Re: [Freesurfer] lGI value is aberrantly high

Wayne, You can try to rerun the surface reconstruction (recon-all -autorecon2-wm -randomness, in order to change the number of vertices, and then recon-all -autorecon3) and then rerun the lgi process (recon-all -lgi), this should solve the problem. If not, please let me know. Marie On Jun 27

[Freesurfer] FNIRT and fslregister

Hi all, regarding the VolumeRoiCorticalThickness pipeline, is it possible to apply non linear transformation as obtained by FNIRT, instead of linear transformation as obtained by FLIRT? If yes, in which way? By using fslregister? Thank you marco ___

[Freesurfer] surface reconstruction of neonatal brain

Hello everybody, I would like to ask you about the topology correction algorithm of freesurfer. I have produced the tissue segmentation for a number of neonatal brains, but as they are not topologically accurate, I would like to try your algorithm to fix the surfaces. As I can see, the mris_fix_to

Re: [Freesurfer] long_mris_slopes

Hi Martin and all, I would like to ask you if by comparing tp1 thickness-spc with tp2 (and comparing tp2 with tp3) using the base brain between tp1,2 and 3 (altogether) I have messed up methodologically. I was expecting a rise in cortical thickness in certain areas between tp1 and tp2 followed by

Re: [Freesurfer] surface reconstruction of neonatal brain

Hi Antonis, you can try running it with the T2 as the brain.mgz and see how it goes. We do this fairly routinely on ex vivo data (which is T2* weighted) and it does ok. Not as well as in vivo where the contrast is what we expect, but it does produce topologically correct and geometrically reas

Re: [Freesurfer] lGI value is aberrantly high

Hi Marie: I have the same problem. I am doing LGI on a group of Genetic High Risk (for Schizophrenia) subjects (n=77). Here is what I got for one brain: * WARNING -- Problem for vertex iV = 57001, lGI value is aberrantly high (lGI=47.4609)... ...lGI computation will be stopped. This may be caused

Re: [Freesurfer] lGI value is aberrantly high

Hi Alan, If you only have this problem with one or just a few subjects, then I am pretty confident that running recon-all -autorecon2-wm -randomness will solve your problem. Otherwise let me know! Marie On Jun 28, 2011, at 3:48 PM, Alan Francis wrote: > Hi Marie: > > I have the same proble

[Freesurfer] sourcing freesurfer

I just installed freesurfer on Mac OSX and everything went smoothly in installation. But now I am trying to source it, and it's not working. I typed 'csh' into the terminal to launch c-shell, and then entered: [115-18-41-155-wireles1x:/Applications/freesurfer] Kat% setenv FREESURFER_HOME /freesu

Re: [Freesurfer] sourcing freesurfer

Hi Kat are you including the < and > in your setenv line? You shouldn't. It should be: setenv FREESURFER_HOME /Applications/freesurfer cheers Bruce On Tue, 28 Jun 2011, Kat Mott wrote: I just installed freesurfer on Mac OSX and everything went smoothly in installation.  But now I am tr

[Freesurfer] MRI_Convert error on recon-all process

Hello, My name is Jordi Casals. I've been trying to process some subjects with recon-all, but the procees is giving me this error: SUBJECT DFF_082 DATE Tue Jun 28 16:58:40 CEST 2011 USER neuro HOST td547.pic.es PROCESSOR x86_64 OS Linux Linux td547.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:

[Freesurfer] Recon-all with mris_fix_topology error

Hello FreeSurfer community, I am Jordi Casals, from Barcelona. After few days trying to process a set of modificactions done to a subject (pial, white matter and control points), I still have this error, about mris_fix_topology. I don't know where is the problem, because I have done a lot of subj

Re: [Freesurfer] MRI_Convert error on recon-all process

Hi Jordi where did your dicoms come from? Bruce On Tue, 28 Jun 2011, Jordi Casals wrote: Hello, My name is Jordi Casals.  I've been trying to process some subjects with recon-all, but the procees is giving me this error: SUBJECT DFF_082 DATE Tue Jun 28 16:58:40 CEST 2011 USER neuro HOST td

Re: [Freesurfer] Recon-all with mris_fix_topology error

Hi Jordi, what is the error? You didn't include it Bruce On Tue, 28 Jun 2011, Jordi Casals wrote: > Hello FreeSurfer community, > I am Jordi Casals, from Barcelona. > > After few days trying to process a set of modificactions done to a subject > (pial, white matter and control points), I still

[Freesurfer] Error using tkmedit

Hello, I have some problems with tkmedit. The recon-all finished without problems, but when using tkmedit the following error occured: /usr/local/freesurfer//tktools/tkmedit.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory T

[Freesurfer] Tkmedit error

-- Dr.Antonella Kis, PhD Clinical Research Project Coordinator The Hospital for Sick Children (SickKids) Diagnostic Imaging Department Neurosciences and Mental Health Sessional Lecturer Life Sciences, Physics Department University of Toronto at Scarborough Hello,

Re: [Freesurfer] Error using tkmedit

Hi Antonella sorry for the delay. Many of the FS developers have been away at the FS/FSL course and/or HBM. We'll try to get back to you today or tomorrow. Sounds like your linux installation is missing this library though and that you will need to install it. cheers Bruce On Tue, 28 Jun 2011

Re: [Freesurfer] Error using tkmedit

Hi Antonella, I found similar problems in the FreeSurfer mailing list archives: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07366.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03433.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07130.html

[Freesurfer] mri_volcluster in single direction

Hello All, I've been using fslstats to create a mask of voxels reaching a certain threshold and then using mri_volcluster to reduce the mask down to just clusters above 3 voxels. Now we're trying to filter them down to just those clusters that have more than 3 contiguous voxels in a single directi

[Freesurfer] mri_glmfit-sim problem...

Hi All, I tried using glmfit-sim to for multiple comparison correction on some previously analyzed data, and I've run into an error I don't understand: Here's the command I used: mri_glmfit-sim --glmdir tal.wrfx.arousal_v_valence_TP0 --cache 1.3 pos This generated the following error: ERROR: ca

Re: [Freesurfer] your mail

Hi Antonella, gzip doesn't recognize your file. Can you just send us a tif? Bruce On Tue, 28 Jun 2011, Antonella Kis wrote: Once again thanks Bruce. I am posting this message also  to the list: I am having problem with tksurfer. When I run:  tksurfer lh inflated for the Freesurfer data

[Freesurfer] Tracula question: group analysis

Hello Tracula Developers & Users, I can follow how to use the diffusion measures from pathstats.overall.txt for each subject to run a group analysis on the tracts. On the other hand I noticed there is also the pathstats.byvoxel.txt which contains various diffusion measures in each voxel along the

[Freesurfer] stats on masked functional data

Hello All, Looks like this question slipped through. I have a functional beta value overlay as a .mgh file and a V1 label file and I want to compute the average beta value within that mask for each subject. How do I do this ? Thanks a lot Ri ___ Fr

Re: [Freesurfer] stats on masked functional data

Hi Ri Doug may have something to do this, but if not it would be easy enough in matlab Bruce On Tue, 28 Jun 2011, Ritobrato Datta wrote: > Hello All, > > Looks like this question slipped through. > I have a functional beta value overlay as a .mgh file and a V1 label file and > I want to compu

[Freesurfer] Trac-all: using bvecs/bvals from FSL folder

Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the di

Re: [Freesurfer] Tracula question: group analysis

Hi Maryam - You could compare the different measures like FA or MD across subjects along the length of the pathway. There will be a different number of points along the pathway for each subject, so you'd have to interpolate the data points from all your subjects to do a point by point comparis

Re: [Freesurfer] Trac-all: using bvecs/bvals from FSL folder

Hi Jared - Have you looked at $FREESURFER_HOME/bin/dmrirc.example? You can specify bvecfile, bvalfile, and nb0. Currently these are assumed to be the same for all subjects. The format is 3 columns for bvecs, single column for bvals. Otherwise you shouldn't have to do anything else to them (hop

[Freesurfer] error in qdec design analyze

Hi Freesurfers, There existed an error "Error in Analyze: Couldn't open file /usr/local/freesurfer/subjects/PD1/surf/lh.thickness.fwhm10.fsaverage.mgh", when I clicked on the button "Analyze" in qdec design. I have only done "recon-all" with my data (PD-MPR group and Controled-MPR group). Did I mi