Re: [Freesurfer] Group level analysis: Specifying contrasts
On 04/12/2016 04:16 PM, Afzal, Afsana wrote: > The source data is from a gambling task that has multiple levels of risk and > reward. The offset refers to the risk level and the slope refers to the > monetary reward for that particular risk level. > > We were doing some parametric modulation in the first level analysis. For the > second levels, currently I'm just looking at the offset values which is why > the slope rows are all zeros. I don't think this makes sense. If you don't want it there, then it must not be in the FSGD file. What are you trying to test at the group level? > > Please let me know if that makes sense, > > Afsana > > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, April 11, 2016 11:19 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts > > What is your source data? It looks like you have two time points per > subject, but the names of "offset" and "slope" suggest some preprocessing? > > Input hc001-lRsk_offset hc001100 > Input hc001-lRsk_slope hc001000 > Input hc001-mRsk_offset hc001010 > Input hc001-mRsk_slope hc001000 > Input hc001-hRsk_offset hc001001 > Input hc001-hRsk_slope hc001000 > > > > On 04/11/2016 10:09 AM, Afzal, Afsana wrote: >> Hi Doug, >> >> I've attached the fsgd file and the contrast matrix file. Thanks for your >> help! >> >> - Afsana >> >> __ >> Afsana Afzal >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> ________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Friday, April 08, 2016 12:07 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts >> >> I don't know what you mean, can you just send the header of the fsgd >> file and the contrast matrix? >> >> On 04/04/2016 11:20 AM, Afzal, Afsana wrote: >>> Hi, >>> >>> I want to perform a linear regression for a task with 3 different risk >>> conditions (low, medium, high) with the following linear trend: low = >>> 1, medium = 2, high = 3. >>> >>> Right now I'm specifying the above weighted under each risk condition >>> in my contrast matrix. Is this the correct approach? I want to make >>> sure I am calculating a regression and not a weighted average. >>> >>> Thank you for your help, >>> >>> Afsana >>> >>> >>> __ >>> *Afsana Afzal* >>> Clinical Research Coordinator >>> Massachusetts General Hospital >>> Division of Neurotherapeutics >>> Department of Psychiatry: Neurosciences >>> 149 13th St, Room 2612 >>> Charlestown, MA 02129 >>> Phone: 617-643-5129 >>> Fax: 617-726-4078 >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
Re: [Freesurfer] Group level analysis: Specifying contrasts
The source data is from a gambling task that has multiple levels of risk and reward. The offset refers to the risk level and the slope refers to the monetary reward for that particular risk level. We were doing some parametric modulation in the first level analysis. For the second levels, currently I'm just looking at the offset values which is why the slope rows are all zeros. Please let me know if that makes sense, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 11, 2016 11:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts What is your source data? It looks like you have two time points per subject, but the names of "offset" and "slope" suggest some preprocessing? Input hc001-lRsk_offset hc001100 Input hc001-lRsk_slope hc001000 Input hc001-mRsk_offset hc001010 Input hc001-mRsk_slope hc001000 Input hc001-hRsk_offset hc001001 Input hc001-hRsk_slope hc001000 On 04/11/2016 10:09 AM, Afzal, Afsana wrote: > Hi Doug, > > I've attached the fsgd file and the contrast matrix file. Thanks for your > help! > > - Afsana > > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, April 08, 2016 12:07 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts > > I don't know what you mean, can you just send the header of the fsgd > file and the contrast matrix? > > On 04/04/2016 11:20 AM, Afzal, Afsana wrote: >> Hi, >> >> I want to perform a linear regression for a task with 3 different risk >> conditions (low, medium, high) with the following linear trend: low = >> 1, medium = 2, high = 3. >> >> Right now I'm specifying the above weighted under each risk condition >> in my contrast matrix. Is this the correct approach? I want to make >> sure I am calculating a regression and not a weighted average. >> >> Thank you for your help, >> >> Afsana >> >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___
Re: [Freesurfer] Group level analysis: Specifying contrasts
What is your source data? It looks like you have two time points per subject, but the names of "offset" and "slope" suggest some preprocessing? Input hc001-lRsk_offset hc001100 Input hc001-lRsk_slope hc001000 Input hc001-mRsk_offset hc001010 Input hc001-mRsk_slope hc001000 Input hc001-hRsk_offset hc001001 Input hc001-hRsk_slope hc001000 On 04/11/2016 10:09 AM, Afzal, Afsana wrote: > Hi Doug, > > I've attached the fsgd file and the contrast matrix file. Thanks for your > help! > > - Afsana > > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, April 08, 2016 12:07 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts > > I don't know what you mean, can you just send the header of the fsgd > file and the contrast matrix? > > On 04/04/2016 11:20 AM, Afzal, Afsana wrote: >> Hi, >> >> I want to perform a linear regression for a task with 3 different risk >> conditions (low, medium, high) with the following linear trend: low = >> 1, medium = 2, high = 3. >> >> Right now I'm specifying the above weighted under each risk condition >> in my contrast matrix. Is this the correct approach? I want to make >> sure I am calculating a regression and not a weighted average. >> >> Thank you for your help, >> >> Afsana >> >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Group level analysis: Specifying contrasts
Hi Doug, I've attached the fsgd file and the contrast matrix file. Thanks for your help! - Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, April 08, 2016 12:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts I don't know what you mean, can you just send the header of the fsgd file and the contrast matrix? On 04/04/2016 11:20 AM, Afzal, Afsana wrote: > Hi, > > I want to perform a linear regression for a task with 3 different risk > conditions (low, medium, high) with the following linear trend: low = > 1, medium = 2, high = 3. > > Right now I'm specifying the above weighted under each risk condition > in my contrast matrix. Is this the correct approach? I want to make > sure I am calculating a regression and not a weighted average. > > Thank you for your help, > > Afsana > > > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer avg.risk.mod.fsgd Description: avg.risk.mod.fsgd weight_avg.mtx Description: weight_avg.mtx ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Group level analysis: Specifying contrasts
I don't know what you mean, can you just send the header of the fsgd file and the contrast matrix? On 04/04/2016 11:20 AM, Afzal, Afsana wrote: > Hi, > > I want to perform a linear regression for a task with 3 different risk > conditions (low, medium, high) with the following linear trend: low = > 1, medium = 2, high = 3. > > Right now I'm specifying the above weighted under each risk condition > in my contrast matrix. Is this the correct approach? I want to make > sure I am calculating a regression and not a weighted average. > > Thank you for your help, > > Afsana > > > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Group level analysis: Specifying contrasts
Hi, I want to perform a linear regression for a task with 3 different risk conditions (low, medium, high) with the following linear trend: low = 1, medium = 2, high = 3. Right now I'm specifying the above weighted under each risk condition in my contrast matrix. Is this the correct approach? I want to make sure I am calculating a regression and not a weighted average. Thank you for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
