Re: [Freesurfer] Coordinate system in mris_convert

Hello all, I'm new to surface analysis. I have 2 groups (patient and healthy control) that i want to check differences between. I want to perform cortical thickness/ surface analysis. My categories are Patients, healthy control, age, TIV, father age, mother age. Where age & TIV are covaria

[Freesurfer] Resampling the parametric map of brain activations onto a surface

Hi All, I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying to overlay a parametric map onto a FreeSurfer surface. Here are the tutorial codes I found: 1. To resample the paramatric map onto the individual's surface: mri_vol2surf --src spm001.img --srcreg register.dat --hemi

Re: [Freesurfer] Brainmask edit error

Hi Ani, I really appreciate the time and effort you are putting in to help me find a solution to this problem. The surface does look much more promising. Following your instructions in the email, I have been playing around with editing the wm.mgz and have been able to generate better wm surfa

Re: [Freesurfer] Coordinate system in mris_convert

I have the following error: unknown option --cras_correction. I am using FreeSurfer 5.3, I don't known if it helps. By the way, I was wondering: why this c_ras vector is not taken into by default e.g. with mris_convert or mri_tesselate ? 2016-06-07 16:54 GMT+02:00 Douglas Greve : > Try adding --

Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header

Hi Doug, I do not believe the files have changed in any way since I started using them; I uploaded some dicoms for you to look at and the recon-all log to the file drop a few minutes ago (with more details). Thank you for all your help! Joseph Aloi Graduate Student, MD/PhD Scholars Program Depa

Re: [Freesurfer] Fwd: bug report

Hello Siya, What version of perl is on your ubuntu system? $> perl --version -Zeke On 06/05/2016 04:30 PM, siya sherif wrote: > > > FREESURFER_HOME: /usr/local/freesurfer > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > Debian version: jessie/sid > > Kernel info: Linux

Re: [Freesurfer] Freesurfer program for 7 Tesla

No. not really. This paper should be useful. Thanks for sending this along. From: Alan Francis [mailto:alandarkene...@gmail.com] Sent: Tuesday, May 24, 2016 9:47 AM To: Freesurfer ; pnucl...@gmail.com Subject: Re: [Freesurfer] Freesurfer program for 7 Tesla Hi Prasad: Hope all is well.

Re: [Freesurfer] errors in wm and pial boundaries

Hello, Have you been able to look at the data I sent over yet? It would be great to get a sense of what we can or cannot do to correct the boundaries. Thanks Corinna On Wed, May 25, 2016 at 12:05 PM, Corinna Bauer wrote: > Hi Bruce, just checking in to see if you have had an opportunity to tak

Re: [Freesurfer] Coordinate system in mris_convert

Try adding --cras_correction to the command line and see if it works. On 6/7/16 10:27 AM, Alexandre Routier wrote: Hello, I would like to work with mesh representation of pial and white surfaces in vtk format. To do that, I use the following syntax: mris_convert lh.pial lh.pial.vtk However,

Re: [Freesurfer] cespct in FS 5.3

Rescaling by the voxel mean will mess up the intensity normalization. Try making your analysis (mkanalysis-sess) with -no-inorm and see if the results are more consistent. They will not be exact because the raw mean time course is not used to create the cespct. Rather it is the regression coe

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Columns (1+2) = Columns (4+5) in the desgin matrix. This causes the error On 6/7/16 5:56 AM, Hao wen wrote: Thanks, Doug: That was a really silly mistake, so right now I can run the cmdline for mri_glmfit but I got the error like this: ERROR: matrix is ill-conditioned or badly scaled, con

[Freesurfer] Coordinate system in mris_convert

Hello, I would like to work with mesh representation of pial and white surfaces in vtk format. To do that, I use the following syntax: mris_convert lh.pial lh.pial.vtk However, there is a small issue after conversion: the vector called 'c_ras' (the RAS at the 'center' of the volume according to m

Re: [Freesurfer] SAVE REG in tkregister2

what is your command line? On 6/7/16 4:46 AM, Hao wen wrote: Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output: register: ### can't create file NULL/rgb/NULL I think maybe this is a very stupid question:)

Re: [Freesurfer] SAVE REG in tkregister2

That will work in version 6 On 6/7/16 4:55 AM, Hao wen wrote: Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized. I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Manual

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Hello: Also, for the contrast matrix, I am a little confused about the explaination in FS wiki: --C contrast1.mat <--C contrast2.mat ...> Specify one or more contrasts to test. The contrast.mat file is an ASCII text file with the contrast matrix in it (make sure the last line is blank). The o

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Thanks, Doug: That was a really silly mistake, so right now I can run the cmdline for mri_glmfit but I got the error like this: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.07053e+07 Possible problem with experimental design: Check for duplicate

Re: [Freesurfer] SAVE REG in tkregister2

Also, in automatic registration with bbregister, you define a flag, --init-rr, but the terminal told me: ERROR: Flag --init-rr unrecognized. I just follow the tutorial, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration FsTutorial/ManualRegistration - Free Surfer Wiki

[Freesurfer] SAVE REG in tkregister2

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output: register: ### can't create file NULL/rgb/NULL I think maybe this is a very stupid question:) But FS is really complicated... Thanks in advance ___

Re: [Freesurfer] Save REG in tkregister2

here is my terminal output: register: ### can't create file NULL/rgb/NULL I think maybe this is a very stupid question:) De : Hao wen Envoyé : mardi 7 juin 2016 10:27:07 À : freesurfer@nmr.mgh.harvard.edu; Bruce Fischl Objet : Save REG in tkregister2 Hello: I

[Freesurfer] Save REG in tkregister2

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in