[Freesurfer] Talairach

Dear FreeSurfers I am pretty new to Freesurfer, and I'm using the workflows which are provided in your website; however, I was wondering If every time, I have to check my Talairach (i.e. and to fix it) Do I have to run the recon-all -autorecon1 ... Which takes hrs, or I have another short option w

RE: [Freesurfer] Talairach

Hi Sharon, Because the talairach is the second step, when you fix it you really do have to run everything else to have it applied. In terms of how long it is taking - it is a long process, the speed of which is dependent on your computer speed and also on the quality of your data. What type of

[Freesurfer] sphere registration

Hi I am using the freesurfer Parcellation, modify the obtained parcels to have a small rois. To validate my parcels subdivision into small rois, I need to know the variation of some roi_gravity_centers. Do you think that with the vertex number on the sphere of a subject (after parcellation) is it

Re: [Freesurfer] sphere registration

Hi Leila, you can use the spherical coordinates, given by the (x,y,z) of the vertex on that subject's sphere.reg (or the lattitude, colongitude). Or you can use send_to_subject in tksurfer to look up the vertex index on the fsaverage sphere.reg if you want. cheers, Bruce On Tue, 10 Jul 20

RE: [Freesurfer] add the gray matter

Dear, Dr. Fischl Thank you for your suggestion. My problems are around hippocampus. The grey/white surface is OK now. but some grey matters are not included in the pial surface. How to change the Pial surface? Thank you again, Xin From: Bruce Fischl [mailto

RE: [Freesurfer] add the gray matter

oh, I wouldn't worry about the surfaces in the hippocampus. They aren't meant to be accurate there. There is too much internal structure there - we model is separately in the aseg.mgz files. cheers, Bruc On Tue, 10 Jul 2007, Wang, Xin wrote: Dear, Dr. Fischl Thank you for your suggestion. My

[Freesurfer] mri_motion_correct.fsl problems

Hi, I'm still having problems with the rawavg.mgz volume being generated with incorrect orientations. I gave Jenni two 00?.mgz volumes and she was able to generate a correctly-oriented rawavg. Our two log files look very different, but I'm not able to figure out the problem by looking a

[Freesurfer] Talairach

I'm trying to use Flirt from FSL to get talairach.xfm. Here are the steps I took: 1) recon-all -autorecon1 -notalairach -subjid $subject 2) mri_convert $SUBJECTS_DIR/$subject/mri/nu.mgz $SUBJECTS_DIR/$subject/mri/nu.img 3) bet $SUBJECTS_DIR/$subject/mri/nu $SUBJECTS_DIR/$subject/mri/nu_brain 4) fsl

Re: [Freesurfer] mri_motion_correct.fsl problems

Yes, the problem is with the matfile. This is rather strange since we generate the matfile. It might be some interaction with osx. Do you have a linux box your can try it out on? This also looks like it might be a fairly old version, can you download a more recent version and see if it works

Re: [Freesurfer] export mgz+label to dicom files

Hi Doug: Is it possible to write out nifti or mgz files with labels+T1.mgz? Thanks! Tao Doug Greve wrote: Sorry, we do not have an option to write out dicoms. doug T. Song wrote: Hi All: After imposing labels to a T1.mgz files in tkmedit, is it possible to write out dicom files with the

[Freesurfer] smoothing and monte carlo sim

Hi Doug, As you suggested, I ran mc simulation data with a threshold taken from fwhm.dat so that the smoothing on the simulation matches the smoothing on the real data. What I was wondering is, if I use the same simulation data for several contrasts (they have the same fsgd, so this seems lik

Re: [Freesurfer] export mgz+label to dicom files

I'm not sure what you mean by "labels+T1". Also "labels" can mean a lot of different things (eg, aseg, aparc, label format). Can you be more specific? T. Song wrote: Hi Doug: Is it possible to write out nifti or mgz files with labels+T1.mgz? Thanks! Tao Doug Greve wrote: Sorry, we do no

Re: [Freesurfer] smoothing and monte carlo sim

If the simulation command-line would be the same across the different contrasts and the contrast matrices have the same number of rows, then you do not have to redo the simulation. Why is the smoothing changing if you are using the same fsgd file? Robert Levy wrote: Hi Doug, As you suggeste

Re: [Freesurfer] MR to MGZ

There appears to be a problem when freesurfer reads in that dicom file. See if this works mri_convert -it dicom /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz Jerry Yeou-Wei Chen wrote: Hello, We have been having

Re: [Freesurfer] Talairach

What you are trying to do is harder than you think as you are trying to go thru several spaces in several software packages (and using ANALYZE to boot). Why not just use the talairaching in freesurfer? Wayne Su wrote: I'm trying to use Flirt from FSL to get talairach.xfm. Here are the steps I

Re: [Freesurfer] MR to MGZ

Thanks for such a prompt reply, Doug. Unfortunately, I still get an error: ===start=== mri_convert -it dicom home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz reading

Re: [Freesurfer] export mgz+label to dicom files

OK. Say, I have a label file saved from a user defined ROI in tksurfer (ascii label). I superimpose the label with a T1.mgz file in tkmedit. Now I get a T1 weighted image with predefined ROI highlighted. Can I save the whole series to a nifti or mgz file? Thanks! Tao Doug Greve wrote: I'm not

Re: [Freesurfer] smoothing and monte carlo sim

Hi, That's a good question. I have no idea why changing only the contrast (and changing nothing anatomical) should result in the smoothing being different. I also learned that previous research assistants in our lab encountered the same exact issue but they didn't solve it. My best guess

Re: [Freesurfer] mri_motion_correct.fsl problems

ok. it seems to be an osx problem. using a more recent version on a mac did not work, but the orientations were fine when i ran it on a linux box. i can just use that machine to do the motion correction for all of these subjects. thanks for your help! -cate > Yes, the problem is with the mat

Re: [Freesurfer] smoothing and monte carlo sim

Oh, sorry, you mean the lower-level contrast? Yes, that can definitely cause difference in smoothness at the higher level because it is a totally different input. Robert Levy wrote: Hi, That's a good question. I have no idea why changing only the contrast (and changing nothing anatomical)

Re: [Freesurfer] export mgz+label to dicom files

You can convert the label into a binary mask (mgz or nii) with mri_label2vol. You can really save a base image and an overlay together. doug T. Song wrote: OK. Say, I have a label file saved from a user defined ROI in tksurfer (ascii label). I superimpose the label with a T1.mgz file in t

Re: [Freesurfer] export mgz+label to dicom files

Thanks! I was able to create a binary mask, and the result looks good. Now how do I save a base image with an overlay, in tkmedit of which command? Tao Doug Greve wrote: You can convert the label into a binary mask (mgz or nii) with mri_label2vol. You can really save a base image and an ov

Re: [Freesurfer] FreeSurfer relevance for studying structures other than the brain

Hi Greg, I think there are certain things you could use, but so much of what we do uses brain-specific information and assumptions that it is going to be rough. What exactly are you trying to achieve? Bruce On Mon, 9 Jul 2007, Greg Soltis wrote: Greetings, I am attempting to use FreeSur