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Can you post your .png and design.fsf files? Also, what exactly are the contents of the .gfeat/cope2.feat directory?
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>Date: Saturday, May 18, 2013 1:03 PM
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] Feat second level zstats maps
MarenHi,I tried both, fixed and mixed effects (EVs set as you wrote), but I stil lonly get one zstat map (for cope1).
On Sat, May 18, 2013 at 8:46 AM, Harms, Michael <[log in to unmask]> wrote:
Well, then I'm confused, because what you wrote that you did in your 2nd level analysis is not what I described to do. (i.e., use Fixed, not Mixed effects; and what is an EV set to 0?)
Did you use the "Inputs are lower level FEAT directories" setting on the Data tab?
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>Date: Friday, May 17, 2013 9:35 PM Subject: Re: [FSL] Feat second level zstats maps
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
That's what I did. It didn't give me a zstat map for each COPE, just for the first one. The question that I posted was how to get a zstat map for each on my COPEs.Maren
On Fri, May 17, 2013 at 6:32 PM, Harms, Michael <[log in to unmask]> wrote:
If you 2nd level analysis is just to effectively average the 1st level copes from the 5 runs in a given subject, then you should do a Fixed Effects Lev2 analysis using a single EV that is a column of 1's, and then you'll get a .gfeat directory for each subject with copeX.feat directories, where X is all your 1st level contrasts.
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, May 17, 2013 2:27 PM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: [FSL] Feat second level zstats maps
Hi,
I am planning an fMRI data analysis using FEAT. I want to look at a pre-post-intervention change between two groups that were trained under two different conditions. At each session, 5 runs of data were acquired. Roughly, what I am planning is to run a first-level and a second-level feat analysis and take the z-stats maps from the second level analysis to do a group x time analysis using randomise. I got stuck at the second level. Also, if there are objections to do this this way, I would appreciate any suggestions.
1. In the first-level feat analysis of individual runs, I set up standard preprocessing parameters and registered the functional data to MNI 1mm space via a high-resolution mprage. In the stats tab, I set up 1 EV for each predictor. In the contrasts, I set up 1 contrast for each EV and a few more additional contrasts to look at differences between conditions in my experiment.
2. In the second-level analysis, I used the lower-level feat directories as inputs. Under stats, I selected Mixed effects, FLAME1. In the Full model set up, I set up one EV (set to 0). This gave me only a zstat map for the COPE of my first EV, whereas I got only log and DoF files for the other 16 EVs. I tried to set up 17 EVs, but that gave me an error message. How do I get a zstat map for each of the COPEs or should I not do this this way at all?
Maren
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.
Can you post your .png and design.fsf files? Also, what exactly are the contents of the .gfeat/cope2.feat directory?
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>Date: Saturday, May 18, 2013 1:03 PM
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] Feat second level zstats maps
MarenHi,I tried both, fixed and mixed effects (EVs set as you wrote), but I stil lonly get one zstat map (for cope1).
On Sat, May 18, 2013 at 8:46 AM, Harms, Michael <[log in to unmask]> wrote:
Well, then I'm confused, because what you wrote that you did in your 2nd level analysis is not what I described to do. (i.e., use Fixed, not Mixed effects; and what is an EV set to 0?)
Did you use the "Inputs are lower level FEAT directories" setting on the Data tab?
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>Date: Friday, May 17, 2013 9:35 PM Subject: Re: [FSL] Feat second level zstats maps
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
That's what I did. It didn't give me a zstat map for each COPE, just for the first one. The question that I posted was how to get a zstat map for each on my COPEs.Maren
On Fri, May 17, 2013 at 6:32 PM, Harms, Michael <[log in to unmask]> wrote:
If you 2nd level analysis is just to effectively average the 1st level copes from the 5 runs in a given subject, then you should do a Fixed Effects Lev2 analysis using a single EV that is a column of 1's, and then you'll get a .gfeat directory for each subject with copeX.feat directories, where X is all your 1st level contrasts.
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, May 17, 2013 2:27 PM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: [FSL] Feat second level zstats maps
Hi,
I am planning an fMRI data analysis using FEAT. I want to look at a pre-post-intervention change between two groups that were trained under two different conditions. At each session, 5 runs of data were acquired. Roughly, what I am planning is to run a first-level and a second-level feat analysis and take the z-stats maps from the second level analysis to do a group x time analysis using randomise. I got stuck at the second level. Also, if there are objections to do this this way, I would appreciate any suggestions.
1. In the first-level feat analysis of individual runs, I set up standard preprocessing parameters and registered the functional data to MNI 1mm space via a high-resolution mprage. In the stats tab, I set up 1 EV for each predictor. In the contrasts, I set up 1 contrast for each EV and a few more additional contrasts to look at differences between conditions in my experiment.
2. In the second-level analysis, I used the lower-level feat directories as inputs. Under stats, I selected Mixed effects, FLAME1. In the Full model set up, I set up one EV (set to 0). This gave me only a zstat map for the COPE of my first EV, whereas I got only log and DoF files for the other 16 EVs. I tried to set up 17 EVs, but that gave me an error message. How do I get a zstat map for each of the COPEs or should I not do this this way at all?
Maren
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.
Can you post your .png and design.fsf files? Also, what exactly are the contents of the .gfeat/cope2.feat directory?
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>Date: Saturday, May 18, 2013 1:03 PM
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] Feat second level zstats maps
MarenHi,I tried both, fixed and mixed effects (EVs set as you wrote), but I stil lonly get one zstat map (for cope1).
On Sat, May 18, 2013 at 8:46 AM, Harms, Michael <[log in to unmask]> wrote:
Well, then I'm confused, because what you wrote that you did in your 2nd level analysis is not what I described to do. (i.e., use Fixed, not Mixed effects; and what is an EV set to 0?)
Did you use the "Inputs are lower level FEAT directories" setting on the Data tab?
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>Date: Friday, May 17, 2013 9:35 PM Subject: Re: [FSL] Feat second level zstats maps
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
That's what I did. It didn't give me a zstat map for each COPE, just for the first one. The question that I posted was how to get a zstat map for each on my COPEs.Maren
On Fri, May 17, 2013 at 6:32 PM, Harms, Michael <[log in to unmask]> wrote:
If you 2nd level analysis is just to effectively average the 1st level copes from the 5 runs in a given subject, then you should do a Fixed Effects Lev2 analysis using a single EV that is a column of 1's, and then you'll get a .gfeat directory for each subject with copeX.feat directories, where X is all your 1st level contrasts.
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: Maren Strenziok <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, May 17, 2013 2:27 PM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: [FSL] Feat second level zstats maps
Hi,
I am planning an fMRI data analysis using FEAT. I want to look at a pre-post-intervention change between two groups that were trained under two different conditions. At each session, 5 runs of data were acquired. Roughly, what I am planning is to run a first-level and a second-level feat analysis and take the z-stats maps from the second level analysis to do a group x time analysis using randomise. I got stuck at the second level. Also, if there are objections to do this this way, I would appreciate any suggestions.
1. In the first-level feat analysis of individual runs, I set up standard preprocessing parameters and registered the functional data to MNI 1mm space via a high-resolution mprage. In the stats tab, I set up 1 EV for each predictor. In the contrasts, I set up 1 contrast for each EV and a few more additional contrasts to look at differences between conditions in my experiment.
2. In the second-level analysis, I used the lower-level feat directories as inputs. Under stats, I selected Mixed effects, FLAME1. In the Full model set up, I set up one EV (set to 0). This gave me only a zstat map for the COPE of my first EV, whereas I got only log and DoF files for the other 16 EVs. I tried to set up 17 EVs, but that gave me an error message. How do I get a zstat map for each of the COPEs or should I not do this this way at all?
Maren
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.