[Freesurfer] Fwd: 7T Facility Fellow Position in Brisbane

2013-03-14 Thread Douglas Greve
FYI Original Message Subject:7T Facility Fellow Position in Brisbane Resent-Date:Thu, 14 Mar 2013 01:01:35 -0400 Resent-From:dgr...@partners.org Date: Thu, 14 Mar 2013 04:59:03 + From: Ross Cunnington r.cunning...@uq.edu.au To: Hello, I'd

[Freesurfer] mri_cvs_register - use of wmparc instead of aseg

2013-03-14 Thread Güllmar , Daniel
Dear Lilla, i'm currently applying mri_cvs_register and I'm very happy with the nice results. Congratulation for this very clever approach. However, some data sets which I work on have still aseg.mgz which are not segmented appropriately. As far as I understand aseg.mgz is not redefined after

[Freesurfer] convert from vtk to Freesurfer surface file format

2013-03-14 Thread Christine Tardif
Hello, I would like to use the surface registration tools in Freesurfer. I first need to convert my vtk surfaces into the Freesurfer format. I tried mris_convert, but this seems to only convert from and not to the Freesurfer file format. Does anyone know of another conversion tool available?

[Freesurfer] Stat doubts

2013-03-14 Thread Gabriel Gonzalez Escamilla
Dear Freesurfers I'm performing regression analyses including confounding variables, and I would like to know how to obtain the following information:A) The squre Rand B) The standarized beta coefficient of an independient variable; and the partial correlation with its p-valuesMany thanks in

Re: [Freesurfer] Stat doubts

2013-03-14 Thread Douglas Greve
Hi Gabriel, I've attached a matlab routine which will compute the PCC. If you cd into the GLM dir, then X = load('Xg.dat'); beta = MRIread('beta.mgh'); C = load('yourcontrast/C.dat'); rvar = MRIread('rvar.mgh'); betamat = fast_vol2mat(beta); rvarmat = fast_vol2mat(rvar); rhomat =

[Freesurfer] Permission denied

2013-03-14 Thread Varghese Chikku
Dear FS team, I dowloaded the latest ML version of FS and tried to run a subject.But this error is coming up.Any suggestions? chikkuvarghese$ recon-all -i /Users/chikkuvarghese/Desktop/BL/raw/image1 -autorecon-all -s BL1 mkdir: /Applications/freesurfer/subjects/BL1: Permission denied

Re: [Freesurfer] Permission denied

2013-03-14 Thread Bruce Fischl
you probably want to specify the SUBJECTS_DIR as being somewhere else that you have write permission to. You can do this with the -sd path on the recon-all command line, or in the environment. cheers Bruce On Thu, 14 Mar 2013, Varghese Chikku wrote: Dear FS team,I dowloaded the latest ML  

[Freesurfer] Coordinates of center of gravity of a cluster in Freesurfer

2013-03-14 Thread Maleki, Nasim
Hi all, I would like to calculate the coordinates of center of gravity of a cluster in Freesurfer. Is there a way to do this in Freesurfer? Thanks, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Estimate of number of manual edits and time to complete in 100subject sample

2013-03-14 Thread Allison Stevens Player
Hi Kev, For the two scenarios you mentioned, here are my best estimates. I assume a healthy, adult population scanned with our recommended sequences. Any other type of dataset (pediatric, one with some type of pathology, one acquired long ago using a less than optimal sequence or coil, etc.)

Re: [Freesurfer] long_qdec_table

2013-03-14 Thread Martin Reuter
Hi Chris, the cross qdec table is messed up ( a single line without line breaks). long_qdec_table has problems reading your long-table because it contains 'tabs', several spaces instead of a single one between other columns and also not the line breaks it expects (the windows format). I

Re: [Freesurfer] long_qdec_table

2013-03-14 Thread Martin Reuter
Hi Chris, try to rename the LongQdecTable.* files in your FS install and place a new LongQdecTable.py file there from here: http://martinos.org/~mreuter/LongQdecTable.py the new one uses universal newline support. Not sure if the Python on your system supports this. Let me know (also what

[Freesurfer] volumetrics questions

2013-03-14 Thread Rashmi Singh
Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the

Re: [Freesurfer] volumetrics questions

2013-03-14 Thread Bruce Fischl
Hi Rashmi of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data. cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Hello experts,    I am doing

Re: [Freesurfer] volumetrics questions

2013-03-14 Thread Rashmi Singh
Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi On 3/14/13 12:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi

Re: [Freesurfer] volumetrics questions

2013-03-14 Thread Bruce Fischl
yes, you should use the longitudinal stream for your analysis. You are probably better off picking the better mprage (i.e. less motion) and analyzing it at each timepoint cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Thank you Bruce. So what should I do. Shall I just take one of

Re: [Freesurfer] volumetrics questions

2013-03-14 Thread Rashmi Singh
Ok I have done that. I did run longitudinal run using each mprage as an individual timepoint. So this way I got the longitudinal run stat output for both time points. So do you suggest I average them out or take the result of the output from one of the long run. Or are you suggesting that I take

[Freesurfer] question about autorecon2-cp, autorecon-pial and autorecon-wm flags

2013-03-14 Thread Mehul Sampat
Hi Folks, I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm flags in recon-all help and also here http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags My interpretation is when I use autorecon-pial, I only need the command: recon-all --autorecon-pial -s subject While for

Re: [Freesurfer] volumetrics questions

2013-03-14 Thread Bruce Fischl
what is your goal? If it is to detect longitidinal change I would advise take the best mprage at each timepoint and run it through cross-sectional then longitudinal analysis Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Ok I have done that. I did run longitudinal run using each mprage as an

Re: [Freesurfer] Xhemi files do not exist in the specified ftp location

2013-03-14 Thread Negar Memarian
Dear Doug, Following up on my yesterday email, I would appreciate if you kindly upload the following files (required for Xhemi) so the ftp download will be possible. I am currently using version 5.1 of FreeSurfer and need the installation of these files in order to be able to run the Xhemi

Re: [Freesurfer] Process flow: ReconAllDevTable

2013-03-14 Thread Mehul Sampat
Hi Nick I have a followup question about Scenario D: Scenario D (for pial edits): 1. recon-all -s subject -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s subject -autorecon-pial I think -autorecon-pial is a subset of

[Freesurfer] Caret to Freesurfer

2013-03-14 Thread Ellspermann, Kara
I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into

Re: [Freesurfer] Xhemi files do not exist in the specified ftp location

2013-03-14 Thread Douglas Greve
It is actually there. I changed the location but did not update the wiki. Look in this dir ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregxhemi-reg On 3/14/13 7:43 PM, Negar Memarian wrote: Dear Doug,

Re: [Freesurfer] mri_cvs_register - use of wmparc instead of aseg

2013-03-14 Thread Lilla Zollei
Hi Daniel. i'm currently applying mri_cvs_register and I'm very happy with the nice results. Congratulation for this very clever approach. However, some data sets which I work on have still aseg.mgz which are not segmented appropriately. As far as I understand aseg.mgz is not redefined

Re: [Freesurfer] Error messages and empty surf files

2013-03-14 Thread Bruce Fischl
Hi Hayley the LINE SEARCH messages can be ignored, but not the watershed one. The watershed error means the skull stripping has failed, possibly because of a talairach normalization problem. Have you checked the talairach.xfm and the brain.mgz? That's where I would start cheers Bruce On

Re: [Freesurfer] Caret to Freesurfer

2013-03-14 Thread Bruce Fischl
Hi Kara I think the answer is yes as there are people at Wash U that do this routinely. Maybe Matt Glasser or someone else can chime in? cheers Bruce On Thu, 14 Mar 2013, Ellspermann, Kara wrote: I am new to Freesurfer, and I am trying to input/process preterm infant brain data

Re: [Freesurfer] Caret to Freesurfer

2013-03-14 Thread Matt Glasser
She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to Caret, which is what I do. Kara, I believe we are meeting tomorrow to discuss the options for this? I don't know anything about the FreeSurfer longitudinal pipeline, but it would take going through the pipeline and finding

[Freesurfer] mri_convert problem

2013-03-14 Thread Valtina Pouegue
Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; -[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc