Re: [HCP-Users] Unresolved: 13-volume mismatch between rsfMRI volumes and trigger file?

[Nicola Toschi]

Hi Greg,

thank you very much for your reply! I understand the source of the issue 
now.

Just to make  sure I take this into account correctly: does the last 
square wave in the physio trigger signal (i.e. the 1187th square wave) 
correspond to the "real" 1187th volume i will find in the .nii.gz file 
(i.e.: the final triggers are missing from the physio log), or to the 
1200th volume (i.e. the initial triggers are missing from the physio log)?

I am asking because from your explanation it would seem that the final 
triggers are missing from the physio log, however the fact that the 
physio log file is "flat" at the end makes me think that it is the 
initial triggers that have been cut off.

Thanks again!

nicola


On 05/22/2015 11:24 PM, Greg Burgess wrote:

The missing triggers (and corresponding physio samples) are cut off 
the end of the scan. The physio files from the scanner have time 
stamps called LogStartMDHTime and LogStopMDHTime, which can be 
synchronized with the DICOM timestamps to ensure that the physio 
measurements are correctly aligned with the BOLD image. The difference 
between the LogStartMDHTime and LogStopMDHTime covers 1200 TRs. 
However, that duration does not appear to compensate for the fact that 
the MB sequences collect a SBRef volume and five dummy scans prior to 
the onset of the first MB BOLD volume. Therefore, when we included 
only the samples that occurred between LogStartMDHTime and 
LogStopMDHTime, it consequently cut off (from the end of the physio 
samples) a duration equivalent to the time to acquire the SBRef and 
dummy BOLD scans, which accounts for the 13 missing TRs at the end.


--Greg
____________________________________________________________________
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology
Email: burge...@pcg.wustl.edu <mailto:burge...@pcg.wustl.edu>

On May 15, 2015, at 3:46 PM, Nicola Toschi <tos...@med.uniroma2.it 
<mailto:tos...@med.uniroma2.it>> wrote:

Dear List,

I have not yet been able to find an explanation to this (I have 
searched the list and bug reports):

For every subject I have checked in the 100 "unrelated" dataset, 
there are only 1187 trigger "up" sections in the physio log file (but 
1200 rs-fMRI volumes). However, the temporal length of the physio 
logs is, as expected, 1200 x TR.

All physio logs I have looked at end like in the attached picture - 
there are about 10 seconds of 0's.

Could anyone help in figuring out which way the misalignment went?

Thanks a lot in advance!

Nicola

<mime-attachment.jpg>
________________________________________________________________
Prof. Nicola Toschi
Associate Professor in Medical Physics
Medical Physics Section, Department of Biomedicine and Prevention
Faculty of Medicine, University of Rome "Tor Vergata"
Via Montpellier 1 - 00133 Rome, Italy
tos...@med.uniroma2.it

Visiting Assistant Professor in Radiology, Assistant in Neurology
Athinoula A. Martinos Center for Biomedical Imaging, Department of 
Radiology
Harvard Medical School
149 Thirteenth Street, Suite 2301, Charlestown, MA 02129
nic...@nmr.mgh.harvard.edu






-------- Forwarded Message --------
Subject: 	Re: [HCP-Users] 13-volume mismatch between rsfMRI volumes 
and trigger file?
Date:   Thu, 14 May 2015 22:59:52 +0200
From:   Nicola Toschi <tos...@med.uniroma2.it>
To: 	Glasser, Matthew <glass...@wusm.wustl.edu>, 
hcp-users@humanconnectome.org <hcp-users@humanconnectome.org>



Hi,

thanks for your quick reply.

I had noticed a bug report (also mentioned in the wiki), but a) it
refers to a 1 or 1.5 second mismatch (not 13 volumes i.e. roughly 10
seconds), b) the wiki says that the files have  been realigned.

https://www.mail-archive.com/hcp-users%40humanconnectome.org/msg00217.html

Any pointers are much appreciated!

Thanks a lot - Nicola

On 05/14/2015 10:52 PM, Glasser, Matthew wrote:
> I believe there has been a reported bug in this, so have a search of the
> mailing list archive for it.
>
> Peace,
>
> Matt.
>
> On 5/14/15, 3:48 PM, "Nicola Toschi"<tos...@med.uniroma2.it>  wrote:
>
>> Dear HCP Staff,
>>
>> I have been looking at the trigger logs (column 1 of the *Physio_log.txt
>> files) in rsfMRI data (both sessions) for the 100 unrelated subjects.
>>
>> While the total temporal length of the physio logs matches the total
>> length of the fMRI data (1200 * TR), in all physio logs I consistently
>> found 1187 (instead of 1200) triggers (i.e. sections with consecutive
>> 1's).
>>
>> Could there be a 13 - volume shift? Or am I missing something (more
>> likely)?
>>
>> Thanks in advance!
>>
>> Nicola
>>
>>
>> _______________________________________________
>> 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 <mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users



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