[HCP-Users] rfMRI BOLD signal

2017-05-27 Thread wtj 
Hi,

After I load the .dtseries.nii file to connectome workbench, there is a
.dynconn.nii connectivity file, which is not in the directory of the
.dtseries.nii file, is the connectivity file generated automatically after I
load the CIFTI dense timeseries file? Does the connectivity file shows rfMRI
function connectivity?

Thanks.


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

Re: [HCP-Users] load cifti file to MATLAB

2017-05-27 Thread Glasser, Matthew 
Use these tools (option 2B):  
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ

Peace,

Matt.

From: 
>
 on behalf of wtj <1257735...@qq.com>
Date: Saturday, May 27, 2017 at 1:28 AM
To: "HCP-Users@humanconnectome.org" 
>
Subject: [HCP-Users] load cifti file to MATLAB

Hi,
I want to load cifti dense timeseries file .dtseries.nii to matlab. First, I 
convert it to GIFTI file, my script is, ./wb_command -cifti-convert 
-to-gifti-ext 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii
 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstgii.gii,
 but I got a file named myfirstgii.gii.data. where’s the problem?
Thanks.

___
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

Re: [HCP-Users] 答复: BOLD signal

2017-05-27 Thread Glasser, Matthew 
That is a CIFTI file.  Have a look in Connectome Workbench (after loading 
appropriate 32k surfaces).

Peace,

Matt.

From: wtj <1257735...@qq.com>
Date: Saturday, May 27, 2017 at 12:05 AM
To: Matt Glasser >
Subject: 答复: [HCP-Users] BOLD signal

Hi,
I open the file with SPM, but I see nothing. How can I map rfMRI BOLD signal 
grayordinates to each region of the functional parcellation?
Thanks.

发件人: Glasser, Matthew [mailto:glass...@wustl.edu]
发送时间: 2017年5月26日 0:23
收件人: wtj <1257735...@qq.com>; 
hcp-users@humanconnectome.org
主题: Re: [HCP-Users] BOLD signal

The database is back up and you can get the parcellation from here: 
https://balsa.wustl.edu/file/show/3VLx

Peace,

Matt.

From: Matt Glasser >
Date: Wednesday, May 24, 2017 at 10:49 AM
To: wtj <1257735...@qq.com>, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] BOLD signal

The HCP has released a cortical areas atlas, but it is unfortunately 
unaccessible due to some IT problems.  Hopefully it will be back up soon.

Peace,

Matt.

From: 
>
 on behalf of wtj <1257735...@qq.com>
Date: Wednesday, May 24, 2017 at 9:28 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] BOLD signal

Hi,
Is there a functional brain region atlas? How can I visualize the BOLD signal 
of every brain region? Take a step back, is there any way to visualize the 
signal?
Thanks.

___
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
Spam detection software, running on the system "mailman02.nrg.mir", has
identified this incoming email as possible spam.  The original message
has been attached to this so you can view it (if it isn't spam) or label
similar future email.  If you have any questions, see
@@CONTACT_ADDRESS@@ for details.

Content preview:  That is a CIFTI file. Have a look in Connectome Workbench
  (after loading appropriate 32k surfaces). Peace, Matt. [...] 

Content analysis details:   (5.7 points, 5.0 required)

 pts rule name  description
 -- --
 3.2 CHARSET_FARAWAY_HEADER A foreign language charset used in headers
 0.0 HTML_MESSAGE   BODY: HTML included in message
 2.5 MIME_CHARSET_FARAWAY   MIME character set indicates foreign language


Spam detection software, running on the system "mailman02.nrg.mir", has
identified this incoming email as possible spam.  The original message
has been attached to this so you can view it (if it isn't spam) or label
similar future email.  If you have any questions, see
@@CONTACT_ADDRESS@@ for details.

Content preview:  That is a CIFTI file. Have a look in Connectome Workbench
  (after loading appropriate 32k surfaces). Peace, Matt. [...] 

Content analysis details:   (5.7 points, 5.0 required)

 pts rule name  description
 -- --
 3.2 CHARSET_FARAWAY_HEADER A foreign language charset used in headers
 0.0 HTML_MESSAGE   BODY: HTML included in message
 2.5 MIME_CHARSET_FARAWAY   MIME character set indicates foreign language

Re: [HCP-Users] 答复: 答复: GIFTI surface data

2017-05-27 Thread Glasser, Matthew 
Perhaps you should specify a specific output directory with -o.

Peace,

Matt.

From: wtj <1257735...@qq.com>
Date: Friday, May 26, 2017 at 11:51 PM
To: Matt Glasser >
Subject: 答复: 答复: [HCP-Users] GIFTI surface data

Hi,
I use melodic commandline of latest version FSL and my command line scrpt is: 
melodic –i 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii

An exception has been thrown
Cannot create directory 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.ica
What’s the problem?
Thanks.
发件人: Glasser, Matthew [mailto:glass...@wustl.edu]
发送时间: 2017年5月25日 8:27
收件人: wtj <1257735...@qq.com>; 
hcp-users@humanconnectome.org
主题: Re: 答复: [HCP-Users] GIFTI surface data

You might need to use the command line version of the latest FSL. The latest 
version of melodic does natively work with CIFTI.

Peace,

Matt.

From: wtj <1257735...@qq.com>
Date: Wednesday, May 24, 2017 at 7:21 PM
To: Matt Glasser >
Subject: 答复: [HCP-Users] GIFTI surface data

Hi,
When I do ICA using MELODIC ICA button in FSL,I selected a .dtseries.nii file, 
then something went wrong.

child process exited abnormally
child process exited abnormally
while executing
"exec sh -c "${FSLDIR}/bin/fslnvols $thefile 2> /dev/null" "
(procedure "feat5:updateimageinfo" line 9)
invoked from within
"feat5:updateimageinfo $w $i 1"
(procedure "feat5:multiple_check" line 63)
invoked from within
"feat5:multiple_check .r 0 1 1 d"
invoked from within
".dialog1.cancel invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .dialog1.cancel"
(command bound to event)

Thanks.

发件人: Glasser, Matthew [mailto:glass...@wustl.edu]
发送时间: 2017年5月24日 9:54
收件人: wtj <1257735...@qq.com>; 
hcp-users@humanconnectome.org
主题: Re: [HCP-Users] GIFTI surface data

No you would use the CIFTI file.  It would be called 
${StudyFolder}/${Subject]/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas.dtseries.nii.
  You would ideally run it through ICA+FIX first before analyzing it.

Peace,
Matt.

From: 
>
 on behalf of wtj <1257735...@qq.com>
Date: Tuesday, May 23, 2017 at 8:49 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] GIFTI surface data

Hi,
I use the lifespan rfMRI data. After preprocessing, there is a file in 
/subject/MNINonLinear/Results/rfMRI_REST1_LR named 
rfMRI_REST1_LR.L.native.func.gii with size, for example, 130576*420. Is this 
file the cortical BOLD signal time series data? Can I use it to do rfMRI 
analysis?
Thanks.

___
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