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

[Glasser, Matthew]

In that case I recommend learning a bit more about ICA and perhaps the command 
line, as you do need to understand what it means to set the ICA dimensionality 
(how many components are you asking for) to use ICA and many of the most 
powerful neuroimaging tools are command line-based.

Peace,

Matt.

From: stargazy pie <1257735...@qq.com>
Date: Monday, May 29, 2017 at 8:56 PM
To: Matt Glasser >
Subject: 回复： 回复：答复: 答复: 答复: [HCP-Users] GIFTI surface data

Hi,
I don't know how to set ICA dimensionality with -d flag, so I just added 
--CIFTI after input file name.
 ./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
 --CIFTI -o 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstica.ica
Could not open file 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstica.ica/eigenvalues_percent
 for writing
terminate called after throwing an instance of 'cifti::CiftiException'
  what():  error opening file 
'/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstica.ica/melodic_IC.nii'
Aborted (core dumped)
By the way, the data's dimenstion is 91282(grayordinate)*420(time point) after 
I converted it to GIFTI, how long does it take to run ICA? how do I set the -d 
flag? In my opinion, after ICA, the result will be something like A(smaller 
than 91282)*420, right?
Thanks.


-- 原始邮件 --
发件人: "Glasser, Matthew";>;
发送时间: 2017年5月29日(星期一) 晚上10:37
收件人: "stargazy pie"<1257735...@qq.com>; 
"hcp-users@humanconnectome.org">;
主题: Re: 回复：答复: 答复: 答复: [HCP-Users] GIFTI surface data

You will need to set the --CIFTI flag and specify an ICA dimensionality with 
the -d flag.

Peace,

Matt.

From: stargazy pie <1257735...@qq.com>
Date: Monday, May 29, 2017 at 9:04 AM
To: Matt Glasser >
Subject: 回复：答复: 答复: 答复: [HCP-Users] GIFTI surface data

Hi,
I use the latest version, v5.0.10
Thanks.

---原始邮件---
发件人: "Glasser, Matthew">
发送时间: 2017年5月29日 10:11:33
收件人: 
"HCP-Users@humanconnectome.org">;"wtj"<1257735...@qq.com>;
主题: Re: 答复: 答复: 答复: [HCP-Users] GIFTI surface data

What version of FSL are you using?

Peace,

Matt.

From: wtj <1257735...@qq.com>
Date: Sunday, May 28, 2017 at 1:34 AM
To: Matt Glasser >
Subject: 答复: 答复: 答复: [HCP-Users] GIFTI surface data

Hi,
I add the –o option, but there are more errors now.
./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
 -o 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/myfirstica.ica
** ERROR: nifti_convert_nhdr2nim: bad datatype
** ERROR (nifti_image_read): cannot create nifti image from header 
'/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.nii'
** ERROR: 
nifti_image_open(/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries):
 bad header info
ERROR: failed to open file 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries
Image Exception : #22 :: ERROR: Could not open image 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries



An exception has been thrown
ERROR: Could not open image 
/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseriesTrace:
 read_volumeROI.

Thanks.

发件人: Glasser, Matthew [mailto:glass...@wustl.edu]
发送时间: 2017年5月27日 22:56
收件人: wtj <1257735...@qq.com>; 
hcp-users@humanconnectome.org
主题: Re: 答复: 答复: [HCP-Users] GIFTI surface data

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 

Re: [HCP-Users] values in myelin maps

[Glasser, Matthew]

They are the ratio of the T1w/T2w images and are a relative measure of myelin 
content.  See this publication for more details:

http://www.jneurosci.org/content/31/32/11597.short

Peace,

Matt.

From: 
>
 on behalf of Lisa Kramarenko 
>
Date: Monday, May 29, 2017 at 5:29 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] values in myelin maps

Hello,

I am not sure what exactly are the values shown for the myelin maps. E.g. on 
the screenshot the values are 0.998 to 1.771. I understand that higher values 
mean higher myelination and vice versa, but what do they mean exactly?
Thanks!

Lisa

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