Re: [Freesurfer] optseq installation

Dear Doug, Thank you for your answer. We run it from shell (a comand window of X11 because we are connected to the server by the way of a MacIntosh) but it isn't recognized. How can we make it executable ? We just upload optseq2 on the Linux server... Le 12 mars 10 à 20:30, Florence POMAR

Re: [Freesurfer] Pial surface- clarification

Thanks Bruce, i don't know much about ftps, do you have a ftp address (FSL they give us some ftp address which you can use to send your images) which you can send it to me and i can upload my images. I am very sorry. Thanks a lot venkat From: freesurfer-bou

Re: [Freesurfer] recon-all fails because of mri_label error

I use v4.5.0, I also downloaded the new version of mri_label and tried it, but I got another error says that " mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/m047599/freesurfer-install/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz /home/m047599/

[Freesurfer] Symmetry on four major cortex lobes on left and right hemisphere

Hello Bruce, Based on Freesurfer segmentation, we calculated the volumes of four major cortex lobes on left and right hemisphere seperately. Now I hope to find some reports illustrate the symmetry stuff using Freesurfer. Do you know where I can find it ? Thanks. Aize

Re: [Freesurfer] recon-all fails because of mri_label error

Hello, Bruce, I loaded the brainmask.mgz, it has a bad skull-stripping results with cerebellum attached. I tried to fix this problem by adjusting the watershed parameters, but the interesting thing is: this is the base template subject which is created by the command line recon-all -base ba

Re: [Freesurfer] selxavg error

Hi Doug, I couldn't find a -no-whiten option in the usage for either selxavg-sess or selxavg3-sess. In any case, when I run the selxavg command, the screen output says: INFO: WhitenFlag = 0 (so I guess it's not whitening?). I also looked for spikes or artifacts as you suggested and the main t

[Freesurfer] Choroid plexus -filling

Hi All, In my "filled.mgz" volume choroid plexus regions are left out in both right and left hemispheres, i am wondering whether i need to fill them or it is ok to leave them unfilled. Thanks venkat === P Please consider the environment before printing this e

Re: [Freesurfer] Choroid plexus -filling

it will fill the choroid that is adjacent to ventricles, but not elsewhere cheers Bruce On Mon, 15 Mar 2010, Rajagopalan, Venkateswaran wrote: > > Hi All, > > In my "filled.mgz" volume choroid plexus regions are left out in both right > and left hemispheres, i am wondering whether i need to fil

Re: [Freesurfer] Choroid plexus -filling

So do i need to fill it in other regions (manual editing) Thanks venkat -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 3/15/2010 1:06 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Choroid plexus -filli

Re: [Freesurfer] Choroid plexus -filling

you shouldn't have to. Is it causing problems? On Mon, 15 Mar 2010, Rajagopalan, Venkateswaran wrote: > So do i need to fill it in other regions (manual editing) > > Thanks > > venkat > > > -Original Message- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Mon 3/15/2010 1

Re: [Freesurfer] Choroid plexus -filling

Thanks, no it is not causing problems i just wanted to know. Thanks again venkat -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 3/15/2010 1:15 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Choroid plex

Re: [Freesurfer] optseq installation

what do you mean it is not recognized? To make it executable, you need to run chmod a+x optseq2 to run it, either put it into your PATH, or cd to where it is located and run ./optseq2 the "./" is necessary if it is not in the PATH doug Florence POMARES wrote: > Dear Doug, > Thank you for yo

Re: [Freesurfer] How to transform brain.mgz back to native space

Liang, You can find instructions on how to do this here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat Sometimes using mri_convert will cause the orientation to be off so you may want to follow those instructions instead. Allison -- On Sat, 13 Mar 2010, Bruce Fischl wrote: > H

Re: [Freesurfer] How to compare conditions scanned within different runs?

Were these all in the same session or different sessions? doug Shahin wrote: > I want to compare 2 different experimental conditions that were > scanned within different runs. For example assume that, in ten runs I > have had conditions 1 and 2 and in another ten runs I have had > conditio

Re: [Freesurfer] recon-all fails because of mri_label error

Hi Guang, yes, this should work: recon-all -base base_id -tp subj1 -tp subj2 -autorecon2 -autorecon3 Let us know how it goes, -Martin On Mon, 2010-03-15 at 10:31 -0500, Guang Zeng wrote: > Hello, Bruce, > > I loaded the brainmask.mgz, it has a bad skull-stripping results with > cerebellum at

Re: [Freesurfer] modification made to longitudinal results

Hi Martin, Just wanted to clarify one question about edits to the longitudinal pipeline. Lets say there is a data-set with 200 subjects with 5 time-points each (1000 scans total). I create the base image and i would only like to make corrections in the 200 base images (if required) and not in th