[Freesurfer] finding closest vertex in matlab

Hi Freesurfers, I have talairach coordinates of electrodes sitting on the brain. I am hoping to use the Desikan-Killiany parcellation scheme to determine which cortical region each electrode lies closest to in standard space. I am using read_annotation in matlab to read the lh.aparc.annot file and

[Freesurfer] which files for thickness and volume stats?

Hi all, I'm wondering which files I should use to find volumetrics data... I need cortical thickness (whole-brain and each hemisphere), GM/WM volumes (cortical) and whole brain volume. I know about asegstats2table but I read that aseg isn't that reliable for WM/GM. What's the difference between

Re: [Freesurfer] Problem registering labels to native space

In that case, try this instead doug # Create a register.dat to fsaverage/mni305 cd $SUBJECTS_DIR/subject/mri tkregister2 --s subject --targ orig.mgz \ --ixfm transforms/talairach.xfm --zero-cras \ --reg transforms/talairach.reg.dat \ --mov $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz \

Re: [Freesurfer] Problem registering labels to native space

Hi Doug, this is indeed an fsfast analysis. I used the fsaverage subject included with the 5.1 distribution. Here is the code that I used to produce the registration matrix for one subject. Note that I did use mri_convert to change the .mgz files into .nii.gz The use of flirt (below) is more of

Re: [Freesurfer] thickness measurement workflow & tksurfer sliver

Hi, I found this - http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis, just after mailing the group. I hope going through and the tutorial on QDEC this will help my cause. Thanks, Jaichander On Mon, Jul 18, 2011 at 3:45 PM, Jaichander S wrote: > Hi freesurfers, > > 1. I am a new

[Freesurfer] re-running recon-all failing

hi all, i'm trying to rerun some subjects processed with 5.0 with 5.1 and am getting the following error on all the subjects. simply executing recon-all -s subjid -all any ideas? cheers, satra -- unfolding failed - restoring original position 0750: dt=0.001250, r

[Freesurfer] thickness measurement workflow & tksurfer sliver

Hi freesurfers, 1. I am a new user of freesurfer. I want to measure,compare cortical thickness in corresponding regions of the cortex in a group of subjects. Is there a description of steps involved in doing this? >From what I have read till now, I know that I can create ROIs and use the instruct

Re: [Freesurfer] Problem registering labels to native space

How did you create it? What is the actual "fsaverage space"? Is this an FSFAST analysis? doug John Richey wrote: > Hi Doug, the .dat file that I mention below had already been converted into > a fs matrix using tkregister2. > > -Original Message- > From: Douglas N Greve [mailto:gr...@n

Re: [Freesurfer] longitudinal version

Hi Natalia, I have never tried it, but don't see a reason why it should not work. Just try it out. Best Martin On Jul 18, 2011, at 5:13 AM, Natalia h wrote: > Dear list, > > I have a question about the longitudinal stream´s version. > I used Freesurfer 4.5 and followed the longitudinal tutor

Re: [Freesurfer] Problem registering labels to native space

Hi Doug, the .dat file that I mention below had already been converted into a fs matrix using tkregister2. -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 12:38 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] FreeSurfer Error during Fix Toplogy

try looking at the ?h.inflated.nofix to see what the big defect is and we can go from there. cheers Bruce On Mon, 18 Jul 2011, Kevin Liu wrote: Hi, I'm relatively new to the FreeSurfer program and have mostly worked with processing adult brains. I am currently working on reconstructing image

Re: [Freesurfer] FreeSurfer Error during Fix Toplogy

Did you check to see whether the cerebellum (or some large bit of skull or brain stem) are still attached? doug Kevin Liu wrote: > Hi, > > I'm relatively new to the FreeSurfer program and have mostly worked > with processing adult brains. I am currently working on reconstructing > images of you

Re: [Freesurfer] FreeSurfer Error during Fix Toplogy

Hi Kevin when you say it hangs, how long do you wait? That is a pretty big defect (7785 vertices, probably 5% of the surface). You can look at the inflated.nofix surface and try to manually correct the defect. The time the topology correction takes goes up as the square of the defect size, so

Re: [Freesurfer] Problem registering labels to native space

You can't use a flirt matrix with mri_label2label. You can convert a flirt matrix to the proper format with tkregister2 using the --fsl option (this will allow you to check the reg as well). doug John Richey wrote: > Hi Bruce, > > The labels that I have fsaverage space are 3D/volume-based and

[Freesurfer] FreeSurfer Error during Fix Toplogy

Hi, I'm relatively new to the FreeSurfer program and have mostly worked with processing adult brains. I am currently working on reconstructing images of young children under 5 and am consistently running into the same error for the two subjects I am running during mris_fix_topology. The error is a

Re: [Freesurfer] Problem registering labels to native space

Hi Bruce, The labels that I have fsaverage space are 3D/volume-based and not surface-based labels. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 12:00 PM To: John Richey Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurf

Re: [Freesurfer] Problem registering labels to native space

Hi John why are you using an affine volume registration for fsaverage? Why not use surface registration? Bruce On Mon, 18 Jul 2011, John Richey wrote: > Hi Bruce - thanks for the reply. > > Here is my command line: > > mri_label2label --srcsubject fsaverage \ > --trgsubject ${SUBJECT} > --src

Re: [Freesurfer] Problem registering labels to native space

Hi Bruce - thanks for the reply. Here is my command line: mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ --regmethod volume \ --reg $SUBJECTS_DIR/$S

Re: [Freesurfer] Problem registering labels to native space

Hi John can you email us your label2label cmdline? cheers Bruce On Mon, 18 Jul 2011, John Richey wrote: > Dear freesurfer experts, > > I have a series of labels corresponding to clusters of significant > activation in fsaverage space. > > I want to map these back to native space using mri_lab

[Freesurfer] Problem registering labels to native space

Dear freesurfer experts, I have a series of labels corresponding to clusters of significant activation in fsaverage space. I want to map these back to native space using mri_label2label, however when I view the individual (native) labels, the registration is way off and the labels do not map in

[Freesurfer] longitudinal version

Dear list, I have a question about the longitudinal stream´s version. I used Freesurfer 4.5 and followed the longitudinal tutorials (the tutorials "before" June 2011) for my data. I saw on the updated version, there are scripts which can do the post-process longitudinal data, like long_mris_slopes