Re: [Freesurfer] Cannot allocate memory

Dear Bruce, I was running: recon-all -autorecon2-cp, after adding control points. When I then look at the surfaces using tkmedit -surfs or inflated surfaces using tksurfer, everything seems to fit and I can open every output I like. Also values for volumes seem reasonable. Thanks in advance. Be

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient). Thank you again for your time! Panos > Hi Panos > > it would certainly be possible to make that measurement, bu

Re: [Freesurfer] EM registration: brain centroid

Yes, I created my own atlas for use with 1-2 year olds. It seems to be happening for all of the subjects. I am wondering if changing the recon-all code to load the manual talairach.lta file for the EM_registration and CA_normalization would possibly fix the problem. It seems strange that the wm/gm

Re: [Freesurfer] EM registration: brain centroid

Hi Mark did you create your own .gca file? If so, why? Does it happen for all your subjects? Bruce On Mon, 12 May 2014, Mark Plantz wrote: As a quick update to this problem, it looks like the wm_mean and gm_mean are reasonable during the #SkullLTA and #SkullStripping steps. However, wm m

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Panos it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain. cheers Bruce On Mon, 12 May 2014, pfot...@nmr.mgh.ha

Re: [Freesurfer] Fwd: Overinclusion of brain volume during segmentation - Question

Hi Christina it's pretty hard to diagnose from just a handful of slices. I also doubt that it's a huge underinclusion - probably if you move click on a point and change to sagittal you'll see it looks less dramatic. In any case, if you upload a dataset we'll take a look. Alternatively you can

Re: [Freesurfer] EM registration: brain centroid

As a quick update to this problem, it looks like the wm_mean and gm_mean are reasonable during the #SkullLTA and #SkullStripping steps. However, wm mean = 0 and gm mean = 0 for the #CA_normalize and #EM_registration steps. Could this have anything to do with using a manual talairach alignment in p

[Freesurfer] Measuring cortical thickness at a specific location

Hi FS experts, I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickne

Re: [Freesurfer] Paradigm files

Yes, you can do that as long as you are not using an FIR analysis. doug On 05/12/2014 04:56 PM, Emily Boeke wrote: > Hi Freesurfers, > > I am doing some analyses for an experiment where paradigm files were > automatically generated by Matlab during stimulus presentation. The script > was desi

[Freesurfer] EM registration: brain centroid

Hi Freesurfers, Does anyone know if it is possible to manually set the brain centroid during the EM Registration step of the recon-all pipeline. I am using a non-default atlas, and have discovered that many of my difficulties have resulted from the brain centroid being incorrectly assigned to a

Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

Hi Christopher I don't think you will be able to draw the geodesic distance in the ribbon in 3D as it will cut across imaging planes unpredictably. If you want the true within-subject geodesic distance there are tools for doing this (I think it was part of Mukund Balasubramanian's Ph.D. disse

Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

Thanx Bruce, I will try out your suggestion and let you know. I think I will get a good estimate of the degree of metric distortions, because I have a lot of subjects tested ;-) If this will not work, or the distortions are to big, I will make use of the Spline Tool in Freeview manually drawin

[Freesurfer] Paradigm files

Hi Freesurfers, I am doing some analyses for an experiment where paradigm files were automatically generated by Matlab during stimulus presentation. The script was designed to make paradigm files for an older version of freesurfer, so the files only have 2 columns. I am going to adjust these fi

Re: [Freesurfer] Viewing functional data on the inflated brain

Hi Douglas, I don’t receive any emails from anyone, I only receive the the digest which is what I “reply” to. So I am not sure what you mean by “try responding to the email that I sent.” This is why I attempted to email you directly as I thought that is what you were asking for. I hope to hav

Re: [Freesurfer] 2x3 DODS analysis question?

I think the last contrast should be of the form 1 -1 0 -1 1 0 1 -1 0 -1 1 0 1 0 -1 -1 0 1 1 0 -1 -1 0 1 but I only looked over it briefly so you should double check that it makes sense. The others look ok doug On 05/09/2014 10:44 AM, Khadka, Sabin wrote: > Hi all, > I am trying to run 2

[Freesurfer] Error running recon-all on hpc computers

Hi all, I'm trying to run recon-all on some data using one of the hpc clusters at my institution using FreeSurfer v. 5.3.0. I've used 4.5.0 without a problem but I'm trying to rerun the data with the new version. I keep getting this error (FreeSurfer's log file is attached here) regarding the mni

Re: [Freesurfer] bbregister to register a .annot file to MNI space

The immediate problem is with permissions. The bigger problem is what you are trying to do. To transfer the label, use mri_label2vol and $FREESURFER_HOME/mni152.register.dat to map aparc+aseg.mgz to mni152 space. But this is not going to work very well because the label is small. Mixing volume

Re: [Freesurfer] bbregister to register a .annot file to MNI space

Nathan, I've run into problems like these before when the fsaverage directory is read only. This may be behind your "permission denied" error. Perhaps try to deconstruct the annotation file into your subjects_dir and do the bbregister command on your label of interest from there - or just copy the

[Freesurfer] bbregister to register a .annot file to MNI space

Hello, I am trying to use bbrestier to take an .annot file of a particular structure and register it to MNI space. I want to be able to use one of the FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and do a fMRI BOLD extraction in FSL in MNI space. Below is the command I us

Re: [Freesurfer] nonlinear models in longitudinal analysis

Hi Martin, Thanks for your reply. I'm not entirely sure what you mean (sorry - I'm new to this!). Do you mean something like this? For examining an increase between timepoint 1 and 2, but the same between timepoint 2 and 3? fsid fsid-base years years-to-years Day1 base 0 0.4 Day2

Re: [Freesurfer] Coomand not found

Ok, could you send the entire terminal output? Thanks. -Louis On Mon, 12 May 2014, Francesca Strappini wrote: > Thanks Louis! > > Yes, I did run tkmedit from the same terminal window I have sourced > freesurfer... > > Francesca > > 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke : >> Hi Francesca

[Freesurfer] A question about installation

Hi, I would like to install "Freesurfer," but I have a problem. I now only have a PC running Windows OS. So I am wondering if I could use "Freesurfer" by windows.(say in "VMware Player") Or should I buy Macintosh or somtehing because of memory problems? Sorry for my really novice question, Ikko K

Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

For #2 you can get the average with mri_segstats passing the mask with the --seg command and using --id 1. If the mask is in fsaverage space, then just apply it to the y.mgh (i,e the input to mri_glmfit passed with --y). Use the --avgwf option to mri_segstats. This will give you the average fo

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table On 05/12/2014 03:41 AM, amirhossein manzouri wrote: > Hi again, > I think I missed my question, How can I get the Mean Thickness of each > hemisphere for several subjects using the aparcstats2table com

Re: [Freesurfer] Coomand not found

Thanks Louis! Yes, I did run tkmedit from the same terminal window I have sourced freesurfer... Francesca 2014-05-12 16:57 GMT+03:00 Louis Nicholas Vinke : > Hi Francesca, > Are you trying to run the tkmedit command in the same terminal window you > have sourced freesurfer? You'll need to sourc

Re: [Freesurfer] Coomand not found

Hi Francesca, Are you trying to run the tkmedit command in the same terminal window you have sourced freesurfer? You'll need to source freesurfer in any new terminal window you open before being able to run any freesurfer commands. It's possible to set it up so that freesurfer is sourced automa

Re: [Freesurfer] distance comparisons across subjects in fsaverage group sphere

Hi Christopher the spherical mapping usually has on the order of 17-20% distortion in distances, and the registration is probably significantly more. I'm not entirely sure what are trying to do, but you can measure the difference in great circle length between the sphere and sphere.reg to get

Re: [Freesurfer] Cannot allocate memory

Hi Kristina you need to give us more context. What command is running when you get that error? cheers Bruce On Mon, 12 May 2014, Mayer Kristina wrote: > Hi there, > > I am using freesurfer on MRI data of children. > In one dataset I have following error appearing, I did not find described > b

[Freesurfer] distance comparisons across subjects in fsaverage group sphere

Dear Freesurfers, In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make. My question now, concerns the comparability of distan

[Freesurfer] Cannot allocate memory

Hi there, I am using freesurfer on MRI data of children. In one dataset I have following error appearing, I did not find described before. MRISalloc(41043678, 76): could not allocate faces Cannot allocate memory Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 x86_6

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Hi again, I think I missed my question, How can I get the Mean Thickness of each hemisphere for several subjects using the aparcstats2table command? On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri wrote: > Dear Doug, > I have read this post( > https://www.mail-archive.com/freesurfer@nmr.mgh