[Freesurfer] Freeview question: using "line profile"

[Albrecht, Daniel S.]

Hello,

I'm having trouble using the "line profile" tool in FreeView. I have a PET 
image overlaid on an MR image, and would like to view a line profile of a 
rectangular ROI on the PET image. I assumed that the "line profile" selection 
in "Tools" would be able to do this, but I haven't been able to get it to work 
and haven't been able to find any documentation on using the tool. Can anyone 
provide any information on this? Thanks,

Dan
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Re: [Freesurfer] Freeview question: using "line profile"

[Albrecht, Daniel S.]

Ok thanks! I was using control points previously, I think that was my problem.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Ruopeng Wang 
[rpw...@nmr.mgh.harvard.edu]
Sent: Wednesday, January 14, 2015 5:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freeview question: using "line profile"

I think you need to create 2 sets of way points as iso-lines. You can do that 
from File -> New Point Set and select 'way point'. Then you should be able to 
use the line profile tool.

On 01/14/2015 04:55 PM, Albrecht, Daniel S. wrote:
Hello,

I'm having trouble using the "line profile" tool in FreeView. I have a PET 
image overlaid on an MR image, and would like to view a line profile of a 
rectangular ROI on the PET image. I assumed that the "line profile" selection 
in "Tools" would be able to do this, but I haven't been able to get it to work 
and haven't been able to find any documentation on using the tool. Can anyone 
provide any information on this? Thanks,

Dan



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[Freesurfer] Using FSL commands through Matlab (Linux)

[Albrecht, Daniel S.]

Hello,

Sorry if this isn’t the right forum for the question, but not sure where to 
direct it.

I’m trying to incorporate some FSL commands into a Matlab script. I’m using a 
Linux machine and running Matlab 7.11.0 (2010b). I tried to access the FSL 
toolbox through Matlab using:

setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
system(‘${FSLDIR}/etc/fslconf/fsl.sh’)

But received a “permissions denied” error. Is there an easier way to access FSL 
through Matlab?

Thanks,

Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging

Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
dsalbre...@mgh.harvard.edu
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[Freesurfer] Spmregister issues

[Albrecht, Daniel S.]

Hello,

I've been using spmregister in order to coregister a static PET image to an 
MPRAGE, typically with good results. A representative run is as follows:

spmregister --mov $file.nii --s $subj --reg SUV_lin_T1.dat --fsvol orig

We then convert *.dat to *.mat with tkregister2, and apply the *.mat to the PET 
with FLIRT.

However, the registration was unsatisfactory for a recent subject. While 
working through a couple different coregistration options, I tried running 
coregister (estimate and reslice) in SPM. The result from this was quite good.
I was confused why this would give a different result from spmregister when I'm 
not changing any of the default parameters in SPM. Any ideas on why running a 
coregistration directly through SPM would give a different result?

And as a secondary follow-up, are there any tools available to convert an SPM 
transformation matrix (e.g. x from x=spm_coreg) to a *.mat that can be used in 
FSL FLIRT?

Thanks,

Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging

Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
dsalbre...@mgh.harvard.edu
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[Freesurfer] Automated extraction of dural/meningeal ROI?

[Albrecht, Daniel S.]

Hello,

We have a PET dataset where we expect to see pathogenic changes in the 
meninges. We'd like to extract the meningeal signal in subject space, and were 
hoping to come up with an automated strategy to create meningeal ROIs, 
containing no brain or scalp.
So my question is: can you suggest any way within the FreeSurfer pipeline that 
we can create a meningeal-only ROI, or alternatively an ROI containing both 
skull and meninges, but still no scalp or brain?

Your help is greatly appreciated!

Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging

Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
dsalbre...@mgh.harvard.edu
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[Freesurfer] Extraction of cortical thickness in native space

[Albrecht, Daniel S.]

Hello,


We are attempting to extract cortical thickness values from a pre-defined ROI 
in MNI space.


Originally, we had followed the instructions detailed here:

https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

for extraction in MNI space, but now wanted to extract thickness from 
individual subject T1 images in native space.


We attempted to use the same pipeline (e.g. register native space T1 to 
fsaverage) but were unable to get a good registration with several different 
tools.


Is there a better way to do this, either by improving the registration to 
fsaverage, or by transforming the ROI to native space (which we have done) and 
projecting that to a surface/label?


Any suggestions are welcome, and we appreciate the help!


Cheers,


Dan

VolumeRoiCorticalThickness - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Cortical Thickness of a Volume-defined ROI. This page describes the workflow to 
extract freesurfer cortical thickness values for a region-of-interest (ROI) 
defined in ...



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Re: [Freesurfer] Extraction of cortical thickness in native space

[Albrecht, Daniel S.]

Thanks, Doug!


I think we were probably going about this the wrong way. If I transform the ROI 
from MNI space back into native space, will the following commands give the 
proper cortical thickness extraction from native space?

mri_vol2surf --mov roi_in_native_space.nii.gz --out rh.roi_in_native_space.mgh 
--hemi rh --regheader ${subj}

#Check surface placement with:
tksurfer ${subj} rh inflated -overlay rh.roi_in_native_space.mgh -fthresh 1

cd $FSdir/$subj/surf
mri_segstats --seg /path_to rh.roi_in_native_space.mgh --in rh.thickness --sum 
segstats-rh.roi_ns.txt

Thanks,


Dan

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[Freesurfer] mri_gtmpvc with amended aparc+aseg

[Albrecht, Daniel S.]

Hello,

I’ve been using PETSurfer for partial volume correction of PET images using the 
RBV option. I’m amending the parcellations/segmentations to add in 
extracortical areas of high PET signal (to prevent spill-in into the brain), 
and after adjusting the *ctab file this runs successfully.

However, I noticed the output resolution of the rbv.nii.gz image is the same as 
the input segmentation mask, not the expected 0.5mm iso. I’ve run a test 
incorporating the --rbv-res 0.5mm flag into the command line. The output 
rbv.nii.gz image is similar to the previous one (without the –rbv-res flag), 
again not as smooth as the typical output image.

Is it satisfactory to run the command with my amended seg image and the 
--rbv-res 0.5mm flag, and are there any additional recommendations for running 
PVC with an amended seg image?

Thanks very much,

Dan

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[Freesurfer] mri_surf2vol -lost cluster

[Albrecht, Daniel S.]

Hello everyone,

I've been using mri_vol2surf to move some activation data in MNI space to the 
fsaverage surface with the following command:

mri_vol2surf --mov MNIvol.nii --projfrac-max 0 1 0.1 --hemi rh --o rh.out.mgz 
--mni152reg

This works well, but I'm losing a small temporal gyrus cluster that sits close 
to pial surface. I was assuming this was due to the proximity to the pial 
surface and resampling, but are there any other options or flags I could use to 
get this to project successfully?

Thanks very much,

Dan
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