Re: [Freesurfer] mri_ca_register from virtual box

I'm going to check with more ram dedicated. Many Thanks Lorenzo Busti 2011/12/5 Nick Schmansky ni...@nmr.mgh.harvard.edu 1.5GB is probably not enough. typically we recommend that recon-all have at least 3GB available to it, which can be very hard to do on a virtual machine (since windows

[Freesurfer] Problems with mri_watershed and creating the BEM geometry file

Dear all, I have successfully run the freesurfer-steps for my subject and completed it without errors. After that I started MNE to create my BEM meshes. The manual tells me, for MNE to do that, the mri_watershed routine from freesurfer is used. Also, this runs fine, as far as the four surfaces

[Freesurfer] make a mask from an annotation file

hi everyone   i have made an annotation file from somme labels and i want to make a mask from the result (from the annotation file). i mean i want keep just the part of the brain covered by the annotation file in order to transform it by mri_convert to nifti format and make my

Re: [Freesurfer] make a mask from an annotation file

you can use mri_mask for this cheers Bruce On Tue, 6 Dec 2011, LAOUCHEDI MAKHLOUF wrote: hi everyone   i have made an annotation file from somme labels and i want to make a mask from the result (from the annotation file). i mean i want keep just the part of the brain covered

[Freesurfer] List of midpoint talairach coordinates for each FreeSurfer cortical region?

Dear FreeSurfers, Anyone out there know of a list of talairach coordinates for FreeSurfer cortical regions (MNI? I suppose)? Thanks! Carl -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center,

[Freesurfer] mri_annotation2label

Dear freesurfers, I have created labels by using the command: mri_annotation2label command (aparc.a2009s): Are these new labels only for the subject I mentioned in the last command or can I use them for other subjects aswell (e.g. in order to measure Volumetry of the auditory Cortex)? THX,

Re: [Freesurfer] List of midpoint talairach coordinates for each FreeSurfer cortical region?

Hi Carl, Do you mean a centroid? I don't know of a list. You could run mri_annotation2label to break the annotation up into individual label files. These files are text and have XYZ in MNI305 space. You could then compute the centroid from that. doug Carl Anderson wrote: Dear FreeSurfers,

Re: [Freesurfer] mri_annotation2label

Only for the subject specified on the command line. doug Klein, Holger wrote: Dear freesurfers, I have created labels by using the command: mri_annotation2label command (aparc.a2009s): Are these new labels only for the subject I mentioned in the last command or can I use them for other

Re: [Freesurfer] Contrasts in GLM

In this case you have 4 class variables and 3 continuous, so you'll have 16 regressors (and so 16 elements in your contrast). Your actual contrast vector depends on the order of your class variables in the fsgd. Assuming that the order is MP, FP, MV, FV, then the regressors will have the

[Freesurfer] mri_surf2surf error - Return code 254

Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval

Re: [Freesurfer] mri_surf2surf error - Return code 254

Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are

Re: [Freesurfer] mri_surf2surf error - Return code 254

What is lh.pial_converted.mgz? How big is it? what do get if you run mri_info on it? doug John Griffiths wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've

Re: [Freesurfer] mri_surf2surf error - Return code 254

surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for

[Freesurfer] Diffusion Tutorial and GroupAnalysis.csh

Dear All, 1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the following scrip: GroupAnalysis.csh with the following instruction: # Assemble input for group analysis set type = CVS-to-avg35# alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' Can you please

[Freesurfer] [FreeSurfer]: mkanalysis-sess

Hi Doug, It seems that there are still problems related to using -per-session. Preproc-sess now finishes apparently fine (correct file names are generated, i.e., fmc.*) but the analyses again defaults to using -per-run at mkanalysis-sess. Specifically, mkanalysis-sess creates an analysis.info

[Freesurfer] Bad registration

Dear All: I was using dtrecon on my DTI data and by default it will register  my diffusion data (fa) on the TAL space so i got the fa-tal.nii file and the fa-tal-nii.reg the file which encodes the transformation while registering to the TAL space. Can you please advise me what is the best

Re: [Freesurfer] Diffusion Tutorial and GroupAnalysis.csh

Hi Antonella, 1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the following scrip: GroupAnalysis.csh with the following instruction: # Assemble input for group analysis set type = CVS-to-avg35# alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' Can you

[Freesurfer] trctrain/trainlist

Hi, I am using TRACULA for the first time, and I am having trouble locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal subjects to enter in for set trainfile command. This is what my Freesurfer home directory looks like: cpdla@ba3:/software/Freesurfer/5.0.0$ ls ASegStatsLUT.txt

Re: [Freesurfer] trctrain/trainlist

Hi - It's $FREESURFER_HOME/trctrain/trainlist.txt. Note the underscore. In any case this is the default, so you don't have to specify trainfile in your dmrirc unless you're using something else. a.y On Tue, 6 Dec 2011, C. Paula de los Angeles wrote: Hi, I am using TRACULA for the first

Re: [Freesurfer] trctrain/trainlist

i dont think those files are in v5.0.0. you will need to download v5.1. n. On Tue, 2011-12-06 at 17:12 -0500, C. Paula de los Angeles wrote: Hi, I am using TRACULA for the first time, and I am having trouble locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal subjects to enter

Re: [Freesurfer] trctrain/trainlist

Oh yeah, that too. Tracula came out in 5.1. On Tue, 6 Dec 2011, Nick Schmansky wrote: i dont think those files are in v5.0.0. you will need to download v5.1. n. On Tue, 2011-12-06 at 17:12 -0500, C. Paula de los Angeles wrote: Hi, I am using TRACULA for the first time, and I am having

Re: [Freesurfer] trctrain/trainlist

thanks! it worked when i updated to 5.1 On Tue, Dec 6, 2011 at 6:13 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Oh yeah, that too. Tracula came out in 5.1. On Tue, 6 Dec 2011, Nick Schmansky wrote: i dont think those files are in v5.0.0. you will need to download v5.1.

[Freesurfer] dt_recon error

Hello, I'm having a problem with dt_recon on data scanned by Siemens TrioTim. I'm using v4.5.0, with Mac OS 10.6.8. dt_recon ran for a while, and stopped with an error ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat I

[Freesurfer] tracula ERROR: must specify brain mask volume for output subject

Hi. I am running into the following error: ERROR: fio_pushd: /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni ERROR: must specify brain mask volume for output subject . I googled this error and it seems like you suggested this to someone else : As for your error, it looks like maybe the

Re: [Freesurfer] mri_glmfit-sim error with v5.0

Thank you Doug, Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: I replaced the /bin/mri_glmfit-sim, but got the same error. [ERROR 1] In line 292: set csdCache =