Re: [HCP-Users] Corrupt Input Data

2019-06-11 Thread Glasser, Matthew 
dcm2bids is not a part of the HCP Pipelines and this seems like a ABCD data 
corruption issue.

Matt.

From:  on behalf of Eric Earl 

Date: Tuesday, June 11, 2019 at 5:59 PM
To: NIMH Data Archive Help Desk 
Cc: Damien Fair , HCPhelp 
Subject: Re: [HCP-Users] Corrupt Input Data

Sveta,

Anders meant the ABCD baseline year 1 data.

~Eric

[OHSU email via VMware Boxer]

On Jun 11, 2019 7:52 AM, NIMH Data Archive Help Desk  
wrote:
## In replies all text above this line is added to the ticket ##

You are registered as a cc on this help desk request and are thus receiving 
email notifications on all updates to the request.
Reply to this email to add a comment to the request.

Sveta Novikova (HELP DESK )

Jun 11, 10:52 AM EDT
Sending this question to HCP support:
I’m finishing up HCP data processing for the year 1 baseline data and I’m left 
with 250 subjects that I am not able to process due to problems with their 
input data. I’ve separated them out into two lists that I attached here.
corrupt_dcms.txt is a list of 138 subjects with at least one corrupt dicom in 
their dataset, which causes dcm2bids to fail. I’ve tried to redownload the tgzs 
but the error persists.
coil_error.txt is a list of 112 subjects that fail dcm2bids conversion 
primarily because the string “Coil Error” is in the series description or there 
is an error with “Slice timing”
I’m wondering if you can take a look at these subjects on your end and see if 
any of these errors can be fixed. My only other solution is to exclude them 
from processing, but often this means excluding the entire subject, which I am 
trying hard not to do.
Please let me know if there’s anything that requires further clarification.

NDA Help Desk


Perronea

Jun 10, 7:05 PM EDT

NDA,

I’m finishing up HCP data processing for the year 1 baseline data and I’m left 
with 250 subjects that I am not able to process due to problems with their 
input data. I’ve separated them out into two lists that I attached here.

corrupt_dcms.txt is a list of 138 subjects with at least one corrupt dicom in 
their dataset, which causes dcm2bids to fail. I’ve tried to redownload the tgzs 
but the error persists.

coil_error.txt is a list of 112 subjects that fail dcm2bids conversion 
primarily because the string “Coil Error” is in the series description or there 
is an error with “Slice timing”

I’m wondering if you can take a look at these subjects on your end and see if 
any of these errors can be fixed. My only other solution is to exclude them 
from processing, but often this means excluding the entire subject, which I am 
trying hard not to do.

Please let me know if there’s anything that requires further clarification.

Thank you,

Anders Perrone

Anders Perrone,

Research Assistant II

Fair Neuroimaging Lab

perro...@ohsu.edu

503-418-1897

Oregon Health & Science University

Mail code:L470

3181 SW Sam Jackson Park Road

Portland, Oregon 97239-3098

Attachment(s)
image001.png
corrupt_dcms.txt
coil_error.txt
'
This email is a service from HELP DESK . Delivered by 
Zendesk
[Z36X8Q-82O2]

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


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
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.

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

Re: [HCP-Users] Corrupt Input Data

2019-06-11 Thread Eric Earl 
Sveta,

Anders meant the ABCD baseline year 1 data.

~Eric

[OHSU email via VMware Boxer]

On Jun 11, 2019 7:52 AM, NIMH Data Archive Help Desk  
wrote:
## In replies all text above this line is added to the ticket ##

You are registered as a cc on this help desk request and are thus receiving 
email notifications on all updates to the request.
Reply to this email to add a comment to the request.

Sveta Novikova (HELP DESK )

Jun 11, 10:52 AM EDT

Sending this question to HCP support:
I’m finishing up HCP data processing for the year 1 baseline data and I’m left 
with 250 subjects that I am not able to process due to problems with their 
input data. I’ve separated them out into two lists that I attached here.
corrupt_dcms.txt is a list of 138 subjects with at least one corrupt dicom in 
their dataset, which causes dcm2bids to fail. I’ve tried to redownload the tgzs 
but the error persists.
coil_error.txt is a list of 112 subjects that fail dcm2bids conversion 
primarily because the string “Coil Error” is in the series description or there 
is an error with “Slice timing”
I’m wondering if you can take a look at these subjects on your end and see if 
any of these errors can be fixed. My only other solution is to exclude them 
from processing, but often this means excluding the entire subject, which I am 
trying hard not to do.
Please let me know if there’s anything that requires further clarification.


NDA Help Desk



Perronea

Jun 10, 7:05 PM EDT

NDA,

I’m finishing up HCP data processing for the year 1 baseline data and I’m left 
with 250 subjects that I am not able to process due to problems with their 
input data. I’ve separated them out into two lists that I attached here.

corrupt_dcms.txt is a list of 138 subjects with at least one corrupt dicom in 
their dataset, which causes dcm2bids to fail. I’ve tried to redownload the tgzs 
but the error persists.

coil_error.txt is a list of 112 subjects that fail dcm2bids conversion 
primarily because the string “Coil Error” is in the series description or there 
is an error with “Slice timing”

I’m wondering if you can take a look at these subjects on your end and see if 
any of these errors can be fixed. My only other solution is to exclude them 
from processing, but often this means excluding the entire subject, which I am 
trying hard not to do.

Please let me know if there’s anything that requires further clarification.

Thank you,

Anders Perrone

Anders Perrone,

Research Assistant II

Fair Neuroimaging Lab

perro...@ohsu.edu

503-418-1897

Oregon Health & Science University

Mail code:L470

3181 SW Sam Jackson Park Road

Portland, Oregon 97239-3098

Attachment(s)
image001.png
corrupt_dcms.txt
coil_error.txt



'
This email is a service from HELP DESK . Delivered by 
Zendesk
[Z36X8Q-82O2]

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