Thanks a lot
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Harms, Michael
Sent: Thursday, October 2, 2014 1:52 PM
To: [log in to unmask]
Subject: Re: [FSL] Motion Parameters
'eddy_correct' will correct for eddy currents and motion prior to inputting the data to 'dtifit'. Separately from that, you could use the motion estimates from that ec_plot.sh script to check if you, for example, have differences in motion between subject groups, or want to use motion estimates as a covariate in a higher level (across-subject) analysis.
cheers,
-MH
--
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: [log in to unmask]
On 10/2/14 12:44 PM, "Alshikho, Mohamad J." <[log in to unmask]>
wrote:
>Thanks a lot Michael,
>So what can I understand right now that we shouldn't use the
>fsl_motion_outliers to calculate the motion parameters in my dMRI data
>because it is designed to fMRI data. What I need to do is to apply that
>script to the output of eddy_current in my dMRI data.
>
>Then I will run dtifit and generate my corrected FA map Is that
>correct?
>
>Mohamad
>
>-----Original Message-----
>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>Behalf Of Harms, Michael
>Sent: Thursday, October 2, 2014 1:11 PM
>To: [log in to unmask]
>Subject: Re: [FSL] Motion Parameters
>
>Search the FSL archives for "eddy current ecclog" and check out item
>#034731
>
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1101&L=FSL&P=R20441&1
>=FS
>L
>&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
>
>
>--
>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: [log in to unmask]
>
>
>
>
>On 10/2/14 11:54 AM, "Harms, Michael" <[log in to unmask]> wrote:
>
>>sorry, meant to say from the output of 'eddy_correct'. Not sure if
>>that same script can be applied to the motion estimates returned by
>>'eddy' as well.
>>
>>--
>>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: [log in to unmask]
>>
>>
>>
>>
>>On 10/2/14 11:37 AM, "Harms, Michael" <[log in to unmask]> wrote:
>>
>>>Hi,
>>>fsl_motion_outliers is for application to fMRI data.
>>>For dMRI data, you should be able to find a script in the archives
>>>that will estimate motion from the output of 'dtifit'.
>>>
>>>cheers,
>>>-MH
>>>
>>>--
>>>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: [log in to unmask]
>>>
>>>
>>>
>>>
>>>On 10/2/14 11:04 AM, "M. alshikho" <[log in to unmask]> wrote:
>>>
>>>>Hi Experts,
>>>>I have a data set of 50 subjects (23 patient and 27 controls) I want
>>>>to check if there is any difference in FA between the two groups. To
>>>>do so I did DTI analysis using FSL pipeline, I did all the steps
>>>>suggested by FSL to generate the FA map. Then I used
>>>>fsl_motion_outliers to calculate the motion parameters for all the
>>>>subjects.
>>>>My question here is about the importance of including the motion
>>>>parameters in my analysis as a confounding (Variable factor) and if
>>>>I do so, are they going to increase the bias in my results?
>>>>
>>>>Looking to learn from you guys
>>>>
>>>>Thanks,
>>>>Mohamad
>>>
>>>
>>>________________________________
>>>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.
>>
>>
>>________________________________
>>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.
>
>
>________________________________
>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.
>
>
>The information in this e-mail is intended only for the person to whom
>it is addressed. If you believe this e-mail was sent to you in error
>and the e-mail contains patient information, please contact the
>Partners Compliance HelpLine at http://www.partners.org/complianceline
>. If the e-mail was sent to you in error but does not contain patient
>information, please contact the sender and properly dispose of the
>e-mail.
________________________________
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.
|