[Freesurfer] QA_tools missing signal to noise calculation

Hi, I have downloaded the latest QA_tools v1.1 from http://surfer.nmr.mgh.harvard.edu/fswiki/QATools. However, when I ran recon_checker, I did not get a signal to noise calculations. I ran recon_checker with -s-dir subjectfile and -snaps-detailed. Is there any option that I missed? Is it poss

[Freesurfer] ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s

Hi, When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128.

Re: [Freesurfer] WM/GM boundary changes and control points

I've been struggling to upload the file to the ftp server, but failed in several times. Sorry for bothering you, but I will send an e-mail when the uploading is done. Best, EK 2012/10/14 Bruce Fischl > I found EK_test.zip, but neither tar nor unzip knows how to uncomress it. > What format is i

Re: [Freesurfer] ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s

Hi Knut you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing the 125 into the 128 geometry (-rl) and go from there. cheers Bruce On Sun, 14 Oct 2012, Knut J Bjuland wrote: > Hi, > > When I import one subject with recon -i dicom -i dicom -s subjec, I get > this error message

Re: [Freesurfer] 3 Factor glm group analysis

Thanks Doug! If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction? Harry From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve

Re: [Freesurfer] 3 Factor glm group analysis

Hi Harry. I have some scripts to compute a slope into the time thickness or volume (linear fits) and then run a standard glm on that . However, we recommend to run a linear mixed effects model (external software). We are working on making that available. Best Martin Harry Hallock wrote: >Th

Re: [Freesurfer] WM/GM boundary changes and control points

I uploaded the EK_test_new.tar file to the ftp incoming folder. I think it might work. Thank you for you time and consideration. 2012/10/15 EK Kim > I've been struggling to upload the file to the ftp server, but failed in > several times. > Sorry for bothering you, but I will send an e-mail

Re: [Freesurfer] ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s

Hi Bruce I converted the dicom into 001.mgz. Then I tried to reslice. mri_convert -rl -i orig/001.mgz -o orig/001.mgz mri_convert -rl -i orig/001.mgz -o orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig/001.mgz... TR=2730.00, TE=3.45, TI=1000.00, flip