Re: [HCP-Users] Hcp Data with non-overlapping parcellations

[Matthew George Liptrot]

Hi again,

The -file–information on the files generated with method (A) and (B) below give 
the same key value for “???”:

# (A) (Changed output of first line to include *.label.*, otherwise the 
-file–information command does not recognise the file format correctly.)
> wb_command -cifti-separate 100307.aparc.32k_fs_LR.dlabel.nii COLUMN -label 
> CORTEX_LEFT aparc32k_fs_LR_dlabel_Separated_CortexLeft.label.gii
> wb_command -gifti-convert ASCII 
> aparc32k_fs_LR_dlabel_Separated_CortexLeft.label.gii 
> aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft.txt
> cp aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft.txt 
> aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft_LabelsOnly.txt
# Strip away all header/footer XML codes from 
aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft_LabelsOnly.txt using 
emacs
> wc -l aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft_LabelsOnly.txt
32492

# (B)
> wb_command -gifti-convert ASCII 100307.L.aparc.32k_fs_LR.label.gii 
> L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft.txt
> cp L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft.txt 
> L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft_LabelsOnly.txt
# Strip away all header/footer XML codes from 
L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft_LabelsOnly.txt using emacs
> wc -l L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft_LabelsOnly.txt
32492

# (A)
> wb_command -file-information 
> aparc32k_fs_LR_dlabel_Separated_CortexLeft.label.gii
Name:   aparc32k_fs_LR_dlabel_Separated_CortexLeft.label.gii
Type:   Label
Structure:  CortexLeft
Data Size:  129.97 Kilobytes
Maps to Surface:true
Maps to Volume: false
Maps with LabelTable:   true
Maps with Palette:  false
Number of Maps: 1
Number of Vertices: 32492

Map   Map Name
  1   100307_aparc

Label table for ALL maps
   KEY   NAME   RED   GREENBLUE   ALPHA
 0   ???  0.000   0.000   0.000   0.000
 1   L_bankssts   0.098   0.392   0.157   1.000
 2   L_caudalanteriorcingulate0.490   0.392   0.627   1.000
 3   L_caudalmiddlefrontal0.392   0.098   0.000   1.000
 4   L_corpuscallosum 0.471   0.275   0.196   1.000
 5   L_cuneus 0.863   0.078   0.392   1.000
...


# (B)
> wb_command -file-information 100307.L.aparc.32k_fs_LR.label.gii
Name:   100307.L.aparc.32k_fs_LR.label.gii
Type:   Label
Structure:  CortexLeft
Data Size:  129.97 Kilobytes
Maps to Surface:true
Maps to Volume: false
Maps with LabelTable:   true
Maps with Palette:  false
Number of Maps: 1
Number of Vertices: 32492

Map   Map Name
  1   100307_L_aparc

Label table for ALL maps
   KEY   NAME   RED   GREENBLUE   ALPHA
 0   ???  0.000   0.000   0.000   0.000
 1   L_bankssts   0.098   0.392   0.157   1.000
 2   L_caudalanteriorcingulate0.490   0.392   0.627   1.000
 3   L_caudalmiddlefrontal0.392   0.098   0.000   1.000
 4   L_corpuscallosum 0.471   0.275   0.196   1.000
 5   L_cuneus 0.863   0.078   0.392   1.000
...

However, what I’m more concerned about is not so much the labels for Key=0, but 
that some of the other vertices have different labels – see lines 22-27 below:

 A   B
10  10
29  29
24  24
28  28
11  11
31  31
27  27
 0  -1
13  13
15  15
35  35
35  35
10  10
10  10
10  10
10  10
10  10
10  10
10  10
10  10
10  10
 0  10
 0  10
 0  10
 0  10
 0  10
 0  10
 0  -1
 0  -1
 0  -1
 0  -1
 0  -1
 0  -1
 0  -1
 0  -1
…

This is just the first few lines, and there are many more differences 
throughout the files. Is this simply a vertex-ordering issue, or is there a 
conversion error?
(Key 10 is “L_isthmuscingulate” in both).

Cheers,

M@


On 18/11/15 22:14 , "Timothy Coalson" > 
wrote:

Sorry, the -*-label-export-table commands don't put the unlabeled key in the 
text file.  Use -file-information on them instead to check what key value the 
"???" label is (it means the unlabled value).

Tim


On Wed, Nov 18, 2015 at 12:54 PM, Timothy Coalson 
> wrote:
Inline replies.

On Wed, Nov 18, 2015 at 8:47 AM, Matthew George Liptrot 
> wrote:
Hi,

Thanks both of you.

On 17/11/15 21:32 , "Timothy Coalson" > 
wrote:
So, cifti is not a 1:1 mapping to surface vertices.  If what you plan to use 
can read gifti, the less error-prone route is probably to use -cifti-separate 
to get a nifti volume and gifti files that do have a 1:1 mapping to vertices.

@Tim: By “not a 1:1 mapping to surface vertices”, do you mean:

  1.  The CIFTI data-value:vertex 

[HCP-Users] qdec error

[LEVI SOLOMYAK]

Dear experts,

I've been attempting to generate a stats data table in qdec, but each time
I get a "Index Error: list index is out of range" error. This is occurring
when it is trying to parse the .stats file.

  I've made sure that the files all line up exactly and that SUBJECTS_DIR
 is properly sourced so I'm not sure how to fix this problem. Any help
would be greatly appreciated!

Thank you,
LS

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[HCP-Users] Has anybody done tractography on HCP diffusion data?

[Joelle Zimmermann]

Hi - I'm a researcher at the McIntosh lab at the Rotman Research Institute.
A few of us here are planning on working with HCP data. I was wondering
whether anybody is working on (or aware of a group working on) fully
preprocessing and tractography on HCP diffusion data, parcellated into some
kind of structural connectivity matrix? Of course we would provide
authorship to whoever is providing the tractographied data.

I'd expect there must be quite a few folks who would be interested in this.

I'm also interested in preprocessed rfMRI functional connectivity matrices
in a matching parcellation.  However, more important is that diffusion data
already undergone tractography and in a certain parcellation in the form of
a SC matrix.

Any direction would really help.
Thanks a lot,
Joelle

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[HCP-Users] Myelin mapping with FLAIR

[Barbara Kreilkamp]

Dear all,

We've now been able to acquire a sagittal B1-Map from the GE templates
protocols (GE 3Tesla 750 Discovery).
I hope this is the right sequence that would tell us where the
high-intensity artifact in the GE myelin maps come from?

The raw data is here:
https://app.box.com/s/3t3o77b1ksrhgfs3hgwi1ryodj0hubp0

These are the related posts (below) and here:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01611.html

The GE physicist has told me that the XETA and CUBE sequence are quite
different now however as well.
I wonder if you could please guide me as to whether the B1-Map looks usable
(unfortunately I have seen some motion/ringing artifact in this
participant, which we normally don't have an issue with) and in which way I
could analyze the issue.

Thank you so much,
Best wishes,
Barbara



On 22/06/2015 21:13, Glasser, Matthew wrote:

I’ve not done that, but perhaps someone else has.

Peace,

Matt.

From: Michael Dwyer 
Date: Monday, June 22, 2015 at 3:12 PM
To: Matt Glasser < glass...@wusm.wustl.edu>
Cc: Gaurav Patel < gauravpa...@gmail.com>, HCP Users

Subject: Re: [HCP-Users] Myelin mapping with FLAIR

Thanks. By the way, have you been able to see any cortical demyelination in
neurological diseases like multiple sclerosis with this myelin mapping
technique, or only used it on healthy controls and neuropsychiatric disease
so far?

On Mon, Jun 22, 2015 at 11:26 AM, Glasser, Matthew 
wrote:

> For the moment one just treats the FLAIR as a T2w scan for the purposes of
> the pipelines.
>
> Peace,
>
> Matt.
>
> From: < 
> hcp-users-boun...@humanconnectome.org> on behalf of Michael Dwyer <
> mgdw...@bnac.net>
> Date: Sunday, June 21, 2015 at 8:24 PM
> To: Gaurav Patel 
>
> Cc: HCP Users 
> Subject: Re: [HCP-Users] Myelin mapping with FLAIR
>
> Thanks, Gaurav, I would be very grateful for any updates on your progress.
>
> On Sun, Jun 21, 2015 at 3:41 PM, Gaurav Patel 
> wrote:
>
>> FYI we're still working on this problem; I'm hoping for a meaningful
>> update soon
>>
>> _
>>  gaurav patel
>>   gauravpa...@gmail.com
>>   www.neurofreak.net
>>
>> On Jun 21, 2015, at 3:04 PM, Harms, Michael < 
>> mha...@wustl.edu> wrote:
>>
>>
>> I don't know.  If the myelin mapping isn't working quite as expected with
>> T1/T2w scans on GE, then its really hard to know what to expect if you use
>> FLAIR instead of T2w.
>>
>> 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  63110 Email: mha...@wustl.edu
>>
>> From: Michael Dwyer < mgdw...@bnac.net>
>> Date: Sunday, June 21, 2015 11:17 AM
>> To: "Harms, Michael" < mha...@wustl.edu>
>> Cc: HCP Users < 
>> HCP-Users@humanconnectome.org>
>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR
>>
>> Thanks, I saw those. We'll certainly have to deal with those issues if we
>> want to do this.
>>
>> Other than that, though, would you recommend doing anything differently
>> with FLAIR than with T2?
>>
>> Best,
>> Mike
>>
>> On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael < 
>> mha...@wustl.edu> wrote:
>>
>>>
>>> Take a look also at the recent posts.  There are unfortunately some
>>> unresolved issues about myelin maps acquired on the GE platform not looking
>>> the same as they do when derived from Siemens data.
>>>
>>> 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  63110 Email: mha...@wustl.edu
>>>
>>> From: Michael Dwyer < mgdw...@bnac.net>
>>> Date: Thursday, June 18, 2015 4:25 PM
>>> To: Gordon Xu < junqian...@mssm.edu>
>>> Cc: HCP Users < 
>>> HCP-Users@humanconnectome.org>
>>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR
>>>
>>> Thanks for the quick reply! Unfortunately, we have a GE scanner, not a
>>> Siemens. Any advice for that? Also any different recommendations for the
>>> post-processing when using FLAIR?
>>>
>>> Best,
>>> Mike
>>>
>>> On Thu, Jun 18, 2015 at 5:04 PM, Xu, Junqian < 
>>> junqian...@mssm.edu> wrote:
>>>
 You can take a look at the UK Biobank project 

Re: [HCP-Users] Hcp Data with non-overlapping parcellations

[Donna Dierker]

Hi Matthew,

I was able to replicate what you are seeing.  The label.gii is encoding the 
medial wall as -1, while the dlabel.nii is encoding it as 0.  The more 
substantive differences are due to the fact that the dlabel.nii has a more 
generous medial wall than the label.gii files do:

http://brainmap.wustl.edu/pub/donna/WUSTL/HCP/Misc/
login pub
password download

I would not have expected this.  I vote for the dlabel.nii route.

Donna


On Nov 19, 2015, at 3:13 AM, Matthew George Liptrot  
wrote:

> Hi again,
> 
> The -file–information on the files generated with method (A) and (B) below 
> give the same key value for “???”:
> 
> # (A) (Changed output of first line to include *.label.*, otherwise the 
> -file–information command does not recognise the file format correctly.)
> > wb_command -cifti-separate 100307.aparc.32k_fs_LR.dlabel.nii COLUMN -label 
> > CORTEX_LEFT aparc32k_fs_LR_dlabel_Separated_CortexLeft.label.gii
> > wb_command -gifti-convert ASCII 
> > aparc32k_fs_LR_dlabel_Separated_CortexLeft.label.gii 
> > aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft.txt
> > cp aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft.txt 
> > aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft_LabelsOnly.txt
> # Strip away all header/footer XML codes from 
> aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft_LabelsOnly.txt using 
> emacs
> > wc -l aparc32k_fs_LR_dlabel_Separated_GiftiConvert_CortexLeft_LabelsOnly.txt
> 32492
> 
> # (B)
> > wb_command -gifti-convert ASCII 100307.L.aparc.32k_fs_LR.label.gii 
> > L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft.txt
> > cp L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft.txt 
> > L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft_LabelsOnly.txt
> # Strip away all header/footer XML codes from 
> L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft_LabelsOnly.txt using emacs
> > wc -l L_aparc32k_fs_LR_label_GiftiConvert_CortexLeft_LabelsOnly.txt
> 32492
> 
> # (A)
> > wb_command -file-information 
> > aparc32k_fs_LR_dlabel_Separated_CortexLeft.label.gii
> Name:   aparc32k_fs_LR_dlabel_Separated_CortexLeft.label.gii
> Type:   Label
> Structure:  CortexLeft 
> Data Size:  129.97 Kilobytes
> Maps to Surface:true
> Maps to Volume: false
> Maps with LabelTable:   true
> Maps with Palette:  false
> Number of Maps: 1
> Number of Vertices: 32492
> 
> Map   Map Name   
>   1   100307_aparc   
> 
> Label table for ALL maps
>KEY   NAME   RED   GREENBLUE   ALPHA   
>  0   ???  0.000   0.000   0.000   0.000   
>  1   L_bankssts   0.098   0.392   0.157   1.000   
>  2   L_caudalanteriorcingulate0.490   0.392   0.627   1.000   
>  3   L_caudalmiddlefrontal0.392   0.098   0.000   1.000   
>  4   L_corpuscallosum 0.471   0.275   0.196   1.000   
>  5   L_cuneus 0.863   0.078   0.392   1.000   
> ...
> 
> 
> # (B)
> > wb_command -file-information 100307.L.aparc.32k_fs_LR.label.gii
> Name:   100307.L.aparc.32k_fs_LR.label.gii
> Type:   Label
> Structure:  CortexLeft 
> Data Size:  129.97 Kilobytes
> Maps to Surface:true
> Maps to Volume: false
> Maps with LabelTable:   true
> Maps with Palette:  false
> Number of Maps: 1
> Number of Vertices: 32492
> 
> Map   Map Name 
>   1   100307_L_aparc   
> 
> Label table for ALL maps
>KEY   NAME   RED   GREENBLUE   ALPHA   
>  0   ???  0.000   0.000   0.000   0.000   
>  1   L_bankssts   0.098   0.392   0.157   1.000   
>  2   L_caudalanteriorcingulate0.490   0.392   0.627   1.000   
>  3   L_caudalmiddlefrontal0.392   0.098   0.000   1.000   
>  4   L_corpuscallosum 0.471   0.275   0.196   1.000   
>  5   L_cuneus 0.863   0.078   0.392   1.000   
> ...
> 
> However, what I’m more concerned about is not so much the labels for Key=0, 
> but that some of the other vertices have different labels – see lines 22-27 
> below:
> 
>  A   B 
> 10  10  
> 29  29  
> 24  24   
> 28  28   
> 11  11   
> 31  31  
> 27  27   
>  0  -1  
> 13  13   
> 15  15   
> 35  35   
> 35  35   
> 10  10   
> 10  10   
> 10  10   
> 10  10   
> 10  10   
> 10  10   
> 10  10   
> 10  10   
> 10  10   
>  0  10   
>  0  10   
>  0  10   
>  0  10   
>  0  10   
>  0  10   
>  0  -1   
>  0  -1   
>  0  -1   
>  0  -1  
>  0  -1   
>  0  -1   
>  0  -1   
>  0  -1   
> …
> 
> This is just the first few lines, and there are many more differences 
> throughout the files. Is this simply a vertex-ordering issue, or is there a 
> conversion error?
> (Key 10 is “L_isthmuscingulate” in both).
> 
> Cheers,
> 
> M@
> 
> 
> On 

Re: [HCP-Users] Myelin mapping with FLAIR

[Gaurav Patel]

Hi!  I'm curious to see how the B1 map will help as well.  Its been a while 
since our team has thought about this, but I'll show this to our MR physicist 
and let you know.  We are continuing to pursue obtaining a GE MPRAGE to see if 
that would help, but its been slow going.  When we do and are able to run some 
tests, we'll post the results

__
  gaurav patel
  gauravpa...@gmail.com
  www.neurofreak.net




On Nov 19, 2015, at 11:27 AM, Barbara Kreilkamp wrote:

> Dear all,
> 
> We've now been able to acquire a sagittal B1-Map from the GE templates 
> protocols (GE 3Tesla 750 Discovery).
> I hope this is the right sequence that would tell us where the high-intensity 
> artifact in the GE myelin maps come from?
> 
> The raw data is here:
> https://app.box.com/s/3t3o77b1ksrhgfs3hgwi1ryodj0hubp0
> 
> These are the related posts (below) and here: 
> https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01611.html
> 
> The GE physicist has told me that the XETA and CUBE sequence are quite 
> different now however as well.
> I wonder if you could please guide me as to whether the B1-Map looks usable 
> (unfortunately I have seen some motion/ringing artifact in this participant, 
> which we normally don't have an issue with) and in which way I could analyze 
> the issue.
> 
> Thank you so much,
> Best wishes,
> Barbara
> 
> 
> 
> On 22/06/2015 21:13, Glasser, Matthew wrote:
>> I’ve not done that, but perhaps someone else has.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Michael Dwyer 
>> Date: Monday, June 22, 2015 at 3:12 PM
>> To: Matt Glasser 
>> Cc: Gaurav Patel , HCP Users 
>> 
>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR
>> 
>> Thanks. By the way, have you been able to see any cortical demyelination in 
>> neurological diseases like multiple sclerosis with this myelin mapping 
>> technique, or only used it on healthy controls and neuropsychiatric disease 
>> so far?
>> 
>> On Mon, Jun 22, 2015 at 11:26 AM, Glasser, Matthew  
>> wrote:
>> For the moment one just treats the FLAIR as a T2w scan for the purposes of 
>> the pipelines.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  on behalf of Michael Dwyer 
>> 
>> Date: Sunday, June 21, 2015 at 8:24 PM
>> To: Gaurav Patel 
>> 
>> Cc: HCP Users 
>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR
>> 
>> Thanks, Gaurav, I would be very grateful for any updates on your progress.
>> 
>> On Sun, Jun 21, 2015 at 3:41 PM, Gaurav Patel  wrote:
>> FYI we're still working on this problem; I'm hoping for a meaningful update 
>> soon
>> 
>> _
>>  gaurav patel
>>  gauravpa...@gmail.com
>>  www.neurofreak.net
>> 
>> On Jun 21, 2015, at 3:04 PM, Harms, Michael  wrote:
>> 
>>> 
>>> I don't know.  If the myelin mapping isn't working quite as expected with 
>>> T1/T2w scans on GE, then its really hard to know what to expect if you use 
>>> FLAIR instead of T2w.
>>> 
>>> 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  63110 Email: mha...@wustl.edu
>>> 
>>> From: Michael Dwyer 
>>> Date: Sunday, June 21, 2015 11:17 AM
>>> To: "Harms, Michael" 
>>> Cc: HCP Users 
>>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR
>>> 
>>> Thanks, I saw those. We'll certainly have to deal with those issues if we 
>>> want to do this.
>>> 
>>> Other than that, though, would you recommend doing anything differently 
>>> with FLAIR than with T2?
>>> 
>>> Best,
>>> Mike
>>> 
>>> On Fri, Jun 19, 2015 at 10:19 PM, Harms, Michael  wrote:
>>> 
>>> Take a look also at the recent posts.  There are unfortunately some 
>>> unresolved issues about myelin maps acquired on the GE platform not looking 
>>> the same as they do when derived from Siemens data.
>>> 
>>> 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  63110 Email: mha...@wustl.edu
>>> 
>>> From: Michael Dwyer 
>>> Date: Thursday, June 18, 2015 4:25 PM
>>> To: Gordon Xu 
>>> Cc: HCP Users 
>>> Subject: Re: [HCP-Users] Myelin mapping with FLAIR
>>> 
>>> Thanks for the quick reply! Unfortunately, we have a GE scanner, not a 
>>>