Re: [Freesurfer] pwd: permission denied

Hi Marcel: Do you using Mac? If so, please unlock your "root" account, then change to the root account (re-login as root or using 'su' command in terminal window). We also have this problem one month ago. It is because that the default setting for root account in OS X 10.7.x is hidden in the begin

[Freesurfer] About new FS version

Dear FS experts I've seeing that a new version of FS is about to be realized, but I'm wondering how soon will be it.Bests,Gabriel-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pab

[Freesurfer] How to find the anatomical slices in the data?

Dear All, Now I have some datas which are including anatomical data and function data,and I want to find the anatomical slices from them to run command 'recon-all'.How can I do? Yours ___ Freesurfer

[Freesurfer] save custom made path on surface as label

Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label fil

[Freesurfer] aparc.a2005s+aseg.mgz

Dear Freesurfer Mavens, After running "recon-all -all" on a set of anatomical data, I wished to used the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to create some ROI masks. I was particularly interested in the subcortical regions contained in the a2005s scheme. However, the ap

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: > Hello, > > I have run the following successfully, but when I have moved on to other > brains I get: > > mri_label2vol --seg chuman_1.mgz --temp orig.

Re: [Freesurfer] How to find the anatomical slices in the data?

if it's Siemens dicoms you can try unpacksdcmdir On Wed, 7 Mar 2012, bowan...@mail.ustc.edu.cn wrote: > Dear All, >Now I have some datas which are including anatomical data and function > data,and I want to find the anatomical slices from them to run command > 'recon-all'.How can I do? >

Re: [Freesurfer] qdec

Hi Julia, Please try deleting the space in 'Left Amygdala' and 'Right Amygdala' in your test.dat file and rerun qdec. Sita. On Wed, 7 Mar 2012, Richter, Julia wrote: > Dear Sir or Madam, > > I have a question concerning FreeSurfer. At the moment I am trying to run a > qdec analysis. I have

Re: [Freesurfer] save custom made path on surface as label

Yes, you probably need to generate a closed path, or a closed cut. I'm not sure if we support saving paths as label files. Anyone know? Bruce On Wed, 7 Mar 2012, Erhan Genc wrote: Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hi Anthony sounds like there is something wrong with one of your volumes. Can you ru mri_info on them? Bruce On Wed, 7 Mar 2012, Anthony Dick wrote: > Hello--I am giving this message a bump. Please let me know if there are > any suggestions. Thanks! > > Anthony > > On 2/15/12 1:43 PM, Anthony D

[Freesurfer] White Matter question

Dear all, I was wondering if you have encountered this issue before: Would you anticipate a difference between the volume calculated by Freesurfer 5.0 in Cerebral-White-Matter volume and the total volume calculated from the regions (defined by the Desikan atlas) in wmparc.stats? In one of my stu

Re: [Freesurfer] Interpreting Results

Hi Allie the real question is whether the surfaces are accurate in that place for that subject. The only way to tell is to visually inspect them. cheers Bruce On Wed, 7 Mar 2012, Allie Rosen wrote: Hi Bruce, I'm not sure if this qualifies as an outlier, but I do have one individual (and t

Re: [Freesurfer] pwd: permission denied

Hallelujah ! Problem solved! Here's what happened: both tcsh pwd and /bin/pwd give errors when a directory is executable (+x) but not readable (-r). And in my case, the colleague of mine fully opened up $SUBJECTS_DIR for me, but (and this is also how it should be done) only provided me with exec

Re: [Freesurfer] pwd: permission denied

Hallelujah ! Problem solved! Here's what happened: both tcsh pwd and /bin/pwd give errors when a directory is executable (+x) but not readable (-r). And in my case, the colleague of mine fully opened up $SUBJECTS_DIR for me, but (and this is also how it should be done) only provided me with exec

Re: [Freesurfer] FS 5.1 control points problem

Hi Tanja, Sorry if I missed something but was the cortex stripped off even before you made any edits. If so, it's probably skull strip error. Please refer to this wiki for instructions to correct the error. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix But if part of the

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hi Anthony, what's in chuman_1.mgz? How many labels? doug Anthony Dick wrote: > Hello--I am giving this message a bump. Please let me know if there are > any suggestions. Thanks! > > Anthony > > On 2/15/12 1:43 PM, Anthony Dick wrote: > >> Hello, >> >> I have run the following successfully, bu

[Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable

Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I check

Re: [Freesurfer] Interpreting Results

Hi Bruce and Doug, Given the fact that all my surfaces for my 16 patients and controls are fine, I'm still left with some basic questions: Since there is this interaction effect for age, how can I actually compare the thickness of the two populations? And should I be worried about the fact that

Re: [Freesurfer] Interpreting Results

Hi Allie perhaps David Salat (ccd) can comment. He definitely saw some areas that thickened with age. They weren't common, but they were definitely in the data. cheers Bruce On Wed, 7 Mar 2012, Allie Rosen wrote: Hi Bruce and Doug, Given the fact that all my surfaces for my 16 patients an

[Freesurfer] FreeSurfer Course in Amsterdam!

Hi everyone, The Department of Radiology at VU University Medical Center in Amsterdam, Netherlands is hosting a FreeSurfer Course on June 27th through June 29th. Registration is now open. You can find details about course as well as the registration form on the following website: http://www.free

Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable

Hi again More on this note: Using the previous stable version 4.3.0 that I have installed here, I have absolutely no problem in running the same process. ian From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian Charest Sent: 07 March 20

Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable

are there other mni tools installed? are the variables from the different freesurfer installs getting mixed? n. On Wed, 2012-03-07 at 19:01 +, Ian Charest wrote: > Hi again > > > > More on this note: > > > > Using the previous stable version 4.3.0 that I have installed here, I > hav

[Freesurfer] Fwd: Qdec Error in analyze: command failed

Hi All, Just wanted to follow up on my message below. Thank you! Laura. -- Forwarded message -- From: Laura Tully Date: Mon, Mar 5, 2012 at 2:03 PM Subject: Qdec Error in analyze: command failed To: freesurfer@nmr.mgh.harvard.edu Hi, I'm getting an error in analyze: command f

Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable

Hi Ian, This is a bug in the CBU's freesurfer wrappers written at the CBU site and not a FreeSurfer bug. Ask them to look into fixing it. Basically, the wrapper doesn't transfer all the variables necessary for FreeSurfer to run properly. The only work around for you at the moment would be to r

[Freesurfer] Cluster-Size in Qdec

Dear Freesurfer experts, I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different neuropsychological parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in diffe

[Freesurfer] recon2 error

Dear FreeSurfer community, I am running Ubuntu 11.10 on an Intel i7 970 3.20Ghz 64bit (11 CPUs) with 12GB DDR3 RAM on a 120GB raid 0 solid state hard drives. I have ran recon-all this summer on some of my subjects and it worked perfectly in 13 hours. I'm trying to run one more analyse (a recon-al

Re: [Freesurfer] recon2 error

Hi Jimmy that isn't an error message - just an informational one. How long did you wait? Are you sure it is not going to terminate if you let it run long enough? cheers Bruce On Wed, 7 Mar 2012, Jimmy Ghaziri wrote: > Dear FreeSurfer community, > > I am running Ubuntu 11.10 on an Intel i7 970

Re: [Freesurfer] recon2 error

I waited a whole night ... I don't recall getting this message last summer. I will run it again and check it back again on Friday just to be sure. Thank you, Jimmy On Wed, Mar 7, 2012 at 15:44, Bruce Fischl wrote: > Hi Jimmy > > that isn't an error message - just an informational one. How long

Re: [Freesurfer] recon2 error

a whole night may not be enough depending on the speed of your machine, and how far from our atlas anatomy your subject is. Those messages are normal and part of the most computationally intensive step in recon-all, so see if it take a day or so to finish On Wed, 7 Mar 2012, Jimmy Ghaziri wro

Re: [Freesurfer] Cluster-Size in Qdec

I don't think tthere is a way in qdec to define either. You can run mri_surfcluster externally to remove clusters under a certain size. With a few tricks you can remove the ones over a certain size too. doug Dusan Hirjak wrote: > Dear Freesurfer experts, > > I am a beginner in using Freesurfer.

Re: [Freesurfer] White Matter question

yes, the cerebral white matter is surface-based, so it can take into account sub-voxel resolution of the surfaces. The WMParc is just counting voxels. Dhinakaran Chinappen wrote: > Dear all, > > I was wondering if you have encountered this issue before: > > Would you anticipate a difference betw

[Freesurfer] "Smart" concatenation in selxavg3-sess?

Hi Freesurfers, The selxavg3-sess's help and Freesurfer documentation say that selxavg3-sess creates a design matrix for each run, fits the glm for each run, and then combines the runs together to give summary data for the subject's whole session. Some of the fsfast 5 slides say it uses "smart" c

Re: [Freesurfer] aparc.a2005s+aseg.mgz

Hi Mark, was aparc.a2009s+aseg.mgz created? That is the new one. doug On 3/7/12 8:43 AM, Kern, Mark wrote: > Dear Freesurfer Mavens, > > After running "recon-all -all" on a set of anatomical data, I wished to used > the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to create some > R

Re: [Freesurfer] "Smart" concatenation in selxavg3-sess?

The runs are brought into alignment during preprocessing. The default is to motion correct each run to the middle time point of the run, then sample the entire run to the common spaces (left hemi fsaverage, right hemi, or the MNI305 for subcortical volume). Once this is done, all the runs are i