[Freesurfer] mri_vol2surf sampling higher resolution

Dear Freesurfer, I have created a ribbon in high resolution like 0.5 x 0.5 x 0.5 mm^3 I selected some of those voxel in the high-res ribbon file. Then I wanted to create a paint file out of volume in that resolution on white or pial. I used the tkregister to register the high-res ribbon file to

Re: [Freesurfer] mri_vol2surf sampling higher resolution

Try using --projfrac 0.5 (halfway into the ribbon). --projfrac 1 samples at the pial, and it may be that you don't have any voxels there. Still, one would expect a few hits. Also, the paint (w) format is pretty old. Consider using mgh format or gifti. doug On 1/16/13 9:55 AM, Rouhollah

[Freesurfer] separate FSAverages and surface-based ROIs

Hello, I have two issues, currently. First, I was wondering if it would be possible to create separate FSAverage brains for different subject groups. I am working with healthy seniors and various stages of Alzheimer's disease, so doing so would be very helpful from the perspective of not

Re: [Freesurfer] separate FSAverages and surface-based ROIs

Hi Paul, On 01/16/2013 10:27 AM, Paul Beach wrote: Hello, I have two issues, currently. First, I was wondering if it would be possible to create separate FSAverage brains for different subject groups. I am working with healthy seniors and various stages of Alzheimer's disease, so doing

[Freesurfer] Error with mri_vol2surf

Hi Freesurfers, Sorry if this is a newbie question. I receive the following error when I use mri_vol2surf to assign values from a subject volume file to each surface vertex and cant fix this ... mris_preproc command exits w/o errors in a previous step: mris_preproc --s AC066 --target fsaverage

[Freesurfer] Speeding up mris_fix_topology

Hello all, I'm processing some high resolution data with an isotropic resolution of 0.5mm and I was wondering if it would be possible to speed up mris_fix_topology somehow. Due to the increased number of vertices and also increased number of defects this stage takes incredibly long (e.g. lots

Re: [Freesurfer] Error with mri_vol2surf

Does /volstat/AC066-rh-volume.mgh exist? what happens when you run ls -l /volstat/AC066-rh-volume.mgh doug On 01/16/2013 11:00 AM, Shantanu Ghosh wrote: Hi Freesurfers, Sorry if this is a newbie question. I receive the following error when I use mri_vol2surf to assign values from a subject

Re: [Freesurfer] Speeding up mris_fix_topology

Hi Bruce, so you use the conformed and fixed ?h.orig during mris_make_surfaces on the .5mm data? Never thought of that. Best, Falk Original-Nachricht Datum: Wed, 16 Jan 2013 11:16:45 -0500 (EST) Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Falk Lüsebrink

Re: [Freesurfer] Speeding up mris_fix_topology

yes On Wed, 16 Jan 2013, Falk Lüsebrink wrote: Hi Bruce, so you use the conformed and fixed ?h.orig during mris_make_surfaces on the .5mm data? Never thought of that. Best, Falk Original-Nachricht Datum: Wed, 16 Jan 2013 11:16:45 -0500 (EST) Von: Bruce Fischl

[Freesurfer] Cortical thickness analysis using *.nii files

Dear members, I am new to Freesurfer and to cortical thickness analysis so I would like to ask a very basic question that I cannot find the answer to online - is it possible to conduct cortical thickness analysis using T1 files in *.nii format? -- Sinead Kelly Neuropsychiatric Genetics Group

Re: [Freesurfer] Cortical thickness analysis using *.nii files

Hi Sinead, sure, just give recon-all the .nii as input with -i instead of the dicoms and you should be all set. cheers Bruce On Wed, 16 Jan 2013, Sinead Kelly wrote: Dear members, I am new to Freesurfer and to cortical thickness analysis so I would like to ask a very basic question that

[Freesurfer] Freesurfer vertex wise area reference

Dear Experts, What references can I use in a write up for the use of area measures in both vertex wise GLM and ROI based analyses. I have looked at the recommended citation blurb on the website but see nothing about specific references for area. I am using FS v5.1 with the modified mris_

[Freesurfer] nu_correct problem

Dear members, when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu _correct. This happens for DICOM but also IMA file type. I tried several brains. Do you have any idea what is wrong? Thanks much, Petr Zach ___ Freesurfer

Re: [Freesurfer] nu_correct problem

Hi Petr, Can you provide us with some more details? Which version of FreeSurfer are you using and on what platform? Could you attach a copy of the recon-all.log file for one of these cases so we can read the full error reported? Have you tried looking at the orig.mgz which is generated

[Freesurfer] [Fwd: Re: Error with mri_vol2surf]

Original Message Subject: Re: [Freesurfer] Error with mri_vol2surf From:Shantanu Ghosh shant...@nmr.mgh.harvard.edu Date:Wed, January 16, 2013 2:05 pm To: Douglas N Greve gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] separate FSAverages and surface-based ROIs

The annotation is the name we give to a surface segmentation (eg, lh.aparc.annot). You can break lh.aparc.annot into its constituent label files. You can then replace the insula label file with posterior and anterior labels that you create. You can then recombine the labels back into a new

Re: [Freesurfer] A question regarding volume calculation

No, the subcortical calculation sums the number of voxels. For voxels on the edge of a structure, there is a partial volume calculation based on the intensity of the voxel and the mean intensities of the adjacent structures. doug On 01/16/2013 05:52 PM, KimMJ wrote:

[Freesurfer] Freesurfer vertex wise area reference

Hi, Sorry to be a little more specific - I am aware of freesurfer area references such as the WInkler reference but basically wanted a few lines, and the most appropriate references, that summarises the technical approach used for group area comparisons in qdec (using updated mris_preproc),