[Freesurfer] mean cortical thickness on N ROIs

Dear FreeSurfers, suppose I should estimate the mean cortical thickness on a number N of ROIs (for instance, the left inferior temporal, the left middletemporal, and the left superior temporal). How would you suggest me to proceed? - Just performing a simple average of the 3 cortical thickness val

[Freesurfer] tracula update link not working

Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry Unive

Re: [Freesurfer] Fwd: mpr2mni305 failed error

Hi all! Sorry for my late answer but I went on holiday and I didn't have access to my mail. The background is normal in original dicoms and it is not an avarage of more than one run. The problem I reported was solved in all cases converting dicoms to nifti with dcm2nii and using the oriented volu

[Freesurfer] labelled tissue segmentation mask back to native

Hello, I was wondering if FS has an output mask (labelled volume) for each tissue types (gm+wm+venctricular_csf) that I can then turn into each subject's native space. I understand I can use aseg.mgz or even aparc+aseg.mgz and then run mri_label2vol. But then how do I get correspondent labelling f

Re: [Freesurfer] tracula update link not working

Hi Kirstie - This was a glitch related to yesterday's storage cluster maintence. It's been fixed now, so please try again. a.y On Wed, 20 Aug 2014, Kirstie Whitaker wrote: > Hi, > > I apologise if this is only on my end but I can't seem to download any of the > updates from http://surfer.nmr

Re: [Freesurfer] tracula update link not working

Yep! Working now - thank you very much :) Kx > On 20 August 2014 12:23, Anastasia Yendiki > wrote: > > Hi Kirstie - This was a glitch related to yesterday's storage cluster > maintence. It's been fixed now, so please try again. > > a.y > > On Wed, 20 Aug 2014, Kirstie Whitaker wrote: > > >

Re: [Freesurfer] tkmedit

Dear Don, Thanks alot for the attachment. I have installed it as recommended and tried the following and I started to get the error message below imaging@imaging-ThinkCentre-20:~$ freeview bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: Permission denied ​When using sudo

[Freesurfer] Some notes on getting Tracula to work for newbies

Hi Anastasia and the freesurfer list, I've been working on getting the latest version of tracula to run and I thought I would post here the errors that I've worked around. It's all been based on looking through the mailing list archives but I thought it would be useful to add them here all in o

Re: [Freesurfer] Some notes on getting Tracula to work for newbies

Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You are a model user :) On Wed, 20 Aug 2014, Kirstie Whitaker wrote: > Hi Anastasia and the freesurfer list, > > I've been working on getting the latest version of tracula to run and I > thought I would post here the errors

[Freesurfer] Creating the FSDG file for more than one discrete variable

Dear Freesurfer gurus, I am trying to create an FSDG file for my data set and I have a question regarding discrete variables. So say this is my data: Two discrete variables (two with two levels, one with eight), one continuous variable. I'm interested in one discrete variable (Patient/Control

Re: [Freesurfer] FreeSurfer platform/performance questions

Thanks for the reply Zeke. I understand what you are saying about the VM. So my question is now, how do we help our users to optimize FreeSurfer for their large scale data sets? We have a couple of Red Hat Enterprise Linux 6 64bit machines with the newest FreeSurfer installed (freesurfer-Linu

[Freesurfer] Open MP parallel processing scaling factor?

Hello all, Traditionally I have only processed FS data using a single core per person, but processing many people at once. Now we have caught up with the backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering if anyone has tested how the speed-up of open-mp vari

Re: [Freesurfer] Creating the FSDG file for more than one discrete variable

Hi Hanna, use #2 doug On 08/20/2014 10:36 AM, Isotalus, Hanna wrote: > > Dear Freesurfer gurus, > > > I am trying to create an FSDG file for my data set and I have a > question regarding discrete variables. > > > So say this is my data: Two discrete variables (two with two levels, > one with ei

Re: [Freesurfer] Custom aseg Color Lookup Table

Try loading aseg.mgz as the aux volume so you can see the number at a particular voxel. If the color is not correct, see what the number is and what it corresponds to in the LUT doug On 08/19/2014 05:57 PM, C.P. Frost wrote: > Hi all, > > I'm trying to use Freeview to display subcortical regio

Re: [Freesurfer] Open MP parallel processing scaling factor?

hi andrew, i haven't done many systematic comparisons but there are a few practical considerations to take into account. in recon-all, i believe a few steps are affected by the openmp option and that creates resource underutilization. processors run idle when those steps are not being run. in my

Re: [Freesurfer] tkmedit

Hi Ali, Sorry it didn’t work “out of the box.” It was kind of a long shot. That interpreter is for an i86 64bit system running linux. If you are running a Mac or have a 32bit os or … it will be a problem. If it’s the right one, it needs to be enabled for execution with the following command: c

[Freesurfer] problem downloading freesurfer

Hi I tried for three days download freesurfer even today but pressing the download link in http://surfer.nmr.mgh.harvard.edu/fswiki/Download These are fallen and message "This web page is not available" I have understood that the site was in maintenance, however the links do not even respond. a

[Freesurfer] GLM: Error Matric-Scale

whiplash.fsgd Description: Binary data group_diff.mtx Description: Binary data Hi there FreeSurferWhen trying the GLM-analysis I keep getting the following error. Could you help me with fixing it?ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08Pos

Re: [Freesurfer] Some notes on getting Tracula to work for newbies

On 20 August 2014 14:27, Anastasia Yendiki wrote: > > Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You > are a model user :) > Thank youalthough unfortunately not quite the best user - I still have problems... I think I lied in my earlier email - I think that the mr

Re: [Freesurfer] Some notes on getting Tracula to work for newbies

> On 20 August 2014 14:27, Anastasia Yendiki > wrote: > > Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You > are a model user :) Thank youalthough unfortunately not quite the perfect user - I still have problems... I think I lied in my earlier email - I think tha

Re: [Freesurfer] problem downloading freesurfer

It appears to work for me. Try this link to download directly: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg Once downloaded, go here for installation notes: http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall This should work on OSX Ma

[Freesurfer] Creating lower resolution surface models

I am running analysis where I am taking fMRI data using Freesurfer to project it onto the cortical surface and load it into Brainstorm to use as a constraint on the source reconstruction. I am able to do all the steps just fine, the problem I am encountering is that Freesurfer creates a surface wi

Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

Hello, The latest version of mri_tessellate can be downloaded using this the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate It would be wise to backup your existing version befor overwriting it with the version contained in the link above. -Ze

[Freesurfer] Fwd: Re: Custom aseg Color Lookup Table

Thanks for the reply, Doug. The main problem is that areas not included in my custom table appear colored in freeview. These areas' numbers correctly correspond to their indices on the default FreeSurferColorLUT, although they don't appear labeled in the info panel, nor are they listed to the left

Re: [Freesurfer] tkmedit

Agreed. Long story short, you need to ask your sys admin to install tcsh and link to it from /bin/tcsh if not already there. -Zeke On 08/20/2014 11:48 AM, Krieger, Donald N. wrote: > Hi Ali, > > Sorry it didn’t work “out of the box.” > > It was kind of a long shot. > > That interpreter is for an

Re: [Freesurfer] Open MP parallel processing scaling factor?

Andrew, I basically agree with everything Satra is saying. Just as an added piece if info, Ive included a chart which did a systematic study of recon-all processing times with different number of cpus in parallel. These results are a bit old (and might be for low-res data) but the general idea

[Freesurfer] Fwd: Re: Open MP parallel processing scaling factor?

Opps... I forgot the attachment. Here it is. -Zeke Original Message Subject: Re: [Freesurfer] Open MP parallel processing scaling factor? Date: Wed, 20 Aug 2014 15:24:14 -0400 From: Z K To: Freesurfer support list , Satrajit Ghosh , aos...@ufl.edu Andrew, I basically agre

Re: [Freesurfer] FreeSurfer platform/performance questions

On 08/20/2014 10:37 AM, Lazarevich, Alexander wrote: > Thanks for the reply Zeke. > We have encouraged our users to use these machines, but they have hesitated > because I think a lot of their data has already been processed on the XUbuntu > VM and they are worried about switching the FreeSurfer

[Freesurfer] bbregister for MRA

Hi Surfers I want to use bbregister to register my MRA scans to the structural scans. The first attempts by using these parameters came out OK but not perfect: bbregister --s --mov MRA.nii --init-fsl --reg register.dat --bold However, there are obvious problems around frontal areas. I ha

Re: [Freesurfer] bbregister for MRA

Using --t2 and --bold will always give identical results. If there is not much G/W contrast in the MRA (and there probably isn't), then you can try using the pial surface instead (maybe more GM/CSF contrast). Use --surf pial --t1. Use --t1 here because the GM will probably be brighter than CSF

[Freesurfer] Extracting Group Means for Cortical Thickness

Dear Mailing List, I have just completed a QDEC (v5.1.0) analysis of the following design: Measure:thickness Smoothing (FWHM):10 Hemisphere:lh 2 Discrete (Fixed Factors):group (2 levels, AtRisk & Control) and gene (2 levels, CC & TTorTC) 1 Nuisance Factos:age On

Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

Thanks Zeke Bruce > On Aug 20, 2014, at 1:55 PM, Z K wrote: > > Hello, > > The latest version of mri_tessellate can be downloaded using this the > following link: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate > > It would be wise to backup your existing

Re: [Freesurfer] no improvement for recon-all result after edits

Hi I am reposting my message, hoping someone can give me some hint to get my problem solved. Thanks in advance!! On Mon, Aug 18, 2014 at 10:42 PM, Jidan Zhong wrote: > Hi Freesurfer experts, > > I was doing some manual editing on our subjects which are patients with > lesions. I managed to cor