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Anita Sinha mailto:amsi...@wisc.edu>>
Date: Thursday, January 17, 2019 at 3:37 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] CIFTI to Matlab



To Whom It May Concern,



I am attempting to open up a dtseries.nii CIFTI file into Matlab to extract the 
time series matrix from rs-fMRI data. I have downloaded workbench and gifti-1.8 
and am following the directions outlined in 
https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63963178 in #2 
"How do you get CIFTI files into Matlab, but it isn't working.



When I run this command:

cii = ciftiopen('path/to/file','path/to/wb_command'); CIFTIdata = cii.cdata



with the appropriate file paths, I keep receiving this error:



Error using read_gifti_file_standalone (line 20)

[GIFTI] Loading of XML file 
C:\Users\...\AppData\Local\Temp\tp904b5934_f040_4259_8a21_0b10e15aecc8.gii 
failed.



Error in gifti (line 100)

this = read_gifti_file_standalone(varargin{1},giftistruct);



Error in ciftiopen (line 34)

cifti = gifti([tmpfile '.gii']);



I have added workbench and gifti to the path and saved everything in the same 
directory to mitigate file directory mismatch, but cannot past this error.



Could you provide some help on how to resolve this?



Thank you for your time.



Regards,



Anita

___
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The materials in this message are private and may contain Protected Healthcare 
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Re: [HCP-Users] CIFTI to Matlab

2019-01-17 Thread Timothy Coalson 
Try doing:

system('/wb_command');

Except using the exact string you are providing to ciftiopen's second
argument.  You should get the usage information for wb_command if the path
is correct and things are working.

Tim


On Thu, Jan 17, 2019 at 4:38 PM Anita Sinha  wrote:

> Matt/Michael,
>
>
> When I run g = gifti, I get g = gifti object 1-by-1. I have confirmed that
> I have the correct file paths to the wb_command, however, it seems to
> duplicate part of a file path string, which is why it cannot find the file.
> Is this a known issue?
>
>
> This is what I'm running:
>
>
> y = '/.../.../CM.dtseries.nii';
> ciftiFile = ciftiopen(y,'Z:/.../workbench/bin_windows64/wb_command');
> CM = ciftiFile.cdata;
>
> and receive the same error:
>
> Error using read_gifti_file_standalone (line 20)
> [GIFTI] Loading of XML file
> C:\Users\AMS217\AppData\Local\Temp\tp366ef3da_4687_4d6e_9b4a_bb7f0ce6fd8e.gii
> failed.
>
> Error in gifti (line 100)
> this = read_gifti_file_standalone(varargin{1},giftistruct);
>
> Error in ciftiopen (line 34)
> cifti = gifti([tmpfile '.gii']);
>
>
> Do I need to convert it to char or something so it is read in correctly?
>
>
> Regards,
>
>
> Anita Sinha
>
> Biomedical Engineering Graduate Student
>
> University of Wisconsin-Madison
>
> amsi...@wisc.edu
> --
> *From:* Glasser, Matthew 
> *Sent:* Thursday, January 17, 2019 4:27:17 PM
> *To:* Harms, Michael; Anita Sinha; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] CIFTI to Matlab
>
> That could also be due to it not finding the file or not finding
> wb_command.
>
> Matt.
>
> From:  on behalf of "Harms,
> Michael" 
> Date: Thursday, January 17, 2019 at 4:05 PM
> To: Anita Sinha , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] CIFTI to Matlab
>
>
>
> Hi,
>
> It sounds like you don’t have the gifti library properly installed.
>
>
>
> Within matlab, what happens when you type
>
> g = gifti
>
>
>
> Do you get a gifti structure?
>
>
>
> Cheers,
>
> -MH
>
>
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> 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 Anita Sinha <
> amsi...@wisc.edu>
> *Date: *Thursday, January 17, 2019 at 3:37 PM
> *To: *"hcp-users@humanconnectome.org" 
> *Subject: *[HCP-Users] CIFTI to Matlab
>
>
>
> To Whom It May Concern,
>
>
>
> I am attempting to open up a dtseries.nii CIFTI file into Matlab to
> extract the time series matrix from rs-fMRI data. I have downloaded
> workbench and gifti-1.8 and am following the directions outlined in
> https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63963178 in
> #2 "How do you get CIFTI files into Matlab, but it isn't working.
>
>
>
> When I run this command:
>
> cii = ciftiopen('path/to/file','path/to/wb_command'); CIFTIdata = cii.cdata
>
>
>
> with the appropriate file paths, I keep receiving this error:
>
>
>
> Error using read_gifti_file_standalone (line 20)
>
> [GIFTI] Loading of XML file
> C:\Users\...\AppData\Local\Temp\tp904b5934_f040_4259_8a21_0b10e15aecc8.gii
> failed.
>
>
>
> Error in gifti (line 100)
>
> this = read_gifti_file_standalone(varargin{1},giftistruct);
>
>
>
> Error in ciftiopen (line 34)
>
> cifti = gifti([tmpfile '.gii']);
>
>
>
> I have added workbench and gifti to the path and saved everything in the
> same directory to mitigate file directory mismatch, but cannot past this
> error.
>
>
>
> Could you provide some help on how to resolve this?
>
>
>
> Thank you for your time.
>
>
>
> Regards,
>
>
>
> Anita
>
> ___
> 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 p

Re: [HCP-Users] CIFTI to Matlab

2019-01-17 Thread Harms, Michael 

Are you actually using 3 dots, instead of 2 dots, to specify your path?

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
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: Anita Sinha 
Date: Thursday, January 17, 2019 at 4:38 PM
To: "Glasser, Matthew" , "Harms, Michael" 
, "hcp-users@humanconnectome.org" 

Subject: Re: [HCP-Users] CIFTI to Matlab


Matt/Michael,



When I run g = gifti, I get g = gifti object 1-by-1. I have confirmed that I 
have the correct file paths to the wb_command, however, it seems to duplicate 
part of a file path string, which is why it cannot find the file. Is this a 
known issue?



This is what I'm running:


y = '/.../.../CM.dtseries.nii';
ciftiFile = ciftiopen(y,'Z:/.../workbench/bin_windows64/wb_command');
CM = ciftiFile.cdata;

and receive the same error:

Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file 
C:\Users\AMS217\AppData\Local\Temp\tp366ef3da_4687_4d6e_9b4a_bb7f0ce6fd8e.gii 
failed.

Error in gifti (line 100)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 34)
cifti = gifti([tmpfile '.gii']);



Do I need to convert it to char or something so it is read in correctly?



Regards,



Anita Sinha

Biomedical Engineering Graduate Student

University of Wisconsin-Madison

amsi...@wisc.edu


From: Glasser, Matthew 
Sent: Thursday, January 17, 2019 4:27:17 PM
To: Harms, Michael; Anita Sinha; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] CIFTI to Matlab

That could also be due to it not finding the file or not finding wb_command.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Thursday, January 17, 2019 at 4:05 PM
To: Anita Sinha mailto:amsi...@wisc.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] CIFTI to Matlab




Hi,

It sounds like you don’t have the gifti library properly installed.



Within matlab, what happens when you type

g = gifti



Do you get a gifti structure?



Cheers,

-MH





--

Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

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<mailto:mha...@wustl.edu>



From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Anita Sinha mailto:amsi...@wisc.edu>>
Date: Thursday, January 17, 2019 at 3:37 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] CIFTI to Matlab



To Whom It May Concern,



I am attempting to open up a dtseries.nii CIFTI file into Matlab to extract the 
time series matrix from rs-fMRI data. I have downloaded workbench and gifti-1.8 
and am following the directions outlined in 
https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63963178 in #2 
"How do you get CIFTI files into Matlab, but it isn't working.



When I run this command:

cii = ciftiopen('path/to/file','path/to/wb_command'); CIFTIdata = cii.cdata



with the appropriate file paths, I keep receiving this error:



Error using read_gifti_file_standalone (line 20)

[GIFTI] Loading of XML file 
C:\Users\...\AppData\Local\Temp\tp904b5934_f040_4259_8a21_0b10e15aecc8.gii 
failed.



Error in gifti (line 100)

this = read_gifti_file_standalone(varargin{1},giftistruct);



Error in ciftiopen (line 34)

cifti = gifti([tmpfile '.gii']);



I have added workbench and gifti to the path and saved everything in the same 
directory to mitigate file directory mismatch, but cannot past this error.



Could you provide some help on how to resolve this?



Thank you for your time.



Regards,



Anita

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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 telepho

Re: [HCP-Users] CIFTI to Matlab

2019-01-17 Thread Anita Sinha 
Matt/Michael,


When I run g = gifti, I get g = gifti object 1-by-1. I have confirmed that I 
have the correct file paths to the wb_command, however, it seems to duplicate 
part of a file path string, which is why it cannot find the file. Is this a 
known issue?


This is what I'm running:


y = '/.../.../CM.dtseries.nii';
ciftiFile = ciftiopen(y,'Z:/.../workbench/bin_windows64/wb_command');
CM = ciftiFile.cdata;

and receive the same error:

Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file 
C:\Users\AMS217\AppData\Local\Temp\tp366ef3da_4687_4d6e_9b4a_bb7f0ce6fd8e.gii 
failed.

Error in gifti (line 100)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 34)
cifti = gifti([tmpfile '.gii']);


Do I need to convert it to char or something so it is read in correctly?


Regards,


Anita Sinha

Biomedical Engineering Graduate Student

University of Wisconsin-Madison

amsi...@wisc.edu


From: Glasser, Matthew 
Sent: Thursday, January 17, 2019 4:27:17 PM
To: Harms, Michael; Anita Sinha; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] CIFTI to Matlab

That could also be due to it not finding the file or not finding wb_command.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Thursday, January 17, 2019 at 4:05 PM
To: Anita Sinha mailto:amsi...@wisc.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] CIFTI to Matlab




Hi,

It sounds like you don’t have the gifti library properly installed.



Within matlab, what happens when you type

g = gifti



Do you get a gifti structure?



Cheers,

-MH





--

Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

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<mailto:mha...@wustl.edu>



From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Anita Sinha mailto:amsi...@wisc.edu>>
Date: Thursday, January 17, 2019 at 3:37 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] CIFTI to Matlab



To Whom It May Concern,



I am attempting to open up a dtseries.nii CIFTI file into Matlab to extract the 
time series matrix from rs-fMRI data. I have downloaded workbench and gifti-1.8 
and am following the directions outlined in 
https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63963178 in #2 
"How do you get CIFTI files into Matlab, but it isn't working.



When I run this command:

cii = ciftiopen('path/to/file','path/to/wb_command'); CIFTIdata = cii.cdata



with the appropriate file paths, I keep receiving this error:



Error using read_gifti_file_standalone (line 20)

[GIFTI] Loading of XML file 
C:\Users\...\AppData\Local\Temp\tp904b5934_f040_4259_8a21_0b10e15aecc8.gii 
failed.



Error in gifti (line 100)

this = read_gifti_file_standalone(varargin{1},giftistruct);



Error in ciftiopen (line 34)

cifti = gifti([tmpfile '.gii']);



I have added workbench and gifti to the path and saved everything in the same 
directory to mitigate file directory mismatch, but cannot past this error.



Could you provide some help on how to resolve this?



Thank you for your time.



Regards,



Anita

___
HCP-Users mailing list
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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.

___
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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. I

Re: [HCP-Users] CIFTI to Matlab

2019-01-17 Thread Glasser, Matthew 
That could also be due to it not finding the file or not finding wb_command.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Thursday, January 17, 2019 at 4:05 PM
To: Anita Sinha mailto:amsi...@wisc.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] CIFTI to Matlab


Hi,
It sounds like you don’t have the gifti library properly installed.

Within matlab, what happens when you type
g = gifti

Do you get a gifti structure?

Cheers,
-MH


--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
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<mailto:mha...@wustl.edu>

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Anita Sinha mailto:amsi...@wisc.edu>>
Date: Thursday, January 17, 2019 at 3:37 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] CIFTI to Matlab

To Whom It May Concern,

I am attempting to open up a dtseries.nii CIFTI file into Matlab to extract the 
time series matrix from rs-fMRI data. I have downloaded workbench and gifti-1.8 
and am following the directions outlined in 
https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63963178 in #2 
"How do you get CIFTI files into Matlab, but it isn't working.

When I run this command:
cii = ciftiopen('path/to/file','path/to/wb_command'); CIFTIdata = cii.cdata

with the appropriate file paths, I keep receiving this error:

Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file 
C:\Users\...\AppData\Local\Temp\tp904b5934_f040_4259_8a21_0b10e15aecc8.gii 
failed.

Error in gifti (line 100)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 34)
cifti = gifti([tmpfile '.gii']);

I have added workbench and gifti to the path and saved everything in the same 
directory to mitigate file directory mismatch, but cannot past this error.

Could you provide some help on how to resolve this?

Thank you for your time.

Regards,

Anita

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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.

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

Re: [HCP-Users] CIFTI to Matlab

2019-01-17 Thread Harms, Michael 

Hi,
It sounds like you don’t have the gifti library properly installed.

Within matlab, what happens when you type
g = gifti

Do you get a gifti structure?

Cheers,
-MH


--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
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 Anita Sinha 

Date: Thursday, January 17, 2019 at 3:37 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] CIFTI to Matlab

To Whom It May Concern,

I am attempting to open up a dtseries.nii CIFTI file into Matlab to extract the 
time series matrix from rs-fMRI data. I have downloaded workbench and gifti-1.8 
and am following the directions outlined in 
https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63963178 in #2 
"How do you get CIFTI files into Matlab, but it isn't working.

When I run this command:
cii = ciftiopen('path/to/file','path/to/wb_command'); CIFTIdata = cii.cdata

with the appropriate file paths, I keep receiving this error:

Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file 
C:\Users\...\AppData\Local\Temp\tp904b5934_f040_4259_8a21_0b10e15aecc8.gii 
failed.

Error in gifti (line 100)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 34)
cifti = gifti([tmpfile '.gii']);

I have added workbench and gifti to the path and saved everything in the same 
directory to mitigate file directory mismatch, but cannot past this error.

Could you provide some help on how to resolve this?

Thank you for your time.

Regards,

Anita

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[HCP-Users] CIFTI to Matlab

2019-01-17 Thread Anita Sinha 
To Whom It May Concern,

I am attempting to open up a dtseries.nii CIFTI file into Matlab to extract the 
time series matrix from rs-fMRI data. I have downloaded workbench and gifti-1.8 
and am following the directions outlined in 
https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63963178 in #2 
"How do you get CIFTI files into Matlab, but it isn't working.

When I run this command:
cii = ciftiopen('path/to/file','path/to/wb_command'); CIFTIdata = cii.cdata

with the appropriate file paths, I keep receiving this error:

Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file 
C:\Users\...\AppData\Local\Temp\tp904b5934_f040_4259_8a21_0b10e15aecc8.gii 
failed.

Error in gifti (line 100)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Error in ciftiopen (line 34)
cifti = gifti([tmpfile '.gii']);

I have added workbench and gifti to the path and saved everything in the same 
directory to mitigate file directory mismatch, but cannot past this error.

Could you provide some help on how to resolve this?

Thank you for your time.

Regards,

Anita

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Re: [HCP-Users] CIFTI and MATLAB

2017-07-31 Thread Harms, Michael 

Yes, unless you want to deal with the NaNs.

--
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 7/31/17, 9:58 AM, "hcp-users-boun...@humanconnectome.org on behalf of Claude 
Bajada"  wrote:

Dear all,

Is this post still valid re: cifti in matlab?

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?

Is cifti-matlab still only recommended for MEG data?

https://github.com/Washington-University/cifti-matlab

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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The materials in this message are private and may contain Protected Healthcare 
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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 
strictly prohibited. If you have received this email in error, please 
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[HCP-Users] CIFTI and MATLAB

2017-07-31 Thread Claude Bajada 
Dear all,

Is this post still valid re: cifti in matlab?

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?

Is cifti-matlab still only recommended for MEG data?

https://github.com/Washington-University/cifti-matlab

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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