[Freesurfer] automatically saving images from tksurfer

Hi folks, Is there anyway to get freesurfer to pop up a surface with an overlay from the command line and get it to just save the image to .tiff and die. Im trying to make a movie from 300 frames of surface with overlay. I can do the popping up the image with overlay from command line of course,

[Freesurfer] kill tksurfer auto

Hi Bruce directed me to the tcl scripting stuff for tksurfer and so with a combi of tcl and bash I have almost got my machinery working to make my movies. Just one little fly in the ointment, it keeps putting up one after another tksurfer invocation piled on top the last. I have tried killing la

[Freesurfer] hippocampal subfield segmentations

I heard from Koen a while back that a new improved version was in the works. I have several projects I would be interested in using it for. Any info on timelines for release or a publication ? thank You ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

[Freesurfer] label to curv .mgh

hello, trying to convert a medial wall label to a curv format .mgh file running mris_convert --label lh.Medial_wall.label lh.white foo.mgh tried a few things but not getting there, what does it want ? thank You ___ Freesurfer mailing list Freesurfe

[Freesurfer] large topological defect

im trying something novel with a veryb young brain, i ran freesurfer standard stream and got decent results and then did some manual editing to fix a skull struip problem and reran and now it is detecting a large defect, is there a way i can look at the data to see what topological defect it is

Re: [Freesurfer] hippocampal subfields

Hi, just wondering if you have a guesstimate on the ETA of the new atlas ? thanks On 03/03/14, Juan Eugenio Iglesias wrote: > Dear Gabor, > the segmentation benefits to some extent from higher resolution data, > but produces decent estimates of the subfields at 1x1x1. We are working > on a new

[Freesurfer] version 5.3 bug fix

In the release notes for 5.3 i find Stable release version 5.3.0 is a bug fix release to correct the problem with pial and white surface creation affecting thickness and area measures. Is this only related to netative thickness values, which i have never found. I have 150 subjects * 3 ti

Re: [Freesurfer] applying Yeo atlas to individual brains

problem with surf2surf is it deals with scalar fields ( data ) so don't think that will do it. problem with label2label is that it deals with a single label which has a diferent structure than anot. so a way to do it 1. mri_annotation2label ... to convert the yeo anotation file to individual

[Freesurfer] flash v.s. mprage

looking at the docs available it seems that in general flash is prefered but it seems that for cortical thickness studies you may still favor the mprage ? all with good parameter setting of course. thanks in advance for any clarifying comments you may have Greg ___

[Freesurfer] LGI radius on outer surface ?

Hello Im preparing an LGI(local gyrification index) manuscript and seems i don't know the default radius that is used for the circular region defined on the outer surface that the boundary of is then projected onto the pial surface to get the corresponding pial region ? hope im clear, not the

Re: [Freesurfer] no aseg

so it seems that i ran make_average_volume which does have a --no-aseg flag make_average_subject really just runs 2 other commands make_average_surface and make_average_volume. bruce the reason i did this is that mike was running a `super` average, i.e. the average subject of 2 different syudies

Re: [Freesurfer] Recent paper on FreeSurfer reliability

bottom line is can we trust freesurfer cortical thickness results and a recent paper my group published seems to give very strong positive answer to the question. paper - cortical thinning in psychopathy, it's on the wiki publication list. All of the areas reported overlap with the areas that ha

[Freesurfer] cortical surface area related measures

Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al

[Freesurfer] is skull strip needed

if there is extra skull left after skull stripping but the pial surface is fine ( i.e. the left skull did not get included in the pial surface ) is it nessesary to adjust watershed parameters or manually remove it and reprocess the data set ? I am thinking it is not needed if it is not causing

[Freesurfer] assembling data

a have a bunch of data stored in the subj_id directories of the subjects for convieniance but it is already in the average surface space, but i want to assemble it into one file so i can run the glm. mris_preproc --fsgd subset.fsgd --target subset_average --hemi lh --meas winkler.mgh --out lh.

[Freesurfer] winkler surf data with qdec ?

Hi , I have winkler variety surface area data that is already smoothed and converted to vertex wise data on my average subject. Each subject has a file rh.ico7.fwhm10.mgh, lh... and Doug gave me a way with mri_concat to assemble the data into a single file so i can run command line mri_glmfit type

[Freesurfer] putamen seg

Hi, tried to use control points to improve the segmentation of the putamen in the difficult area between putamen,claustrum & insula. adding some white matter control points does not seem to insluence the aseg segmentation. control points are set to 110 after reprocessing with recon-all -autore

[Freesurfer] mri_glmfit-sim fwhm error

run mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos get cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir SURFACE: subset_average lh log file is lh.lgi.glmdir/cache.mri_glmfit-sim.log cd /study5/aa-scratch/UTAH/

Re: [Freesurfer] nu_correct problem

Petr why do you keep trying to name your input files something.mgz, when you were in wisconsin i told you the inputs always need to be 001.mgz at this point i think you need to get invited to upload one of your data sets to ugh and see if there is a problem with the data or is it a problem with

[Freesurfer] mri_vol2vol call problem

Greetings lords of freesurfer! I am having a problem getting a combined cvs warp+bbregister to map an FA volume onto a template. mri_vol2vol --targ 816 --m3z combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff

[Freesurfer] mri_vol2vol call

Hi I found my old notes ( re my message earlier) I think this is now correct for mapping subject 822 FA onto my template 816, I know the cvs technology is recent, so just asking to make sure there is now a newer/prefered way. mri_vol2vol --targ /study5/aa-scratch/TEENEMO/twins_freesurfer/816/

[Freesurfer] -hippo-subfields

we have freesurfer set up on our big condor cluster, i asked that the -hippo-subfields be added. they have it set up to run in 3 stages autorecon1 autorecon2 autorecon3 they added the flag to all 3, i think it would only be needed on autorecon3, but don't think it would cause harm, just be ign

[Freesurfer] make movies of non eeg/meg temporal data ?

I would like to make a movie of the temporal evolution of data on the cortical surface from something im doing. similar to what mne_make_movie does, but it's not eeg/meg data. is there a way to make and display movies of data in tksurfer or freeview ? or i guess i could `trick` mne and display m

Re: [Freesurfer] Surface Viewer Issue.

i saw this problem on one redhat installation, not on any others, seems something with the X library orientation information and openGL greg On 10/08/14, Jamie Hanson wrote: > Hi Freesurfer List, > > > I had a (hopefully quick) question about surface viewers and data orientation > in tksurfe

[Freesurfer] unsupported slice timing pattern 5 ?

hi, started working with a new data set to tracula proc. right off the bat it dies on mri_convert with unsupported slice timing pattern 5 if i simply do mri_convert data.nii.gz dwi_orig.nii.gz it dies with same, it's from a siemens 1.5 mobile scanner.  somebody else converted this data to .nii

[Freesurfer] please help, unsupported slice timing

i am trying to run tracula on a large number of subjects,  tracula dies quicklyin -prep stage when mri_convert tries to copy/rename the diffusion data, the error actually comes from the data read function. the data is already in .nii format the error is 'unsupported slice timing pattern 5' t

[Freesurfer] gray scale inflated surf rendering prob

send a question that martina asked before and we have not solved the prob. on macs when we run tksurfer xxx lh inflated for example the surf comes up looking smoother,low resolution rendered. if we load something like curvature that displays in color the surface looks fine, so the problem is on

[Freesurfer] bbregister coordinates

Happy new year folks, i would like to get info on which axis the transformation info in the fregister_XXX.dat.param is w.r.t. comparing the log files with the values i think the first 3 are the translations and the next 3 the rotations. but i did not see w.r.t. which directions, i.e. LR,AP,IS

[Freesurfer] cvs register mri_aparc2aseg running 22 hours ?

im running mri_cvs_register --step2, running it in a shell, not in the background. the process returned but top shows mri_aparc2aseg  still running at 100% cpu for 1320 minutes. seems something is not running correctly ? greg ___ Freesurfer mailing lis

[Freesurfer] problem applying morph with mri_vol2vol

Hi i am trying to transform/morph a tract created with tracula into my cvs template subject space, using v.5.0 i am thinking the bb register transformation i am using is not the correct one, but it seems the logical choice, but obviously not working good as forceps minor ends up wraped around t

[Freesurfer] white matter hyper intensities

a collaborator just got a grant review that claimed  There's a possibility that changes in cortical thickness in the insula might be a consequence of lesions (MR-hyperintensities) in the white matter. i would think that white matter hyper intensities would tend to enhance freesur

Re: [Freesurfer] white matter hyper intensities

On 04/05/12, Bruce Fischl wrote: > Hi Greg, > > yes, that can happen where they are hyper-intense on T2 and hypo-intense on > T1 and thus look like GM on the T1. It's not that common since they are > usually deeper, but we have seen it. > > sorry > Bruce >