We've been having some problems with our MNI registration of the fMRI data.
After going through the PreFS, FS, PostFS, and the GenericfMRIbatch scripts, we
get a 4D dataset: subjectID/MNINonLinear/Results/taskname/taskname.nii.gz
I'm assuming those 4D images should be registered to the MNI
[mailto:glass...@wusm.wustl.edu]
Sent: Thursday, April 16, 2015 12:56 PM
To: Book, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii
Perhaps you should post your fMRIVolume and fMRISurface calls.
Peace,
Matt.
From: Book, Gregory
gregory.b
For this task, there are only single runs. So, yes, I don't need to combine
multiple runs. I was also planning to do second level stats outside of the HCP
pipelines.
From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Friday, April 17, 2015 1:06 PM
To: Book, Gregory; hcp-users
be the cause of the fMRISurface pipeline error?
Thanks,
-G
From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Thursday, April 16, 2015 12:20 PM
To: Book, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii
Did you run the fMRISurface pipeline yet
I'm running the TaskfMRIAnalysisBatch script against data that was processed
using the PreFS,FS,PostFS, and GenericfMRI batch scripts.
It doesn't get far and gives an error that it can't find _Atlas.dtseries.nii:
Wed Apr 15 16:38:04 EDT 2015 - TaskfMRILevel1.sh - Use wb_command to calculate
it have a negative effect?
-Greg
-Original Message-
From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Tuesday, March 03, 2015 1:09 PM
To: Book, Gregory
Subject: Re: [HCP-Users] manual AC-PC realignment
Hi Greg,
If you use the files I specified from MNINonLinear
stage) before re-running this script
From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Thursday, January 08, 2015 2:07 PM
To: Book, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] fieldmap processing error
Probably the easiest thing to do would be to fix the outlying
We've noticed an error while processing some fMRI data through the HCP
pipeline. Several series are failing with the following message:
Phase and Magnitude images must have the same number of voxels and voxel
dimensions
Current dimensions are:
Phase image: 80 x 80 x 48 with dims of
We're using dcm2nii. What's weird is that run 1 works fine, but runs 2-5 do
not, even though they reference the same fieldmap images.
From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Thursday, January 08, 2015 2:07 PM
To: Book, Gregory; hcp-users@humanconnectome.org
Subject: Re
, December 15, 2014 5:41 PM
To: Book, Gregory; Harms, Michael; Glasser, Matthew;
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] spin echo phase encoding direction
Hi Greg,
Ultimately, getting all the signs right is a complicated combination of (1) how
the manufacturer implements its PE
We also experienced a problem with the FLIRT based motion correction. We fixed
it by using mcflirt instead. I can also post our version of the
MotionCorrection.sh script if that would be helpful.
-Greg
Dear all,
I have made changes to two files to make use of FSL's mcflirt instead
parameters
From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Tuesday, December 16, 2014 1:34 PM
To: Book, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion
correction
I'd be interested in seeing your mcflirt call. I've
Would that be the *.dInPlaneRot value for each slice in the CSA header?
From: Harms, Michael [mailto:mha...@wustl.edu]
Sent: Monday, December 15, 2014 10:11 AM
To: Book, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] spin echo phase encoding direction
The value
: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Monday, December 15, 2014 2:33 PM
To: Book, Gregory; Harms, Michael; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] spin echo phase encoding direction
If your phase encoding directions are inverted, I would recommend swapping
: Monday, December 15, 2014 4:10 PM
To: Book, Gregory; Glasser, Matthew; Harms, Michael;
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] spin echo phase encoding direction
Hi,
If you had AP with Invert RO/PE Polarity checked, then that would be the
same as if you had set PA and Invert RO/PE
We've run into a weird problem when using the GenericfMRIVolume batch script to
process more than 2 tasks at a time. When we setup any more than 2 tasks (we've
tried 3 and 4 tasks), the first 2 run correctly and without error, but any
after that crash in the TopUp section with the following
: Glasser, Matthew [mailto:glass...@wusm.wustl.edu]
Sent: Tuesday, December 09, 2014 3:33 PM
To: Book, Gregory; hcp-users@humanconnectome.org
Cc: Brown, Tim
Subject: Re: [HCP-Users] error when processing more than 2 tasks with
GenericfMRIVolume script
You need to expand the PhaseEncodinglist
When I run the GenericfMRIVolume(Surface)ProcessingPipelineBatch.sh script with
the SpinEchoPhaseEncodeNegative and SpinEchoPhaseEncodePositive containing a SE
image, the script processes fine. But when I set those fields to NONE, the
script fails
Here is the last bit of log before the error:
Neuroinformatics Database is an all purpose storage and retrieval system for
imaging data. NiDB is geared toward neuroimaging research, but can store any
modality of data. NiDB is released in an open-source format:
http://nidb.sourceforge.nethttp://nidb.sourceforge.net/, but now offers a
cloud
I'm trying to run the gradient unwarping step in the HCP fMRIVolume script
again, using the .grad file from our Skyra. It appears to be reading the .grad
file successfully, and writes out the trilinear.nii.gz file. It then crashes
because it is missing the
.
How would I run the HCP motion correction using the middle timepoint instead of
either the sbref or the mean of the first 10 images?
-G
-Original Message-
From: Harms, Michael [mailto:mha...@wustl.edu]
Sent: Wednesday, October 29, 2014 10:45 AM
To: Book, Gregory; Harms, Michael; hcp-users
, Junqian
Cc: Book, Gregory; HCP Users
Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion
correction
I agree with Mike and Gordon. Our best guess right now is that the motion
correction registration target (i.e., SBRef) is corrupted, and that is
affecting the efficacy of motion
11:40 AM
To: Book, Gregory; Greg Burgess; Xu, Junqian
Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion
correction
Hi Greg,
I'm a little confused by what you are showing in your gif. Is the original
(top) the uncorrected (raw) time series, and the final
(bottom) the result
I'm continuing to fine-tune our preFS script for our data, and I'm running into
trouble with the gradient unwarping step. I've obtained the .grad file from our
Skyra scanner and running the HCP with it. It runs the gradient unwarp step,
but seems to fail right after. If I set the
I'm processing our own raw data, collected on our stock Skyra. Our data was
collected using the HCP sequence recommendation.
-G
From: Harms, Michael [mailto:mha...@wustl.edu]
Sent: Thursday, October 16, 2014 11:08 AM
To: Book, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users
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