[Freesurfer] recon-all

Dear Freesurfer expert, I am using Freesurfer version 5.1.0. After I ran the freesurfer recon-all -autorecon-all and checked the data I saw that the skull wasn't removed as a whole (yet it is not part of the pial or white matter margin). I was wondering if it just doesn't look good or that

[Freesurfer] No result differences v5.1.0 between MacOSX 10.6 and 10.7

Hi, For your information: for version 5.1.0 we have found no differences in the results between MacOSX 10.6 and 10.7 (53 subjects). Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] average measure of cortical thickness

Hi Douglas, Well, I usually use aparcstats2table with -m thickness, but what I get is the thickness for all those 34 hemisphere regions, but not that measure of mean thickness for the hemisphere. Could I be missing something? thanks Daniel Message: 15 Date: Tue, 30 Oct 2012 11:17:56 -0400 From:

[Freesurfer] Hurricane Sandy

Hi Bruce and colleagues, I hope you did survive Sandy without too much damage. Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

[Freesurfer] Phase-Sensitive Inversion Recovery

Hi all Our local team of physicists recommend Phase-Sensitive Inversion Recovery instead of MPRAGE for anatomical imaging in 7T. So far, I have had no issues with 7T MPRAGEs with regard to freesurfer processing. I am not sure about PSIR and freesurfer compatibility. Does anyone have experience

Re: [Freesurfer] Hurricane Sandy

Thanks Ed It wasn't as bad here as elsewhere Bruce On Oct 31, 2012, at 5:53 AM, Ed Gronenschild ed.gronensch...@np.unimaas.nl wrote: Hi Bruce and colleagues, I hope you did survive Sandy without too much damage. Cheers, Ed ___ Freesurfer

Re: [Freesurfer] recon-all

Hi Efrat if it's not messing up the surfaces or the aseg then you don't have to worry about it cheers Bruce On Wed, 31 Oct 2012, Efrat Kliper wrote: Dear Freesurfer expert, I am using Freesurfer version 5.1.0. After I ran the freesurfer recon-all  -autorecon-all  and checked the data I saw

Re: [Freesurfer] Phase-Sensitive Inversion Recovery

Hi Lena sorry, I havne't heard of Phase-Sensitive Inversion Recovery. I'll cc Jon Polimeni who might have some thoughts. cheers Bruce On Wed, 31 Oct 2012, Lena Palaniyappan wrote: Hi all Our local team of physicists recommend Phase-Sensitive Inversion Recovery instead of MPRAGE for

Re: [Freesurfer] Phase-Sensitive Inversion Recovery

Bruce, thanks a lot. I will look forward for Jonathan's reply. On 31/10/2012 13:11, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lena sorry, I havne't heard of Phase-Sensitive Inversion Recovery. I'll cc Jon Polimeni who might have some thoughts. cheers Bruce On Wed, 31 Oct 2012, Lena

[Freesurfer] SPM VBM and Freesurfer group analysis

Hi, I did a SPM VBM (using dartel) analysis as well as a freesurfer group analysis. After correcting for multiple comparisons. Both maps give me pretty different results. From the literature review both sets of results make sense but the fact that the results don't agree is troubling me. I have

Re: [Freesurfer] average measure of cortical thickness

Is the last item in the list lh_MeanThickness_thickness This is the mean thickness across the hemisphere. doug On 10/31/2012 05:16 AM, Daniel Ferreira wrote: Hi Douglas, Well, I usually use aparcstats2table with -m thickness, but what I get is the thickness for all those 34 hemisphere

Re: [Freesurfer] FW: TRACULA some fiber volumes being too small

If FSL isn't happy with the directions, that's going to be fatal b/c trac-all relies on bedpostx running properly. I'm going to look into this further to try to figure out what it is about this data that's causing the discrepancy. On Wed, 31 Oct 2012, Fernando Ventrice wrote: Dear

[Freesurfer] Error during recon-all with notal-check on

I have a MRI data which has a lesion on the left side .  recon-all fails with errors . I was hoping to recover from this error . The last few lines of the log file is as follows'___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Error during recon-all with notal-check on

The lines are as follows Computing Initial Surface Statistics       -face       loglikelihood: -9.5176  (-4.7588)       -vertex     loglikelihood: -7.1428  (-3.5714)       -normal dot loglikelihood: -3.5493  (-3.5493)       -quad curv  loglikelihood: -6.1889  (-3.0944)       Total Loglikelihood

Re: [Freesurfer] fieldsign-sess problem in retinotopy

Hi, Doug Thank you for your reply. I have tried exporting SUBJECTS_DIR to the directory of upper fold, retinotopy or SUBJ01 But none of them works. Still the same error msg. So what should SUBJECTS_DIR be exported to for this analysis? Best Wei Hi Wei, this is a bug in the error msg. It

Re: [Freesurfer] fieldsign-sess problem in retinotopy

What is the name of FreeSurfer subject? This is not necessarily the same as SUBJ01 in your command line below. That is the session (which may or may not be the same as the subject name). What ever the subjectname is, does $SUBJECTS_DIR/subjectname exist? On 10/31/2012 03:07 PM, Zhou, Wei