Re: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

[Harms, Michael]

Are you sure that there is duplication of actual *data* on the different 
drives?  Just because a subject ID appears on multiple drives doesn’t mean that 
data under that subject ID is the same on the drives.

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 "Glasser, Matthew" 

Date: Friday, June 7, 2019 at 6:01 PM
To: "Fales, Christina L" , 
"hcp-users@humanconnectome.org" 
Cc: "Cler, Eileen" 
Subject: Re: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?


  1.  I don’t know, but perhaps someone from NRG can answer.
  2.  Those are different smoothing levels.  I do not recommend using more than 
s4 and personally don’t use anything but s2.  You can see Coalson et al 2018 
PNAS: https://www.pnas.org/content/115/27/E6356.short for the deleterious 
effects of spatial smoothing, which are worst in the volume in 3D, but still 
problematic on the surface when large kernels are used.

Matt.

From:  on behalf of "Fales, Christina L" 

Date: Friday, June 7, 2019 at 5:40 PM
To: "hcp-users@humanconnectome.org" 
Cc: "Fales, Christina L" 
Subject: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

Hi HCP gurus:

I’m reposting the following question(s) in hopes that one of you knows the 
answer.

(1)
On looking through the data, it appears that there is duplication between the 
drives delivered. Is that intentional? We received 12 drives, but four of them 
appear to be duplicates. Specifically, in the pairs below, every subject on the 
first drive (eg, “sde1”) also occurs on the second (“sdi1”).  Files look the 
same (ie, have same file size). What is the difference between the people on 
corresponding drives in each pair?

sde1, sdi1
sdd1, sdh1
sdc1, sdg1
sdf1, sdk1

Subjects on drives sdb1, sdj1, sdbl1, and sdbm1 appear to be unique.

(2)
I cannot find anywhere an explanation of the differences between 
“analysis_s12”, “analysis_s8”, “analysis_s4”, and “analysis_s2”. What is the 
difference between these?

Thanks very much….
-Christina Fales

Christina Fales, PhD
Research Scientist
Division of Psychiatry Research
Zucker Hillside Hospital
Feinstein Institute for Medical Research
Glen Oaks, NY 11004

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Re: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

[Glasser, Matthew]

  1.  I don’t know, but perhaps someone from NRG can answer.
  2.  Those are different smoothing levels.  I do not recommend using more than 
s4 and personally don’t use anything but s2.  You can see Coalson et al 2018 
PNAS: https://www.pnas.org/content/115/27/E6356.short for the deleterious 
effects of spatial smoothing, which are worst in the volume in 3D, but still 
problematic on the surface when large kernels are used.

Matt.

From:  on behalf of "Fales, Christina L" 

Date: Friday, June 7, 2019 at 5:40 PM
To: "hcp-users@humanconnectome.org" 
Cc: "Fales, Christina L" 
Subject: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

Hi HCP gurus:

I’m reposting the following question(s) in hopes that one of you knows the 
answer.

(1)
On looking through the data, it appears that there is duplication between the 
drives delivered. Is that intentional? We received 12 drives, but four of them 
appear to be duplicates. Specifically, in the pairs below, every subject on the 
first drive (eg, “sde1”) also occurs on the second (“sdi1”).  Files look the 
same (ie, have same file size). What is the difference between the people on 
corresponding drives in each pair?

sde1, sdi1
sdd1, sdh1
sdc1, sdg1
sdf1, sdk1

Subjects on drives sdb1, sdj1, sdbl1, and sdbm1 appear to be unique.

(2)
I cannot find anywhere an explanation of the differences between 
“analysis_s12”, “analysis_s8”, “analysis_s4”, and “analysis_s2”. What is the 
difference between these?

Thanks very much….
-Christina Fales

Christina Fales, PhD
Research Scientist
Division of Psychiatry Research
Zucker Hillside Hospital
Feinstein Institute for Medical Research
Glen Oaks, NY 11004

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are hereby notified that any dissemination, distribution, copying or disclosure 
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The materials in this message are private and may contain Protected Healthcare 
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[HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

[Fales, Christina L]

Hi HCP gurus:

I'm reposting the following question(s) in hopes that one of you knows the 
answer.

(1)
On looking through the data, it appears that there is duplication between the 
drives delivered. Is that intentional? We received 12 drives, but four of them 
appear to be duplicates. Specifically, in the pairs below, every subject on the 
first drive (eg, "sde1") also occurs on the second ("sdi1").  Files look the 
same (ie, have same file size). What is the difference between the people on 
corresponding drives in each pair?

sde1, sdi1
sdd1, sdh1
sdc1, sdg1
sdf1, sdk1

Subjects on drives sdb1, sdj1, sdbl1, and sdbm1 appear to be unique.

(2)
I cannot find anywhere an explanation of the differences between 
"analysis_s12", "analysis_s8", "analysis_s4", and "analysis_s2". What is the 
difference between these?

Thanks very much
-Christina Fales

Christina Fales, PhD
Research Scientist
Division of Psychiatry Research
Zucker Hillside Hospital
Feinstein Institute for Medical Research
Glen Oaks, NY 11004


The information contained in this electronic e-mail transmission and any 
attachments are intended only for the use of the individual or entity to whom 
or to which it is addressed, and may contain information that is privileged, 
confidential and exempt from disclosure under applicable law. If the reader of 
this communication is not the intended recipient, or the employee or agent 
responsible for delivering this communication to the intended recipient, you 
are hereby notified that any dissemination, distribution, copying or disclosure 
of this communication and any attachment is strictly prohibited. If you have 
received this transmission in error, please notify the sender immediately by 
telephone and electronic mail, and delete the original communication and any 
attachment from any computer, server or other electronic recording or storage 
device or medium. Receipt by anyone other than the intended recipient is not a 
waiver of any attorney-client, physician-patient or other privilege.
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Re: [HCP-Users] wb_command -convert-matrix4-to-workbench-sparse

[Timothy Coalson]

Tractography visualization is somewhat rough around the edges.  What was
the full probtrackx command you used?  Do you have bingham parameter
volumes for the fiber orientations (mean, stdev, theta, phi, psi, ka, kb),
or only the fiber orientation sample volumes?

Tim


On Fri, Jun 7, 2019 at 7:48 AM DE CASTRO Vanessa 
wrote:

> Good morning, I would like to transform my data obtained with fsl's
> probtackx, to visualized them with wb_view. But the instructions to run the
> command is not clear for me. I've tried several choices but there is always
> something missing or nor recognized (I'm very naive with all this.. just
> starting). Could you show a practical example to run it, please?
>
> Thank you very much
>
>
> *--*
>
> *Vanessa DeCastro, PhD*
>
> *Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS
> Pavillon Baudot CHU Purpan
> 31052 Toulouse Cedex 03, France *
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] A minor question regarding HCP 7T movie data

[Harms, Michael]

Hi,
It isn’t surprising that data will be missing in some subjects, due either to 
problems at the scanner, or problems during processing.

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 Reza Rajimehr 

Date: Friday, June 7, 2019 at 11:00 AM
To: Keith Jamison , hcp-users 
Subject: Re: [HCP-Users] A minor question regarding HCP 7T movie data

Thanks Keith! I am currently working with the Movie Task fMRI 2mm/32k 
FIX-Denoised (Compact) dataset, and I noticed the issues below:

1) Two subjects (126931 and 74) do not have MSMAll-registered time-series 
data.

2) Five subjects (181636, 473952, 536647, 552241, and 973770) have two runs 
(MOVIE1 and MOVIE2).

3) One subject (585256) has three runs (MOVIE1, MOVIE3, and MOVIE4).

Best,
Reza

On Mon, Jun 3, 2019 at 8:33 PM Keith Jamison 
mailto:kjami...@umn.edu>> wrote:
Hi Reza,

Your interpretation of the timing is correct. The validation segment in each 
movie scan was shifted by 40-200ms for the "v2" version. This was done in order 
to make that final 83 second clip begin precisely at the start of the next TR 
for all 4 movie sessions.

Given HRF variability, ignoring this change will probably not adversely impact 
most analyses.

-Keith


On Fri, May 31, 2019 at 9:05 PM Reza Rajimehr 
mailto:rajim...@gmail.com>> wrote:
Hi,

The HCP S1200 Reference Manual says that there are two versions of 4 movie 
files. Some subjects have been scanned with one version, and the remaining 
subjects have been scanned with another version. Version 2 includes these 
changes:

7T_MOVIE1_CC1_v2 remains unchanged.

7T_ MOVIE2_HO1_v2 removed 1 frame of rest before the validation clip.

7T_MOVIE3_CC2_v2 removed 5 frames of rest before the validation clip.

7T_MOVIE4_HO2_v2 added 4 frames of rest before the validation clip.

Here *frame* is a frame of the movie, right?

Assuming that the movies are ~25 frames per second, the deviations are between 
0 and ~200 ms in each movie file. Considering the TR of one second and the slow 
hemodynamic BOLD responses, these deviations are negligible, and we can 
possibly ignore them when concatenating time-series data across all subjects. 
Would you agree?

Thanks,
Reza

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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 
immediately notify the sender via telephone or return mail.

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Re: [HCP-Users] A minor question regarding HCP 7T movie data

[Reza Rajimehr]

Thanks Keith! I am currently working with the Movie Task fMRI 2mm/32k
FIX-Denoised (Compact) dataset, and I noticed the issues below:

1) Two subjects (126931 and 74) do not have MSMAll-registered
time-series data.

2) Five subjects (181636, 473952, 536647, 552241, and 973770) have two runs
(MOVIE1 and MOVIE2).

3) One subject (585256) has three runs (MOVIE1, MOVIE3, and MOVIE4).

Best,
Reza

On Mon, Jun 3, 2019 at 8:33 PM Keith Jamison  wrote:

> Hi Reza,
>
> Your interpretation of the timing is correct. The validation segment in
> each movie scan was shifted by 40-200ms for the "v2" version. This was done
> in order to make that final 83 second clip begin precisely at the start of
> the next TR for all 4 movie sessions.
>
> Given HRF variability, ignoring this change will probably not adversely
> impact most analyses.
>
> -Keith
>
>
> On Fri, May 31, 2019 at 9:05 PM Reza Rajimehr  wrote:
>
>> Hi,
>>
>> The HCP S1200 Reference Manual says that there are two versions of 4
>> movie files. Some subjects have been scanned with one version, and the
>> remaining subjects have been scanned with another version. Version 2
>> includes these changes:
>>
>> 7T_MOVIE1_CC1_v2 remains unchanged.
>>
>> 7T_ MOVIE2_HO1_v2 removed 1 frame of rest before the validation clip.
>>
>> 7T_MOVIE3_CC2_v2 removed 5 frames of rest before the validation clip.
>>
>> 7T_MOVIE4_HO2_v2 added 4 frames of rest before the validation clip.
>>
>> Here *frame* is a frame of the movie, right?
>>
>> Assuming that the movies are ~25 frames per second, the deviations are
>> between 0 and ~200 ms in each movie file. Considering the TR of one second
>> and the slow hemodynamic BOLD responses, these deviations are negligible,
>> and we can possibly ignore them when concatenating time-series data across
>> all subjects. Would you agree?
>>
>> Thanks,
>> Reza
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>

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[HCP-Users] wb_command -convert-matrix4-to-workbench-sparse

[DE CASTRO Vanessa]

Good morning, I would like to transform my data obtained with fsl's probtackx, 
to visualized them with wb_view. But the instructions to run the command is not 
clear for me. I've tried several choices but there is always something missing 
or nor recognized (I'm very naive with all this.. just starting). Could you 
show a practical example to run it, please?

Thank you very much


--

Vanessa DeCastro, PhD

Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS
Pavillon Baudot CHU Purpan
31052 Toulouse Cedex 03, France


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