Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

FreeSurferColorLUT for FSL
by Nasim Maleki 17 Nov '09

17 Nov '09

Dear all, I would like to view the aparc.a2009s+aseg files in FSL and therefore I need to make LUTs for FSL from the FreeSurferColorLUT. I was just curious to know if any of you has ever done this and if there is an easy way around it. Thanks for your help in advance, Nasim

2 1

reply
by Jared Price 17 Nov '09

17 Nov '09

Doug, I tried mri_vol2vol --mov .../orig/001.mgz --targ ...orig/001.mgz --regheader -o ... This created a volume but the same issue remained. When I load a segmentation on top of the created volume, tkmedit won't let me alter the segmentation. If I use "new segmentation" as opposed to loading a previous segmentation (e.g. the aseg.mgz volume) then the segmentation works fine. Anyway, what I would like to do is put a volume as similar to the original dicoms as possible upon which a manual segmentation can be performed in tkmedit. Any other thoughts? Jared

2 1

extract aparc.anot area
by simon 17 Nov '09

17 Nov '09

Hi everyone, I need to draw Heschl gyri on freesurfer pial surface of my subjects but its not easy because this area is not directly visible. So: 1. Is there a simple mean to cut the surface to see more internal areas with freesurfer tools (or other???) ? 2. Is it possible to extract only desired areas from the aparc.annot.a2005s files and how to modify them manually? Thanks Grégory SIMON

2 1

moving 001.mgz to anatomical space
by Jared Price 17 Nov '09

17 Nov '09

.... I see the mistake I made. Works well now. Thanks for the help. Jared

1 0

follow-up
by Jared Price 17 Nov '09

17 Nov '09

...Also, I should mention that slice thickness in the MRI acquisition sequence was 1.3 mm so the native voxels are not 1x1x1.

1 0

?h CC_* volumes
by Freesurfer Local Archive 16 Nov '09

16 Nov '09

Dear Freesurfers, I was wondering if there is any way to compute volumes of the CC_* callosal patitions separately for left and right hemispheres? I noticed that there are separate labels for the left and right lateral portions of the corpus callosum (e.g. ctx-lh-corpuscallosum vs. ctx-rh-corpuscallosum and wm-lh-corpuscallosum vs. wm-rh-corpuscallosum) but not for the CC_* callosal partitions. Thank you in advance for all your help. -gerard

2 1

reply
by Jared Price 16 Nov '09

16 Nov '09

I guess I am not entirely sure what the contrast properties of orig.mgz are. After looking at the recon-all DevTable I don't see anything that explicitly mentions any intensity normalization occurring before this point so I imagine it would work. I guess I will just ask you for your suggestion. For this particular task I would like the grayscale image to be as close to the original dicom images as possible with perhaps the one exception of reslicing. Jared

3 2

manually segment with 001.mgz as main volume?
by Jared Price 16 Nov '09

16 Nov '09

Hi all, I want to do a manual segmentation of the putamen in tkmedit, but rather than using brainmask.mgz as the main volume, I wanted to use 001.mgz. This is because the intensity normalization step can in certain cases brighten lighter areas of the putamen to 110. Anyway, when I load the 001.mgz volume it will allow me to load a segmentation on top of it, but it won't allow me to modify the segmentation. In other words, I load a segmentation volume and configure the segmentation brush but it won't respond whenever the 001.mgz file is loaded. Anyone know why, or know a workaround? Jared

3 2

(no subject)
by Dalwani, Manish 16 Nov '09

16 Nov '09

Hi All, I am getting the following error after running the simulation script generated by QDEC. ERROR: dimension mismatch between X and contrast /usr/local/freesurfer/subjects/ qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has 2 cols, C has 6 cols Kindly advise! Regards, Manish

2 1

(no subject)
by Dalwani, Manish 16 Nov '09

16 Nov '09

2 1

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