[Freesurfer] preproc-sess error with -per-session flag

Dear Freesurfers, I ran into an issue while trying to preprocess some resting state data. As I wished to use the first slice to correct for motion, I typed in this command : preproc-sess -s 5167/ -fsd bold -stc down -surface fsaverage lhrh -mni305-2mm -fwhm 6 -*per-session. * The error message

Re: [Freesurfer] Yeo_JNeurophysiol11_FreeSurfer networks

Hi Thomas, Thank you for your answer, I will try to project your parcellation in fsaverage space to BASGU space first. Regards, Yolanda 2011/11/26 Thomas Yeo yeoye...@gmail.com Hi Yolanda, Just to understand what you are doing, you have run BASGU through recon-all and you are trying to

[Freesurfer] Number of maximal permutations / pooled variance estimates

Dear FS experts I have a question regarding the number of maximal permutations. I compare a single patient versus a group of six control subjects. Intuitively, I guess that only six different permutations are possible. However, when running 100 permutations in FS with mri_glmfit-sim, I get

[Freesurfer] longitudinal processing edema from lesion causing skewed registration

Hi, I am doing longitudinal processing of multiple subjects (each with 3 sessions) post stroke. However, some of the lesions are so extensive in the first session that they cause edema and push the brain midline. This greatly affects the pial surface on the lesioned hemishpere after

Re: [Freesurfer] running recon-all after editing aseg.mgz

If you only made edits to the aseg, then you can run: recon-all -s subject_name -autorecon2-aseg -autorecon3 which omits some stages that don't need to be redone (but which would otherwise be included if you use the -autorecon2 flag). If you in addition added control points, then you would run

Re: [Freesurfer] subjects with contrast medium

do you mean gado? If so, it should work although things like dura and choroid that get very bright may need some extra manual editing. cheers Bruce On Mon, 28 Nov 2011, LAOUCHEDI MAKHLOUF wrote: hi everyone i am working on traumatic brain injury and noticed that some exams

[Freesurfer] Surface X, Y, Z to Tailarach or Volume Index

Dear all, I wrote my own function to show the 3D surfaces in Matlab, works splendidly. I now however want to be able to point out Tailarach/MNI coordinates on the 3D surface. I however only have the x, y, z format that is saved in the asc files, which is just where a certex is located in space,

[Freesurfer] Freesurfer projecting vector results for segmented cortical regions

hello we are trying to project a vector of results for segmented cortical regions (i.e.,... lh_middletemporal_thickness 0.000757119 rh_middletemporal_thickness 8.06E-05 lh_parahippocampal_thickness -0.000510407 rh_parahippocampal_thickness 0.000625997 lh_pericalcarine_thickness

Re: [Freesurfer] Freesurfer projecting vector results for segmented cortical regions

Thanks for the help. We don't have matlab here in our lab, but we do have R. Is there a way to use R and get the same desired result? On 11/28/11 11:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brian, I guess you can use read_annotation.m in matlab and set every vertex within the

[Freesurfer] Surface Area from mri_surfcluster versus mri_segstats

I've noticed that if I run mri_surfcluster to produce a label file, then merge the labels into a single label using mri_mergelabels, then mri_segstats with the slabel option with the fsaverage subject; I get different surface areas from mri_surfcluster (summed all the cluster areas) and

[Freesurfer] create an annotation file

hi everyone    i am new in freesurfer and i want to create a masque of some color made of somme régions labels (say for ex. the post central gyrus and precentral gyrus or any combination of geri and sulcus) to put it as a layer on an a pial or inflated surface. how can i

[Freesurfer] Installation FS

Dear FreeSurfer Group I have some problem for installing the FS. Using following links, I downloaded and installed freesurfer-Darwin-leopard. For next step, in terminal when I write source $FREESURFER_HOME/SetUpFreeSurfer.sh or source $FREESURFER_HOME/SetUpFreeSurfer.csh it says that No such file

Re: [Freesurfer] trac-all Error: bvecs and bvals don't have the same number of entries

Sorry for the delay in responding, I wanted to try every permutation that I could think of. I updated the tracula binaries for snow leopard (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.html) and that gives me some of the same, and some different issues that may

Re: [Freesurfer] trac-all Error: bvecs and bvals don't have the same number of entries

Hi Peter - The format for the bvec and bval files is explained in: $FREESURFER_HOME/bin/dmrirc.example If you've structured your dmrirc following this example file and you're still getting this error, please send the following so I can debug this: - your exact trac-all command

Re: [Freesurfer] FSGD for dtrecon group analysis

Hi Antonella, 1) I will be very grateful if you let me know what data I should use for my fsgd when I run the GLM group analysis: the dti data after running the dtrecon (for example for my first control I called this directory C01_dti or the FS data after running recon-all on the structural

Re: [Freesurfer] Installation FS

Hi Nooshin, Did you include the full path to your freesurfer directory when setting the FREESURFER_HOME variable with the 'setenv' command? -Louis On Mon, 28 Nov 2011, nooshin n.zade wrote: Dear FreeSurfer Group I have some problem for installing the FS. Using following links, I downloaded

Re: [Freesurfer] Freesurfer projecting vector results for segmented cortical regions

If you've got any Python users in the lab, this shouldn't be to hard to accomplish with pysurfer: pysurfer.github.com I'm happy to walk you through the steps if you're interested. Michael On Mon, Nov 28, 2011 at 8:52 AM, Weisinger, Brian (NIH/NIMH) [F] brian.weisin...@nih.gov wrote: Thanks