Re: [Freesurfer] Talairach transformation

Hi Bruce, thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and DCM-Modeling with my data, I guess the correct

Re: [Freesurfer] Recon-all Error: _FindFacePath

Hi Daniel, Usually when I get the FindFacePath error, the wm.mgz is very bad. You can try placing control points on the wm and rerun -autorecon2 and -autorecon3. That worked for me. -Khoa On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote: Dear Bruce and experts, I would really

[Freesurfer] Big Ventricles on v4.0

Hi everyone, I'm using a frozen version of FS v4.0 and I have a subject with rather large ventricles that don't get filled properly (surfaces and aseg are off) during recon. I can't really find a good fix in previous messages besides to upgrade FS, since it seems like the newer versions will

Re: [Freesurfer] Big Ventricles on v4.0

Hi Andrew, you can fill them in the aseg.mgz with tkmedit if you want. The newer versions do better with large ventricles, but if they are big enough we may still mislabel some of it. cheers Bruce On Tue, 13 Sep 2011, Andrew Dumas wrote: Hi everyone, I'm using a frozen version of FS v4.0

Re: [Freesurfer] Talairach transformation

Hi Maria you can use tkregister2 to check the accuracy of the talairach.xfm transform (xform for short), and correct it if you want. cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote: Hi Bruce, thanks for the first response. I tried to find some information on the webpage about xform,

[Freesurfer] Talairach transformation

Hi Bruce, so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a

[Freesurfer] Converting a cluster to a ROI without manually drawing

Hi all, In qdec, is there a way to convert a cluster to an ROI without manually drawing the ROI? I'm talking about selecting clusters on the mc-z maps. Thanks, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Converting a cluster to a ROI without manually drawing

Hi all, I figured it out. This is easily doable using TkSurfer. Thanks, Nasim On Sep 13, 2011, at 12:37 PM, Nasim Maleki wrote: Hi all, In qdec, is there a way to convert a cluster to an ROI without manually drawing the ROI? I'm talking about selecting clusters on the mc-z maps. Thanks,

[Freesurfer] Longitudinal 5.0 with data from earlier version

Hi all, Does anyone have experience running a longitudinal analysis in version 5.0, using .mgz files generated from the last version of freesurfer? My understanding is that the only major differences between the previous and current versions were in the longitudinal stream. Any input would be

Re: [Freesurfer] Longitudinal 5.0 with data from earlier version

no, there are other differences as well. Bruce On Tue, 13 Sep 2011, Erica Griffith wrote: Hi all, Does anyone have experience running a longitudinal analysis in version 5.0, using .mgz files generated from the last version of freesurfer? My understanding is that the only major differences

Re: [Freesurfer] Longitudinal 5.0 with data from earlier version

Alright, thanks. Would you recommend against using the new longitudinal stream with data generated from a previous version though? That is my main question. On Tue, Sep 13, 2011 at 4:17 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: no, there are other differences as well. Bruce On Tue,

Re: [Freesurfer] Longitudinal 5.0 with data from earlier version

Hi Erica, I'm not sure what you mean. Why not just run it through all the way? And we would *strongly* recommend using the 5.1 longitudinal instead of 5.0 cheers Bruce On Tue, 13 Sep 2011, Erica Griffith wrote: Alright, thanks. Would you recommend against using the new longitudinal stream

Re: [Freesurfer] Longitudinal 5.0 with data from earlier version

Hi Bruce, We are working with a cohort of several hundred subjects, and all of the data has already been processed using the last version of FS. It would take quite a while for us to go through all of that data again, so we're trying to figure out if it would be okay to go ahead and use the

Re: [Freesurfer] Longitudinal 5.0 with data from earlier version

its ok to use just the longitudinal stream of 5.1 with your existing data. that is, you dont need to rerun the cross-sectional part of the three-stage longitudinal process, just -base stage and then the -long stage. n. Hi Bruce, We are working with a cohort of several hundred subjects, and

[Freesurfer] using mri_label2label with full path

I have a tricky situation where we can't use symbolic links ( cifs/smb mounts ) and it doesn't make sense to copy the fsaverage to the SUBJECTS_DIR. The subjects_dir is actually a separate directory for every subject when trying to run things through the connectome toolkit. I've edited my

[Freesurfer] mri_mcsim and mri_glmfit-sim

I am trying to figure out how to cluster some data on the cortical surface; however, I've run into a few issues: (1) I can't seem to find a description or examples for running mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST to create my statistical maps. (2) A previous email