[Freesurfer] (no subject)

2015-04-10 Thread Ashkan Faghiri
hello, I have two question: 1- I use GNU-parallel to run recon-all on my computer. i have 50 or so subject but after processing around 10 subject i get this error: "rm no match found", and the process won't continue. it only give me this error one after another.do you know what is my problem? 2-

[Freesurfer] (no subject)

2015-05-31 Thread Ashkan Faghiri
Hello all, I have two question. 1- I am unable to read a surface to matlab, can you please give me an example. how should i load a surface with overlay to matlab and display it (e.g. do it for bert) 2- another question, can we use another test in place of t-test? how? WRG A.Faghiri _

[Freesurfer] (no subject)

2015-05-31 Thread Ashkan Faghiri
Hello again, I forgot to ask one of my main questions: averaging subjects to fsaverage. if i run recon-all with -qcache all my subjects will be averaged to fsaverage subject, right? then will the fsaverage change after i do this, and if it change doesn't it affect my future projects? WRG A.Faghir

[Freesurfer] fsaverage problem

2015-06-03 Thread Ashkan Faghiri
Hello Bruce, thank you for your reply, and sorry that i couldn't reply on your mail (i don't know how). What do you mean by mapping an image to fsaverage space? do you mean we get a matrix of transformation? and if yes do we have access to this matrix? or do mean that when a subject is added the f

[Freesurfer] comparison between two hemisphere in single subject

2016-02-11 Thread Ashkan Faghiri
Hello, I want to compare the two hemisphere in one subject (thickness for example). should I use? surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi then what? how can I compare the two hemisphere of one subject? Regards, Ashkan -- -- Ashkan

Re: [Freesurfer] comparison between two hemisphere in single

2016-02-13 Thread Ashkan Faghiri
his vector is 0 so mri_glmfit returns "ERROR: DOF = 0". which is correct I think. I believe I can't do this procedure for single subject. I want to check if there is thickening or thinning between two hemisphere for one subject. what should I do exactly? Regards, Ashkan -- --

[Freesurfer] curved Surface projection

2016-02-13 Thread Ashkan Faghiri
tool to do this. Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harv

[Freesurfer] comparison between two hemisphere in single

2016-02-19 Thread Ashkan Faghiri
gards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees

[Freesurfer] comparison between two hemisphere in single

2016-02-20 Thread Ashkan Faghiri
urface if you > want to display it there. > doug > > On 2/19/16 9:18 AM, Ashkan Faghiri wrote: > > Hello, > > > > sorry for asking this again > > > > I want to calculate the difference between the thickness of one > > subjects different hemispheres and sho

[Freesurfer] quality check of T1 scans

2014-12-22 Thread Ashkan Faghiri
hello. we have some T1 scans from a previous experiment. before starting to analyse them i wanted to know if there is any way to check if the quality of the images are good enough for a morphometric analysis. WRG A.Faghiri ___ Freesurfer mailing list Fr