[Freesurfer] Order of edits for longitudinal data

Dear All, I was would like to double check the order of edits for longitudinal data. I did edits for my cross-sectional data, and for my base data, I did the following: 1. skull strips edits (if necessary) 2. control points edits 3. white matter edits 4. pial edits 5.brain final surfs edits. I

[Freesurfer] questions regarding longitudinal processing

Hi All, This may seem to be an easy question, I would just like to confirm... I have two groups that underwent different types of training and were measured at two time points (before and after training). My understanding is that I should use the longitudinal scheme in freesurfer to run recon-

Re: [Freesurfer] questions regarding longitudinal processing

them in the post-processing stream? Or should I just update my v5.0 to v5.3 and start running my -base -long in v5.3 using the data that was processed in the v5.0? Thanks in advance, Catherine From: Martin Reuter To: Rongxiang Tang Cc: "frees

[Freesurfer] error during longitudinal -base stream

Hi All, I found an error during the longitudinal -base stream: #@# Ex-vivo Entorhinal Cortex Label lh Wed Sep  4 19:35:00 CDT 2013  mris_spherical_average -erode 1 -orig white -t 0.4 -o 611 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject

Re: [Freesurfer] error during longitudinal -base stream

I ended up fixing the error through symlink. From: Rongxiang Tang To: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, September 4, 2013 8:04 PM Subject: error during longitudinal -base stream Hi All, I found an error during the longitud

[Freesurfer] talairach transformation troubleshooting problem

Dear All, When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside the green line. Instead of drawing the green line to include all of the white matter of the whole brain, it somehow only includes the bottom half of the white matte

Re: [Freesurfer] talairach transformation troubleshooting problem

Hi Bruce, The aseg is also problematic for several slicesI uploaded the subject dir on theMatinos center file drop...since the file is too big, I separated into two parts. Thanks, Catherine From: Bruce Fischl To: Rongxiang Tang Cc: "frees

Re: [Freesurfer] talairach transformation troubleshooting problem

gt; > I was thinking that if it is ok to use stable version for most of the > subjects and use dev version for the two subjects that have problems, and > finally run group analysis with the whole data set? > > Thanks, > Catherine > > > > > On Feb 19, 2013, at

[Freesurfer] Some basic cortical thickness questions

Dear All, I have some basic questions about groups analysis for cortical thickness, and I looked over the list and tutorial, but still have questions. I have two groups, experimental and control, and both were tested before and after training... I plan to use qdec to run the group analysis, and

[Freesurfer] wmparc.mgz transformation

External Email - Use Caution Dear All, I would like to transform individual wmparc.mgz into MNI space for each of my subjects. I have tried using this command:mri_vol2vol --targ /data/mri/wmparc.mgz --mov /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --inv --reg /usr/local/

[Freesurfer] freesurfer masks for fsl processed data

External Email - Use Caution Dear All, I ran fsl feat on my functional data and have all my data transformed into standard MNI space. However, I would like to use freesurfer generated white matter parcellation (wmparc.mgz) to extract white matter signals from my MNI space functi

[Freesurfer] Could I run several freesurfers at the same time?

Dear All, I was wondering if I can run several freesurfers in my virtualbox simultaneously by setting up several virtual machines...my computer has 16G RAM and it's Windows 7 64-bit. Would working multiple freesurfers at the same time slow down the calculations? Moreover, I was wondering if my c

Re: [Freesurfer] Could I run several freesurfers at the same time?

virtual machine, should I just open several terminals, and enter in separate commands? If I understand correctly... Thanks Again! Catherine --- On Thu, 4/21/11, Bruce Fischl wrote: From: Bruce Fischl Subject: Re: [Freesurfer] Could I run several freesurfers at the same time? To: "

[Freesurfer] Change the default SUBJECTS_DIR...

Dear All, All my data is on a USB hard drive and I do not want to put them in the "/home/virtualuser/apps/freesurfer/subjects" directory, which is the default... Also, I would like to save all my results on that USB hard drive... I was wondering if I would be able to do that... I tried this: Fre

Re: [Freesurfer] Change the default SUBJECTS_DIR...

Hi Bruce,   Thanks for your prompt reply. I'm running the freesurfer in a virtual box in windows 7. When I plug the usb in, the computer just called it (E:)...and i just directly copy that directory"E:\data\Ventricle-freesurfer\ben\1.3.12.2.1107.5.2.7.20418.300901051836502528507" to the

Re: [Freesurfer] Change the default SUBJECTS_DIR...

CTS_DIR... To: "Bruce Fischl" Cc: "Rongxiang Tang" , freesurfer@nmr.mgh.harvard.edu Date: Saturday, April 23, 2011, 4:28 PM Hi Catherine You need to mount the external harddisk inside the virtualbox and give its path as $SUBJECTS_DIR. The path starting with E:\d

[Freesurfer] Tksurfer slow loading.....

Dear all, I met a problem when I tried to load the tksurfer...it doen't give any error, just extremely slow...I also tried the "straces -f",still very slow... FreeSurfer:~> tksurfer ben lh pial subject is ben hemi    is lh surface is pial surfer: current subjects dir: /home/virtualuser/apps/f