[Freesurfer] contrast matrix

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I

[Freesurfer] contrast matrix

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1)

[Freesurfer] error in analyze command failed: mri_concat

Hello Freesurfer experts, I have got some problems with qdec. For testing my data i make an design with age, sexe and right and left hippocampus. The same design as the tutorial on the freesurfer wiki. When starting anlalyze i get an Error in Analyze: command failed: mri_concat

[Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi everyone, I recently switched the phase encoding direction of the functional sequence I've been using from F H to R L and ran into a problem with epidewarp.fsl (in version 4). The unwarping was still happening along the F H axis in the new images where phase encoding was R L.

[Freesurfer] bankssts label

Dear Freesurfers, Does anyone know why sometimes the bankssts (banks of the superior temporal sulcus) is only found in the sulcus, and sometimes occupies a sizeable part of an adjacent gyrus (superior temporal / inferior parietal)? The dark-green area is generally only visible in the inflated

Re: [Freesurfer] segmentation problem.

the intensity normalization has a region growing component that is bounded by intensity gradients. In images like MPRAGE, where SNR is traded for CNR it can help to raise the threshold for stopping so that more white matter is included (that's what the -b 20 does, I think the default it 10 or

Re: [Freesurfer] bad acquisition and noise problem.

what is the bandwidth? The typical way to fix it is to increase the bandwidth. You can probably recover some of the SNR you will lose by reducing your flip angle, which is pretty far from the Ernst angle. Also, minimize your TE (if 4ms is not already the min) cheers Bruce On Tue, 13 Nov 2012,

[Freesurfer] gstro...@ggmail.com, analysis-b...@nmr.mgh.harvard.edu

Hi Freesurferers or Experts, I have been trying to convert the watershed bem brain surfaces to vol with mri_fill and mri_surf2vol but not succeed. My main aim is to create mask for outer_skull, inner_skull and other from their respective surfaces. Is there any other method to use? Azeez Azeez

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi Clark, the phase encode direction is always lost since that information is not represented in the nifti header. epidewarp.fsl always assumes that the phase encode direction is in the row direction. doug On 11/13/2012 07:32 AM, Clark Fisher wrote: Hi everyone, I recently switched the phase

Re: [Freesurfer] error in analyze command failed: mri_concat

Hi Stan, can you run that mri_concat command from the terminal command line and send me the resulting terminal output? I've put the command below doug mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

hi doug, just to follow up on this. if i had the phase encode direction (we currently store various dicom attributes in a nifti header extension), where would i provide it? cheers, satra On Tue, Nov 13, 2012 at 11:27 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Clark, the phase

Re: [Freesurfer] contrast matrix

That contrast will do what you want but a more general one would be [1 -1 0 0 0 0 0 0 0 0 0 0] [0 0 0 1 -1 0 0 0 0 0 0 0] [1 0 -1 0 0 0 0 0 0 0 0 0] [0 0 0 1 0 -1 0 0 0 0 0 0] This will return positive if there is any difference between the genotypes regardless of gender. In your contrast, you

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

actually, I have no idea:). This is a wrapper around the FSL programs. I wrote the code always assuming that the phase encode direction was the row direction. Usually, it gets unpacked that way. Is the data getting reoriented along the way? doug On 11/13/2012 11:34 AM, Satrajit Ghosh wrote:

Re: [Freesurfer] gstro...@ggmail.com, analysis-b...@nmr.mgh.harvard.edu

Hi Azeez, try using mris_fill. cheers Bruce On Tue, 13 Nov 2012, Azeez Adebimpe wrote: Hi Freesurferers or Experts, I have been trying to convert the watershed bem brain surfaces to vol with mri_fill and mri_surf2vol but not succeed.  My main aim is to create mask for outer_skull,

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

I'm a little confused as to why the rows are not the phase encode direction to begin with. What did you use to convert the dicoms to nifti? doug On 11/13/2012 11:59 AM, Clark Fisher wrote: Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before

Re: [Freesurfer] volume conversion problem

Yes, the problem is rawavg.mgz. When was it created? How many runs do you have in this data set? You can also try using your input volume subject/mri/orig/001.mgz (or what ever it is called). If you only have one run, then rawavg.mgz should just be a copy of 001.mgz doug On 11/12/2012 11:54

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious though. On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote: I'm a little confused as to why the rows are not the phase encode direction to begin with.

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi Clark, hi Doug fugue has an option that might help here. Here is the relevant excerpt rom calling fugue on the command line (as in fugue of fsl 5.0.1 but I am sure this was also present in fsl 4.1.n): --unwarpdirspecifies direction of warping [x/y/z/x-/y-/z-] (default y) it seems that

Re: [Freesurfer] Qdec - longitudinal. File missing

Hello Martin, thanks again for your help. We created the .Qdecrc file in the qdec directory. It still gives the same error. Also we made some changes to the .Qdecrc file, for example we changed the ...long.thickness.. to ...long-thickness..., but the error remaines the same. We performed

Re: [Freesurfer] bankssts label

Hi Vincent, sorry, I'm not sure. This is an area that Ron Killiany and Marilyn Albert had found sizable effects in prodromal AD patients, which is why Ron included it in his parcellation, but I'm not sure how they decided the extent and location of it. You could email Rahul Desikan and ask him

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

I guess it is possible that Siemens is doing something funny with the images. I've never used sagittal before. On 11/13/2012 12:51 PM, Clark Fisher wrote: I'm using a script that calls unpacksdcmdir. Maybe there is some setting in our config file that forces the orientation? Nothing obvious

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl

Hi Doug, All other things being equal, if you switch from AP to RL phase encoding in an axial acquisition, then the PE direction will switch from the y-axis to the x-axis in the images. It doesn't really have anything to do with Siemens, since the images are written out in a standard anatomical

[Freesurfer] Subgenual ACC - part of the Desikan rostral ACC?

Hello all - I'm unclear on whether the subgenual ACC gets included in the rostral ACC when running parcellations from the Desikan atlas. From the Desikan paper's description and images, it appears to me that the rACC area curves under the genu of the CC and that the caudal boundary there at the

Re: [Freesurfer] Subgenual ACC - part of the Desikan rostral ACC?

Rahul? On Tue, 13 Nov 2012, Amanda Schlesinger wrote: Hello all - I'm unclear on whether the subgenual ACC gets included in the rostral ACC when running parcellations from the Desikan atlas. From the Desikan paper's description and images, it appears to me that the rACC area curves under

Re: [Freesurfer] Qdec - longitudinal. File missing

Hi Martin, Yes, that's it, I wasn't changing the Measure in the Design tab ! Thank you very much for the advice and support ! Sincerely, Alex Le 13/11/2012 3:41 PM, Martin Reuter a écrit : Hi Alex, just tested it with our dev version and it works for me. When you setup the subjectsdir

Re: [Freesurfer] bad acquisition and noise problem.

I'm not engaged in obtaining images, so I don't have any details about the images. I wonder the method which you commented can be applied to images I already earned. If it's not, is there any way to recover SNR after image scanning? Thanks, Youngmin Huh. 2012/11/13 Bruce Fischl

Re: [Freesurfer] bad acquisition and noise problem.

it's not a question of SNR, the problem appears to me to be that the B0 distortions are so bad that a bunch of the temporal lobe is piled up on top of itself. There's no way to fix that posthoc. If you upload the full volume I'm happy to take a look On Wed, 14 Nov 2012, youngmin huh wrote:

[Freesurfer] Fwd: bad acquisition and noise problem.

-- Forwarded message -- From: youngmin huh ymin1...@gmail.com Date: 2012/11/14 Subject: Re: bad acquisition and noise problem. To: Bruce Fischl fis...@nmr.mgh.harvard.edu Thanks for your comment. I would appreciate if you could take a look. Do you want a whole folder of the

Re: [Freesurfer] aparc+aseg voxels labeled as unknown

What is the aseg label for them? On Nov 13, 2012, at 4:30 PM, Nikhil Chandra nsc2...@columbia.edu wrote: Hello, After completing the FreeSurfer Recommended Reconstruction, we have noticed that in aparc+aseg, many subjects exhibit small clusters of voxels in the medial temporal lobe