Phillips lab - Revision history

imported>Nmp: /* Cross Group Analysis from fsl to full brain image */

2013-07-16T17:43:57Z

Cross Group Analysis from fsl to full brain image

← Older revision		Revision as of 17:43, 16 July 2013
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	See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].		See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].

			For final reconstruction stage: need to go to new folders (see Russ's new code)

			In fsl, in the anatomy directory, there should be a folder “fs average”
			The overlays should come from the the group overlays.
			Use the average t1 and average surfaces from this folder.
			Can use fs-average mgh files.

	===Calculating Threshold for Reconstructed Data based on False Discovery Rate (FDR)===		===Calculating Threshold for Reconstructed Data based on False Discovery Rate (FDR)===

imported>Nmp: /* Calculating Threshold for Reconstructed Data based on False Discovery Rate (FDR) */

2013-07-16T17:40:44Z

Calculating Threshold for Reconstructed Data based on False Discovery Rate (FDR)

← Older revision		Revision as of 17:40, 16 July 2013
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	===Calculating Threshold for Reconstructed Data based on False Discovery Rate (FDR)===		===Calculating Threshold for Reconstructed Data based on False Discovery Rate (FDR)===

			False Discovery Rate (FDR) is a new approach to the multiple comparisons problem. Instead of controlling the chance of any false positives (as Bonferroni or random field methods do), FDR controls the expected proportion of false positives among suprathreshold voxels. A FDR threshold is determined from the observed p-value distribution, and hence is adaptive to the amount of signal in your data.
			FDR is more sensitive than traditional methods simply because it is using a more lenient metric for false positives. However, if there is truly no signal anywhere in the brain, a FDR-controlling method has the same control as standard methods. That is, if the null hypothesis is true everywhere, a FDR procedure will control the chance of a false positive anywhere in the brain at the specified level.

			Anywhere between 1% and 10% is considered reasonable for FDR

			Suggested 5%

			FDR relevant links:
			http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDR
			https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferWorkingWithData/TkSurferOverlay

			Setting threshold in tksurfer:
			View → configure → overlay
			Use value of .05 (aka 5%)
			https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferWorkingWithData/TkSurferOverlay

			You can’t do fdr directly on cope files; you have to convert them to p files
			You need to create an image where each voxel is a p-value...

			Right now, our Cope files are the log 10 of p, as directed by tk surfer -- it makes more sense to view the log 10 of p, but when doing actual analysis, we must do the actual p. This will spit out your p-value threshold. (You could then do the log 10 of that if you wanted to.)
			http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDR
			All you should need, really, is the p-value image.
			We’ll have to go back to the nifti format files to get this.

			There’s an FDR tool in freesurfer that may be easier to use; you just run it in the command line

	=Lab Equipment Notes=		=Lab Equipment Notes=

imported>Nmp: /* Data Analysis Notes */

2013-07-16T17:39:11Z

Data Analysis Notes

← Older revision		Revision as of 17:39, 16 July 2013
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	See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].		See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].

			===Calculating Threshold for Reconstructed Data based on False Discovery Rate (FDR)===

	=Lab Equipment Notes=		=Lab Equipment Notes=

imported>Nmp: /* Cross Group Analysis */

2013-04-03T20:29:39Z

Cross Group Analysis

← Older revision		Revision as of 20:29, 3 April 2013
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	===Cross Group Analysis===		===Cross Group Analysis===

			I think this is old (update?)

	Go into fsl		Go into fsl

imported>Nmp: /* Data Analysis Notes */

2013-04-03T20:08:34Z

Data Analysis Notes

@@ Line 31: / Line 31: @@
      Linux: cd Documents/nmp-data
      To View Data for s01 to s18: ./runViewer.sh [s01] [regular/flipped] [pial/inflated]
 ===Parse the PsychoPy log file===

imported>Nmp: /* Cross Group Analysis from fsl to full brain image */

2013-04-03T18:50:54Z

Cross Group Analysis from fsl to full brain image

← Older revision		Revision as of 18:50, 3 April 2013
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	If you use fslhd, give it one file, it'll give you the information about that one file. You have to RUN THIS FIRST to figure out how many time points there are. Then command (1) will allow us to crop things out.		If you use fslhd, give it one file, it'll give you the information about that one file. You have to RUN THIS FIRST to figure out how many time points there are. Then command (1) will allow us to crop things out.

			"dim4" is the only thing we care about -- this is the length of the 4th dimension. It will be some number. That's how many time points there are for that subject. So you'll tell fslroi to start at frame 10, say, and then you keep "total minus 10" -- this lets you keep total minus the first ten. If you tell it to start at frame 10 and keep "total minus 20" you'll keep the total minus the first ten and the last ten. Natalie: "cutting ten would mean cutting 20 seconds."

			Doing this cropping means you'll have to change all the other stuff we ran. (?) Refer back to Psychopy. Keep in mind that people are reading at different speeds. We may have to rerun all of the psychopy versions that would then be entered.

	Bob recommends going through the fsl course. Take a good tutorial. In fsl support, select fsl course.		Bob recommends going through the fsl course. Take a good tutorial. In fsl support, select fsl course.

imported>Nmp: /* Cross Group Analysis from fsl to full brain image */

2013-04-03T18:47:31Z

Cross Group Analysis from fsl to full brain image

← Older revision		Revision as of 18:47, 3 April 2013
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	2.) fslhd fmri_all.nii.gz		2.) fslhd fmri_all.nii.gz

			If you use fslhd, give it one file, it'll give you the information about that one file. You have to RUN THIS FIRST to figure out how many time points there are. Then command (1) will allow us to crop things out.

	Bob recommends going through the fsl course. Take a good tutorial. In fsl support, select fsl course.		Bob recommends going through the fsl course. Take a good tutorial. In fsl support, select fsl course.

imported>Nmp: /* Cross Group Analysis from fsl to full brain image */

2013-04-03T18:45:24Z

Cross Group Analysis from fsl to full brain image

← Older revision		Revision as of 18:45, 3 April 2013
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	So for those coordinates, on the right it's millimeters, and on the left it's voxels. The intensity is a number "stored" in the voxel. It's for the statistical map. This is the result. This is what's being mapped in black and white. So if it's negative it's black, etc. (See above.) To reiterate: the intensity will later be correlated to our brain activity; after a threshold is applied, regions of certain intensity will be red and others will be blue, etc. It's all here in the raw data.		So for those coordinates, on the right it's millimeters, and on the left it's voxels. The intensity is a number "stored" in the voxel. It's for the statistical map. This is the result. This is what's being mapped in black and white. So if it's negative it's black, etc. (See above.) To reiterate: the intensity will later be correlated to our brain activity; after a threshold is applied, regions of certain intensity will be red and others will be blue, etc. It's all here in the raw data.

			Again: Positives are non-thresholded raw data where there is more bloodflow (our comparison) for close v pleasure reading. And negatives are places where there's more activity for pleasure reading.

			If we opened cope2, we'd be seeing the same thing, but for reading vs. not reading rather than close vs. pleasure.

			What Russ needs to do is get into these cope files.

			Bob:

			There are two ways to map group data onto a surface. They're two versions of the same method, essentially. Basically, you have to take the individual subjects analyses; there's a command in the tutorial that has you map them to the group space; there's one command that will generate the group average statistical map.

			Natalie:

			I will send those tutorials to Russ. What I understand is... I need to think of fsl and freeview as two separate things. Freeview needs to be able to not just access group information, but also access the cope files, because these have the raw data for each individual subject for cross group analysis. We did fsl and got our group analysis, which got us a cope file for group analysis.

			Bob:

			This tutorial thing won't use the fsl group average cope file. The tutorial will show you how to create an average using freesurfer tools. It's the same idea as fsl -- you give it all the cope files for individual subjects, and then there's one command that will [...].

			Natalie:

			Talking about cropping the beginning and the end of scans... We know time course data isn't all that reliable for just that one voxel. Is there a way to get time course data for an "average" voxel?

			Command line:

			Terminal --> fslroi

			This will let you crop in time.

			We want to crop the fsl to feat. We're cropping off time. The input is a 4-dimensional data set: 3 spatial plus time. We don't want to crop anything in space, so... Bob suggests we take some time to use fslview to view the "fmri all" input. Get used to fslview and play around with it. It lets you see space, but it also lets you click through the different time points. Then try this fslroi; you're going to have to crop a different amount from each subject -- you'll want to crop the same time points, but each subject has a different length, because people read at different speeds.

			Bob:

			One example command: If you don't want to crop in space, you would use these two commands.

			1.) fslroi fmri_all.nii.gz fmri_all_cropped.nii.gz 0 -1 0 -1 0 -1 10 80

			2.) fslhd fmri_all.nii.gz

			Bob recommends going through the fsl course. Take a good tutorial. In fsl support, select fsl course.



	See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].		See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].

imported>Nmp: /* Cross Group Analysis from fsl to full brain image */

2013-04-03T18:27:13Z

Cross Group Analysis from fsl to full brain image

← Older revision		Revision as of 18:27, 3 April 2013
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	- Type fslview cope1.nii.gz		- Type fslview cope1.nii.gz

			So now we should have opened fslview and are able to see some brain images.

			The crosshairs isolate a voxel. Each voxel has a location, mapped by xyz coordinates. Each voxel has a number.

			White means positive numbers, gray means zero, and black means negative numbers.

			So for those coordinates, on the right it's millimeters, and on the left it's voxels. The intensity is a number "stored" in the voxel. It's for the statistical map. This is the result. This is what's being mapped in black and white. So if it's negative it's black, etc. (See above.) To reiterate: the intensity will later be correlated to our brain activity; after a threshold is applied, regions of certain intensity will be red and others will be blue, etc. It's all here in the raw data.
	See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].		See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].

imported>Nmp: /* Cross Group Analysis from fsl to full brain image */

2013-04-03T18:21:03Z

Cross Group Analysis from fsl to full brain image

← Older revision		Revision as of 18:21, 3 April 2013
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	Special instructions:		Special instructions:

	- Open terminal		Open terminal
	- Type cd /
	~~- type~~ ls		Type cd /
	- Type cd Volumes
			ype ls

			Type cd Volumes

	- Type cd lc		- Type cd lc

	- Type cd nmp-data		- Type cd nmp-data

	- Type cd nmp-subjects-original		- Type cd nmp-subjects-original

	- Type cd s01		- Type cd s01

	- Type cd regular.feat		- Type cd regular.feat

	- Type cd stats		- Type cd stats

	- Type fslview cope1.nii.gz		- Type fslview cope1.nii.gz


	See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].		See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer freesurfer/FSL tutorial] and the [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer relevant FSL wiki page].