subject:"Re\: \[HCP\-Users\] Where are per\-subject netmats\?"

Re: [HCP-Users] Where are per-subject netmats?

2017-06-01 Thread Stephen Smith

Hi - yes that's all correct.  IIRC for that PTN release (as opposed to the 
previous one) we thought it wasn't worth having subject-specific netmat pconn 
files, but just put all the information in the text files.

Cheers.


> On 1 Jun 2017, at 16:36, Habib Ganjgahi <h.ganjg...@gmail.com> wrote:
> 
> Hi Steve,
> 
> I've extracted the "netmats_3T_HCP820_MSMAll_ICAd15_ts2.tar.gz" file from the 
> HVP_PTN820 folder but it doesn't contain subject specific pconn files. This 
> is what i see inside it:
> 
> Mnet1.pconn.nii 
> 
> Mnet2.pconn.nii
> 
> hierarchy.png
> 
> netmats1.txt
> 
> netmats2.txt
> 
> each pconn file dimension is 15x15 and each text file is a 820x225 matrix. I 
> think each row of the matrix corresponds to different subject netmat matrix, 
> Am i right? if so, is the order of rows as same as the "subjectIDs.txt" file? 
> 
> 
> 
> Bests,
> 
> Habib
> 
> 
> On Thu, Jun 1, 2017 at 3:25 PM, Stephen Smith <st...@fmrib.ox.ac.uk 
> <mailto:st...@fmrib.ox.ac.uk>> wrote:
> Probably clearest to use both terms for clarity, e.g.   "ICA maps, i.e., 
> ICA-based parcellations"
> 
> 
> 
>> On 1 Jun 2017, at 15:21, Harms, Michael <mha...@wustl.edu 
>> <mailto:mha...@wustl.edu>> wrote:
>> 
>> 
>> Would it perhaps be less confusing if the links said “CIFTI Subject-specific 
>> ICA maps for XXX dimensionality”, rather than “Parcellations” ?
>> 
>> -- 
>> 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 <mailto:mha...@wustl.edu>
>> 
>> From: <hcp-users-boun...@humanconnectome.org 
>> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Stephen Smith 
>> <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>
>> Date: Thursday, June 1, 2017 at 9:07 AM
>> To: Thomas Nichols <t.e.nich...@warwick.ac.uk 
>> <mailto:t.e.nich...@warwick.ac.uk>>
>> Cc: HCP Users <hcp-users@humanconnectome.org 
>> <mailto:hcp-users@humanconnectome.org>>, Habib Ganjgahi 
>> <h.ganjg...@gmail.com <mailto:h.ganjg...@gmail.com>>
>> Subject: Re: [HCP-Users] Where are per-subject netmats?
>> 
>> Hi - subject netmats are in the main PTN download.
>> Cheers.
>> 
>> 
>>> On 1 Jun 2017, at 15:05, Thomas Nichols <t.e.nich...@warwick.ac.uk 
>>> <mailto:t.e.nich...@warwick.ac.uk>> wrote:
>>> 
>>> Hi Jenn,
>>> 
>>> Sorry for the slow reply on this.  We tried downloading the links you 
>>> pointed us to <https://db.humanconnectome.org/data/projects/HCP_1200>:
>>>> 
>>>> The following links contain subject-specific CIFTI maps: subject-specific 
>>>> versions of the group-ICA parcellations, with various ICA dimensionalities 
>>>> applied. These are z-statistic maps generated using dual-regression.
>>>> 
>>>>  CIFTI Subject-specific Parcellations for 10-, 25-, 50-, 
>>>> 100-dimensionalities (57GB) 
>>>> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=GroupAvg=HCP_S900_PTNmaps_d15_25_50_100.zip>
>>>>  CIFTI Subject-specific Parcellations for 200-dimensionality (55GB) 
>>>> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=GroupAvg=HCP_S900_PTNmaps_d200.zip>
>>>>  CIFTI Subject-specific Parcellations for 300-dimensionality (85GB 
>>>> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=GroupAvg=HCP_S900_PTNmaps_d300.zip>but
>>>>  they only contain the *dtseries.nii, while in previous releases there 
>>>> were *pconn.nii files that had the "NetMat" matrices.
>>> 
>>> To be clear, the previous *pconn.nii files had #dim rows, #dim cols, while 
>>> these *dtseries have #Elm rows and #dim cols.
>>> 
>>> Is there some place that NetMats are currently released?  I'm not finding 
>>> them.  I know they're not impossible to recreate but I'd like to minimize 
>>> effort and chance of error by using the standard released product.
>>> 
>>> -Tom
>>> 
>>> 
>>> PS: Note that the webpage is incorrectly indicates that the parcellation 
>>> size is 10, 25, 50 and 100, when instead it is 15,

Re: [HCP-Users] Where are per-subject netmats?

2017-06-01 Thread Habib Ganjgahi

Hi Steve,

I've extracted the "netmats_3T_HCP820_MSMAll_ICAd15_ts2.tar.gz" file from
the HVP_PTN820 folder but it doesn't contain subject specific pconn files.
This is what i see inside it:

Mnet1.pconn.nii

Mnet2.pconn.nii

hierarchy.png

netmats1.txt

netmats2.txt

each pconn file dimension is 15x15 and each text file is a 820x225 matrix.
I think each row of the matrix corresponds to different subject netmat
matrix, Am i right? if so, is the order of rows as same as the "subjectIDs.txt"
file?


Bests,

Habib

On Thu, Jun 1, 2017 at 3:25 PM, Stephen Smith <st...@fmrib.ox.ac.uk> wrote:

> Probably clearest to use both terms for clarity, e.g.   "ICA maps, i.e.,
> ICA-based parcellations"
>
>
>
> On 1 Jun 2017, at 15:21, Harms, Michael <mha...@wustl.edu> wrote:
>
>
> Would it perhaps be less confusing if the links said “CIFTI
> Subject-specific ICA maps for XXX dimensionality”, rather than
> “Parcellations” ?
>
> --
> 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: <hcp-users-boun...@humanconnectome.org> on behalf of Stephen Smith <
> st...@fmrib.ox.ac.uk>
> Date: Thursday, June 1, 2017 at 9:07 AM
> To: Thomas Nichols <t.e.nich...@warwick.ac.uk>
> Cc: HCP Users <hcp-users@humanconnectome.org>, Habib Ganjgahi <
> h.ganjg...@gmail.com>
> Subject: Re: [HCP-Users] Where are per-subject netmats?
>
> Hi - subject netmats are in the main PTN download.
> Cheers.
>
>
> On 1 Jun 2017, at 15:05, Thomas Nichols <t.e.nich...@warwick.ac.uk> wrote:
>
> Hi Jenn,
>
> Sorry for the slow reply on this.  We tried downloading the links you pointed
> us to <https://db.humanconnectome.org/data/projects/HCP_1200>:
>
>
> The following links contain subject-specific CIFTI maps: subject-specific
> versions of the group-ICA parcellations, with various ICA dimensionalities
> applied. These are z-statistic maps generated using dual-regression.
>
>  CIFTI Subject-specific Parcellations for 10-, 25-, 50-,
> 100-dimensionalities (57GB)
> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=GroupAvg=HCP_S900_PTNmaps_d15_25_50_100.zip>
>
>  CIFTI Subject-specific Parcellations for 200-dimensionality (55GB)
> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=GroupAvg=HCP_S900_PTNmaps_d200.zip>
>
>  CIFTI Subject-specific Parcellations for 300-dimensionality (85GB
> <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=GroupAvg=HCP_S900_PTNmaps_d300.zip>
>
> but they only contain the *dtseries.nii, while in previous releases there
> were *pconn.nii files that had the "NetMat" matrices.
>
> To be clear, the previous *pconn.nii files had #dim rows, #dim cols, while
> these *dtseries have #Elm rows and #dim cols.
>
> Is there some place that NetMats are currently released?  I'm not finding
> them.  I know they're not impossible to recreate but I'd like to minimize
> effort and chance of error by using the standard released product.
>
> -Tom
>
>
> PS: Note that the webpage is incorrectly indicates that the parcellation
> size is 10, 25, 50 and 100, when instead it is *15*, 25, 50 & 100.
>
>
>
> On Tue, May 16, 2017 at 1:12 PM, Elam, Jennifer <e...@wustl.edu> wrote:
>
>> Hi Tom,
>> Due to size, we have the individual subject parcellations available in
>> three separate downloads for different dimensionalities under the main PTN
>> download on this page in the DB: https://db.humanconnectome.org
>> /data/projects/HCP_1200
>>
>> Best,
>> Jenn
>>
>> Jennifer Elam, Ph.D.
>> Scientific Outreach, Human Connectome Project
>> Washington University School of Medicine
>> Department of Neuroscience, Box 8108
>> 660 South Euclid Avenue
>> St. Louis, MO 63110
>> 314-362-9387
>> e...@wustl.edu
>> www.humanconnectome.org
>>
>> --
>> *From:*hcp-users-boun...@humanconnectome.org <
>> hcp-users-boun...@humanconnectome.org> on behalf of Thomas Nichols <
>> t.e.nich...@warwick.ac.uk>
>> *Sent:* Tuesday, May 16, 2017 5:16:15 AM
>> *To:* HCP Users
>> *Subject:* [HCP-Users] Where are per-subject netmats?
>>
>> Hi folks,
>>
>> When poking through the PTN download for the netmats, we're having
>> trouble finding the netmat for each sub

Re: [HCP-Users] Where are per-subject netmats?

2017-06-01 Thread Stephen Smith

Hi - subject netmats are in the main PTN download.
Cheers.


> On 1 Jun 2017, at 15:05, Thomas Nichols  wrote:
> 
> Hi Jenn,
> 
> Sorry for the slow reply on this.  We tried downloading the links you pointed 
> us to :
> 
> The following links contain subject-specific CIFTI maps: subject-specific 
> versions of the group-ICA parcellations, with various ICA dimensionalities 
> applied. These are z-statistic maps generated using dual-regression.
> 
>  CIFTI Subject-specific Parcellations for 10-, 25-, 50-, 100-dimensionalities 
> (57GB) 
> 
>  CIFTI Subject-specific Parcellations for 200-dimensionality (55GB) 
> 
>  CIFTI Subject-specific Parcellations for 300-dimensionality (85GB 
> 
> but they only contain the *dtseries.nii, while in previous releases there 
> were *pconn.nii files that had the "NetMat" matrices.
> 
> To be clear, the previous *pconn.nii files had #dim rows, #dim cols, while 
> these *dtseries have #Elm rows and #dim cols.
> 
> Is there some place that NetMats are currently released?  I'm not finding 
> them.  I know they're not impossible to recreate but I'd like to minimize 
> effort and chance of error by using the standard released product.
> 
> -Tom
> 
> 
> PS: Note that the webpage is incorrectly indicates that the parcellation size 
> is 10, 25, 50 and 100, when instead it is 15, 25, 50 & 100.
> 
> 
> 
> On Tue, May 16, 2017 at 1:12 PM, Elam, Jennifer  > wrote:
> Hi Tom, 
> Due to size, we have the individual subject parcellations available in three 
> separate downloads for different dimensionalities under the main PTN download 
> on this page in the DB: https://db.humanconnectome.org/data/projects/HCP_1200 
> 
> 
> Best, 
> Jenn
> 
> Jennifer Elam, Ph.D.
> Scientific Outreach, Human Connectome Project
> Washington University School of Medicine
> Department of Neuroscience, Box 8108
> 660 South Euclid Avenue
> St. Louis, MO 63110
> 314-362-9387
> e...@wustl.edu 
> www.humanconnectome.org 
> 
> From: hcp-users-boun...@humanconnectome.org 
>  
>  > on behalf of Thomas Nichols 
> >
> Sent: Tuesday, May 16, 2017 5:16:15 AM
> To: HCP Users
> Subject: [HCP-Users] Where are per-subject netmats?
>  
> Hi folks,
> 
> When poking through the PTN download for the netmats, we're having trouble 
> finding the netmat for each subject.
> 
> As per the S1200 release manual 
> ,
>  pp 99-100, it says when we extract one of the flies like
>   netmats_3T_HCP820_MSMAll_ICAd*_ts*.tar.gz
> we should get a *_netmat1 directory filled with "One netmat file per subject, 
> computed using full correlation, Z-transformed", and another variant in 
> *_netmat2.  
> 
> Instead, we find that these tar.gz files only have 5 files, in a directory 
> netmats/3T_HCP820_MSMAll_ICAd*_ts*.  Two of these are netmat{1,2}.txt files, 
> but these are a single column and have a very strange number of rows (e.g. 
> for d=50 it has 820 rows).  (There are also Mnet?.pconn.nii files, but these 
> are tiny).
> 
> Where can we find the per-subject netmat files that were in previous releases?
> 
> -Tom
> 
> 
> -- 
> __
> Thomas Nichols, PhD
> Professor, Head of Neuroimaging Statistics
> Department of Statistics & Warwick Manufacturing Group
> University of Warwick, Coventry  CV4 7AL, United Kingdom
> 
> Web: http://warwick.ac.uk/tenichols 
> Email: t.e.nich...@warwick.ac.uk 
> Tel, Stats: +44 24761 51086, WMG: +44 24761 50752
> Fx,  +44 24 7652 4532 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org 
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> 
> 
> 
> -- 
> __
> Thomas Nichols, PhD
> Professor of Neuroimaging Statistics
> Oxford Big Data Institute
> Li Ka Shing Centre for Health Information and Discovery
> University of Oxford
> 
> Interim Contact Info:
> Web:

Re: [HCP-Users] Where are per-subject netmats?

2017-06-01 Thread Thomas Nichols

Hi Jenn,

Sorry for the slow reply on this.  We tried downloading the links you pointed
us to :


The following links contain subject-specific CIFTI maps: subject-specific
versions of the group-ICA parcellations, with various ICA dimensionalities
applied. These are z-statistic maps generated using dual-regression.

 CIFTI Subject-specific Parcellations for 10-, 25-, 50-,
100-dimensionalities (57GB)


 CIFTI Subject-specific Parcellations for 200-dimensionality (55GB)


 CIFTI Subject-specific Parcellations for 300-dimensionality (85GB


but they only contain the *dtseries.nii, while in previous releases there
were *pconn.nii files that had the "NetMat" matrices.

To be clear, the previous *pconn.nii files had #dim rows, #dim cols, while
these *dtseries have #Elm rows and #dim cols.

Is there some place that NetMats are currently released?  I'm not finding
them.  I know they're not impossible to recreate but I'd like to minimize
effort and chance of error by using the standard released product.

-Tom


PS: Note that the webpage is incorrectly indicates that the parcellation
size is 10, 25, 50 and 100, when instead it is *15*, 25, 50 & 100.



On Tue, May 16, 2017 at 1:12 PM, Elam, Jennifer  wrote:

> Hi Tom,
> Due to size, we have the individual subject parcellations available in
> three separate downloads for different dimensionalities under the main PTN
> download on this page in the DB: https://db.humanconnectome.
> org/data/projects/HCP_1200
>
> Best,
> Jenn
>
> Jennifer Elam, Ph.D.
> Scientific Outreach, Human Connectome Project
> Washington University School of Medicine
> Department of Neuroscience, Box 8108
> 660 South Euclid Avenue
> St. Louis, MO 63110
> 314-362-9387
> e...@wustl.edu
> www.humanconnectome.org
>
> --
> *From:* hcp-users-boun...@humanconnectome.org  humanconnectome.org> on behalf of Thomas Nichols <
> t.e.nich...@warwick.ac.uk>
> *Sent:* Tuesday, May 16, 2017 5:16:15 AM
> *To:* HCP Users
> *Subject:* [HCP-Users] Where are per-subject netmats?
>
> Hi folks,
>
> When poking through the PTN download for the netmats, we're having trouble
> finding the netmat for each subject.
>
> As per the S1200 release manual
> ,
> pp 99-100, it says when we extract one of the flies like
>   netmats_3T_HCP820_MSMAll_ICAd*_ts*.tar.gz
> we should get a *_netmat1 directory filled with "One netmat file per
> subject, computed using full correlation, Z-transformed", and another
> variant in *_netmat2.
>
> Instead, we find that these tar.gz files only have 5 files, in a directory
> netmats/3T_HCP820_MSMAll_ICAd*_ts*.  Two of these are netmat{1,2}.txt
> files, but these are a single column and have a very strange number of rows
> (e.g. for d=50 it has 820 rows).  (There are also Mnet?.pconn.nii files,
> but these are tiny).
>
> Where can we find the per-subject netmat files that were in previous
> releases?
>
> -Tom
>
>
> --
> __
> Thomas Nichols, PhD
> Professor, Head of Neuroimaging Statistics
> Department of Statistics & Warwick Manufacturing Group
> University of Warwick, Coventry  CV4 7AL, United Kingdom
>
> Web: http://warwick.ac.uk/tenichols
> Email: t.e.nich...@warwick.ac.uk
> Tel, Stats: +44 24761 51086, WMG: +44 24761 50752
> Fx,  +44 24 7652 4532 <024%207652%204532>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>



-- 
__
Thomas Nichols, PhD
Professor of Neuroimaging Statistics
Oxford Big Data Institute
Li Ka Shing Centre for Health Information and Discovery
University of Oxford

Interim Contact Info:
Web: http://warwick.ac.uk/tenichols
Email: t.e.nich...@warwick.ac.uk

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

Re: [HCP-Users] Where are per-subject netmats?

2017-05-16 Thread Thomas Nichols

Thanks Jenn!  Sorry I missed that.

-Tom

On Tue, May 16, 2017 at 1:12 PM, Elam, Jennifer  wrote:

> Hi Tom,
> Due to size, we have the individual subject parcellations available in
> three separate downloads for different dimensionalities under the main PTN
> download on this page in the DB: https://db.humanconnectome.
> org/data/projects/HCP_1200
>
> Best,
> Jenn
>
> Jennifer Elam, Ph.D.
> Scientific Outreach, Human Connectome Project
> Washington University School of Medicine
> Department of Neuroscience, Box 8108
> 660 South Euclid Avenue
> St. Louis, MO 63110
> 314-362-9387
> e...@wustl.edu
> www.humanconnectome.org
>
> --
> *From:* hcp-users-boun...@humanconnectome.org  humanconnectome.org> on behalf of Thomas Nichols <
> t.e.nich...@warwick.ac.uk>
> *Sent:* Tuesday, May 16, 2017 5:16:15 AM
> *To:* HCP Users
> *Subject:* [HCP-Users] Where are per-subject netmats?
>
> Hi folks,
>
> When poking through the PTN download for the netmats, we're having trouble
> finding the netmat for each subject.
>
> As per the S1200 release manual
> ,
> pp 99-100, it says when we extract one of the flies like
>   netmats_3T_HCP820_MSMAll_ICAd*_ts*.tar.gz
> we should get a *_netmat1 directory filled with "One netmat file per
> subject, computed using full correlation, Z-transformed", and another
> variant in *_netmat2.
>
> Instead, we find that these tar.gz files only have 5 files, in a directory
> netmats/3T_HCP820_MSMAll_ICAd*_ts*.  Two of these are netmat{1,2}.txt
> files, but these are a single column and have a very strange number of rows
> (e.g. for d=50 it has 820 rows).  (There are also Mnet?.pconn.nii files,
> but these are tiny).
>
> Where can we find the per-subject netmat files that were in previous
> releases?
>
> -Tom
>
>
> --
> __
> Thomas Nichols, PhD
> Professor, Head of Neuroimaging Statistics
> Department of Statistics & Warwick Manufacturing Group
> University of Warwick, Coventry  CV4 7AL, United Kingdom
>
> Web: http://warwick.ac.uk/tenichols
> Email: t.e.nich...@warwick.ac.uk
> Tel, Stats: +44 24761 51086, WMG: +44 24761 50752
> Fx,  +44 24 7652 4532 <024%207652%204532>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>



-- 
__
Thomas Nichols, PhD
Professor, Head of Neuroimaging Statistics
Department of Statistics & Warwick Manufacturing Group
University of Warwick, Coventry  CV4 7AL, United Kingdom

Web: http://warwick.ac.uk/tenichols
Email: t.e.nich...@warwick.ac.uk
Tel, Stats: +44 24761 51086, WMG: +44 24761 50752
Fx,  +44 24 7652 4532

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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Re: [HCP-Users] Where are per-subject netmats?

2017-05-16 Thread Elam, Jennifer

Hi Tom,
Due to size, we have the individual subject parcellations available in three 
separate downloads for different dimensionalities under the main PTN download 
on this page in the DB: https://db.humanconnectome.org/data/projects/HCP_1200

Best,
Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org


From: hcp-users-boun...@humanconnectome.org 
 on behalf of Thomas Nichols 

Sent: Tuesday, May 16, 2017 5:16:15 AM
To: HCP Users
Subject: [HCP-Users] Where are per-subject netmats?

Hi folks,

When poking through the PTN download for the netmats, we're having trouble 
finding the netmat for each subject.

As per the S1200 release 
manual,
 pp 99-100, it says when we extract one of the flies like
  netmats_3T_HCP820_MSMAll_ICAd*_ts*.tar.gz
we should get a *_netmat1 directory filled with "One netmat file per subject, 
computed using full correlation, Z-transformed", and another variant in 
*_netmat2.

Instead, we find that these tar.gz files only have 5 files, in a directory 
netmats/3T_HCP820_MSMAll_ICAd*_ts*.  Two of these are netmat{1,2}.txt files, 
but these are a single column and have a very strange number of rows (e.g. for 
d=50 it has 820 rows).  (There are also Mnet?.pconn.nii files, but these are 
tiny).

Where can we find the per-subject netmat files that were in previous releases?

-Tom


--
__
Thomas Nichols, PhD
Professor, Head of Neuroimaging Statistics
Department of Statistics & Warwick Manufacturing Group
University of Warwick, Coventry  CV4 7AL, United Kingdom

Web: http://warwick.ac.uk/tenichols
Email: t.e.nich...@warwick.ac.uk
Tel, Stats: +44 24761 51086, WMG: +44 24761 50752
Fx,  +44 24 7652 4532


___
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___
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Re: [HCP-Users] Where are per-subject netmats?

Re: [HCP-Users] Where are per-subject netmats?

Re: [HCP-Users] Where are per-subject netmats?

Re: [HCP-Users] Where are per-subject netmats?

Re: [HCP-Users] Where are per-subject netmats?

Re: [HCP-Users] Where are per-subject netmats?

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