[Freesurfer] A question about coordinates

Dear experts I have a simple question. To my knowledge, Freesurfer uses Talrairach coordinates. After doing 1 permutations, I found that the resulting file *.sig.cluster.summary contained MNIX, MNIY, MNIZ coordinates. Are these coordinates in MNI space? Thank you in advance for your answer.

Re: [Freesurfer] mri_convert ERROR: could not determine file

Hi Morgan that is odd. I think Doug is traveling which may slow down his normal rapid response time. Bruce On Sat, 27 Jul 2013, Morgan Hough wrote: Hi there, I am trying to run reg-feat2anat and having a bit of an odd problem. It runs but doesn't produce a anat2exf.register.dat. If I look

[Freesurfer] Combining non accelerated and accelerated MRIs

Dear Freesurfer experts I am using Freesurfer to process part of the ADNI 2 database which includes non accelerated and accelerated images. Images have different voxel sizes. Is there any litterature to guide me what should I do, ie combining or not these scans. Stephane

Re: [Freesurfer] Combining non accelerated and accelerated MRIs

Hi Stephane you might look at this paper: https://surfer.nmr.mgh.harvard.edu/pub/articles/reliability_wonderlick.pdf cheers Bruce On Sun, 28 Jul 2013, Stéphane Poulin wrote: Dear Freesurfer experts I am using Freesurfer to process part of the ADNI 2 database which includes non

Re: [Freesurfer] A question about coordinates

Those are MNI305 coordinates. doug On 7/28/13 9:58 AM, jh kim wrote: Dear experts I have a simple question. To my knowledge, Freesurfer uses Talrairach coordinates. After doing 1 permutations, I found that the resulting file *.sig.cluster.summary contained MNIX, MNIY, MNIZ coordinates.

Re: [Freesurfer] A question about coordinates

Thanks, Doug Kim 2013/7/29 Douglas Greve gr...@nmr.mgh.harvard.edu Those are MNI305 coordinates. doug On 7/28/13 9:58 AM, jh kim wrote: Dear experts I have a simple question. To my knowledge, Freesurfer uses Talrairach coordinates. After doing 1 permutations, I found that the

[Freesurfer] dPSD and ev duration

Hi Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of 3 seconds, but would like to reduce my TR from 3 down to 2.5, but I can't seem to input the correct numbers for optseq to help me. thanks in

Re: [Freesurfer] dPSD and ev duration

Hi Ella, it has an internal clock that events have to be syncrhonized to. Try setting the dPSD to 0.5 doug On 7/28/13 4:05 PM, Ella Hinton wrote: Hi Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of

[Freesurfer] cvs_avg35

Hi, Would you tell me where I can find cvs_avg35 brain template. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Error

Dear Community, I got the following error every time I try to calculate the cortical thickness of my MRI data: bmssa-desktop:~ recon-all -i /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm -subject sub02 -all -qcache WARNING: tcsh