[Freesurfer] cespct in FS 5.3

2016-06-06 Thread S.V.Shepherd [work]
Hi all, I ran an analysis on data after dividing each voxel mean across the run, and then multiplying by 100. (My intuition was that the percent signal change should be more consistent across varying SNR that the non-normalized betas). I had naively expected ces.nii and cespct.nii to be equivalen

[Freesurfer] converting Tracula outputs to Wavefront OBJ files

2016-06-06 Thread David Allan Ziegler
Dear Freesurfer/Tracula team, I would like to convert some of the outputs from Tracula into wavefront objects in order to render them in Unity. Does anyone have any advice on how to do so? Based on previous threads and looking into Brainder.org's aseg2surf, I assume I need to use a combination o

[Freesurfer] CORRECTING DEFECT

2016-06-06 Thread maryam koochaki
Hi Bruce,I am wondering if you saw my last email, about uploading my subject in your ftp server.I uploaded the subject  "test_emc_039.tar.gz".I appreciate any help. Thank you, Maryam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http

Re: [Freesurfer] CORRECTING DEFECT

2016-06-06 Thread maryam koochaki
Hi Bruce,Did you get my email regarding to the subject I upload in fft server? Best,Maryam   Regards,Maryam Kouchakidivkolaei On Friday, June 3, 2016 10:16 PM, maryam koochaki wrote: Hi Bruce,I already uploaded it.File name:  test_emc_039.tar.gz Thanks,Maryam   Regards,Maryam

Re: [Freesurfer] Longitudinal Studies Question

2016-06-06 Thread Martin Reuter
Hi Carolyn, not sure what you are asking. You want to do statistics on N=1 subject ? Anyway, in order to use QDEC, you'd have to reduce the longitudinal data (thickness, measured at different time points) to a single number: the slope of a linear fit. This is called the 2-stage-approach. Or

Re: [Freesurfer] volumetric difference between 1.5 T and 3.0 T...

2016-06-06 Thread Jovicich, Jorge
Hi Gonzalo, indeed, here are the references Bruce is refering to: http://www.ncbi.nlm.nih.gov/pubmed/19233293 http://www.ncbi.nlm.nih.gov/pubmed/16651008 Image contrast to noise ratio per unit time of acquisition is different because of different T1s and lower SNR. Different scan durations will

Re: [Freesurfer] Build fsaverage

2016-06-06 Thread Douglas N Greve
fsaverage is distributed with freesurfer. Do you have freesurfer installed on your new computer? If so, then just create a symbolic link with cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage On 06/04/2016 04:44 PM, shi yao wang wrote: > Hello, Thank you very much for the reply! > > 1.

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

2016-06-06 Thread Douglas N Greve
looks like you put your command on two different lines On 06/06/2016 05:16 AM, Hao wen wrote: > Sorry, if you received my email, cuz I really stucked here, and i > didnt find the related topics in the freesurfer support archive! > Thank you in advance > ---

Re: [Freesurfer] volumetric difference between 1.5 T and 3.0 T...

2016-06-06 Thread Bruce Fischl
Hi Gonzalo we seek to minimize these explicitly, but given the difference in T1s at different field strength it's pretty hard to get rid of them completely. Xiao Han wrote a paper on this, and I think Jorge Jovicich did as well cheers Bruce On Mon, 6 Jun 2016, Gonzalo Rojas Costa wrote:

[Freesurfer] volumetric difference between 1.5 T and 3.0 T...

2016-06-06 Thread Gonzalo Rojas Costa
Hi: There exist any difference between the volumetric values obtained using 1.5T and 3.0T images ? Any paper about it ? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. T

Re: [Freesurfer] Longitudinal Studies Question

2016-06-06 Thread Carolyn Drobak
Hello, I have six scans for a single subject. I have performed "group analysis," but wish to use longitudinal data analysis. In particular, I was able to get a base for the subjects, so can view in freeview and all of that. My issue arises when I try to use QDEC. Because QDEC can't use my long.qde

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

2016-06-06 Thread Hao wen
Sorry, if you received my email, cuz I really stucked here, and i didnt find the related topics in the freesurfer support archive! Thank you in advance De : Hao wen Envoyé : mercredi 1 juin 2016 19:32:24 À : freesurfer@nmr.mgh.harvard.edu Objet : RE: [Freesurfer] C