[Freesurfer] consult

Dear FS expert： Today i put two contrast in the file {subjects},and run the command line "recon-all -s mgz -all", several minutes later,the terminal tells error,it says: [brain@localhost ~]$ recon-all -s mgz -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: frees

[Freesurfer] consult

转发邮件信息 发件人："传玺" 发送日期：2012-04-11 19:26:41 收件人：freesurfer 主题：[Freesurfer] consult Dear FS expert： Today i put two contrast in the file {subjects},and run the command line "recon-all -s mgz -all", several minutes later,the terminal tells error,it says: [brain@localhost

[Freesurfer] -cm switch error

Hello When I run recon-all with -cm switch, that generates error as follows: /* mri passed volume size is different from the one used to create M3D data ERROR: mri_ca_register with non-zero status 0 */ Without -cm switch, recon-all completes all processing without error. Any help would be appre

[Freesurfer] longitudinal processing (base-tps error)

HI all, I ran longitudinal processing with reco-all -base -tp -tp -all but in base-tps file of template ID I found the subject ID of MRI_T1 twice instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able to do for MRI_T1 but could not do the same for MRI_T2. ANy help would be

Re: [Freesurfer] consult

are your data really .46 mm in plane? It looks you are running out of memory, but even if you weren't it's very hard to reconstruct data that is that anisotropic (0.4688, 0.4688, 1.19996). You are better off getting 1mm isotropic and using it, which these days with 3T and 32 channels is only 4-

Re: [Freesurfer] -cm switch error

Hi Hiroyuki what size is your original data? Bruce On Wed, 11 Apr 2012, Oya, Hiroyuki (UI Health Care) wrote: Hello   When I run recon-all with ?cm switch, that generates error as follows:   /* mri passed volume size is different from the one used to create M3D data ERROR: mri_ca_regi

Re: [Freesurfer] consult

Hi haochuanxi please post to the list so that others can help! It looks to me like your voxel size is  (0.4688, 0.4688, 1.19996). Is that the case? If so, it's going to be har to reconstruct good surfaces even if you find a machine with enough memory. "in plane" means the resolution of your da

Re: [Freesurfer] longitudinal processing (base-tps error)

Hi Sabin, If the base-tps file contains a time point twice, that indicates that it has been created by passing the same time point twice, probably a typo. You need to remove the base and tp1.long and run again with the correct parameters. Best Martin On Apr 11, 2012, at 9:31, Sabin Khadka wrot

[Freesurfer] consult

Dear FS expert： Today I put two contrast in the file {subjects},and run the command line "recon-all -s mgz -all", several minutes later,the terminal tells error,it says: [brain@localhost ~]$ recon-all -s mgz -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: frees

Re: [Freesurfer] Clarification on centos version/updates/patches

H i Nick, Will the centos5 build of v5.1 work with centos6? I'm getting a new workstation and want to know which version of centos is better to install. On 04/10/2012 10:08 AM, Nick Schmansky wrote: > Wil, > > Hi, the contents of that 'misc' directory is just a filedrop of sorts to > supply fixes

Re: [Freesurfer] Clarification on centos version/updates/patches

Chris, yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it in-house). when the v5.2 release of freesurfer is ready (hopefully at the end of may) you will want to use the centos6 build, as it will get a bit better performance because of the compiler and some openmp options. n.

Re: [Freesurfer] Stylus Input for Cortical Edits

Hi Wil: The model we use for manual morphometry is the Wacom BAMBOO (pen) : Model CTL-460. best, Alan On Mon, Apr 9, 2012 at 12:22 PM, Irwin, William wrote: > Hi- > > ** ** > > I have been considering this option, and these comments pretty much make > it a given. > > ** ** > > Could y

[Freesurfer] Extraction Longitudinal Stats

Hi everybody, I have a question about FS longitudinal post-processing. Currently I obtained some corrected results comparing a Control vs. an Experimental group (pre-post). What i would like to know is if there's a thinning in the control group or a increase in the thickness of the experimental gro

[Freesurfer] mri_label2vol

Hi Can someone tell me please in*_details_*what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz thanks -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., U

[Freesurfer] longitudinal processing for lgi comparison

Hi all, Is there a longitudinal processing stream to compare local gyrification index (lgi) across two time points. -Sabin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inform

Re: [Freesurfer] mri_label2vol

Hi Johnson I believe it resamples the aseg to have the same geometry as the original scan. cheers Bruce On Wed, 11 Apr 2012, Johnson wrote: Hi Can someone tell me please in details what does this line do?  mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header

[Freesurfer] mri_segstats memory corruption error

Hello FreeSurfers, I ran the following command: mri_glmfit-sim --glmdir rhFwhm12Sig13 --sim mc-z 1 1.3 mc-z.abs.13.jls --sim-sign abs --overwrite When it gets to the part to do mri_segstats, it throws this error: 0 1*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2f30248

Re: [Freesurfer] mri_label2vol

And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote: > Hi Johnson > > I believe it resamples the aseg to have the same geometry as the > original scan. > > cheers > Bruce > On Wed, 11 Apr 2012, Johnson wrote:

Re: [Freesurfer] mri_label2vol

it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct On Wed, 11 Apr 2012, Johnson wrote: > And it exactly does that, does it register them together or use a pre-known > transformation matrix > On 04/11/2012 3:46 PM, Bru

Re: [Freesurfer] Extraction Longitudinal Stats

Yes, just extract the stats on each time point as done in a cross sectional analysis (but instead on the ?.long.base directories) do a paired t (or a t on the difference) to see if there is increase or decrease. If you look at one of the reported ROI's (e.g. caudate volume, or pre-central thicknes

Re: [Freesurfer] longitudinal processing for lgi comparison

No, should be very similar across time, or not? But the surfaces will be more reliable after longitudinal processing, can't you just run the lgi analysis on the tp?.long.base directories? Best, Martin On Wed, 2012-04-11 at 15:49 -0400, Sabin Khadka wrote: > Hi all, > Is there a longitudinal proc

Re: [Freesurfer] mri_label2vol

great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ? On 04/11/2012 4:40 PM, Bruce Fischl wrote: > it registers them based on the header information, but sin

Re: [Freesurfer] mri_label2vol

Yes, that is correct. On 04/11/2012 06:54 PM, Johnson wrote: > great, so if I can read the header from the aseg file and the header > from the rawavg header file I would be able to transfer any point from > the aseg space to the rawavg space is that correct ? > > On 04/11/2012 4:40 PM, Bruce Fisch

Re: [Freesurfer] mri_label2vol

yes On Wed, 11 Apr 2012, Johnson wrote: > great, so if I can read the header from the aseg file and the header from the > rawavg header file I would be able to transfer any point from the aseg space > to the rawavg space is that correct ? > > On 04/11/2012 4:40 PM, Bruce Fischl wrote: >> it regi

Re: [Freesurfer] mri_segstats memory corruption error

Hard to say. Can you send the full terminal output? You can just run it like: mri_glmfit-sim --glmdir rhFwhm12Sig13 --sim mc-z 1 1.3 mc-z.abs.13.jls --sim-sign abs --overwrite |& glmfitsim.log Then send me the log file. doug On 04/11/2012 05:14 PM, Jeff Sadino wrote: > Hello FreeSurfers, >

Re: [Freesurfer] mri_label2vol

there are two transformation matrices one in aseg and one in rawavg, how do I use them ? On 04/11/2012 6:12 PM, Bruce Fischl wrote: > yes > On Wed, 11 Apr 2012, Johnson wrote: > >> great, so if I can read the header from the aseg file and the header from the >> rawavg header file I would be able

[Freesurfer] freeview command line generic overlay colormap question

Hi all, I have a question about controlling freeview from the command line. I would like to overlay some z-score maps for individual subjects on the fsaverage inflated surface. I would like to use the 'color wheel' color scale setting and threshold the images between -1 and 1 standard deviations

Re: [Freesurfer] mri_label2vol

Invert one and compose it with the other On Apr 11, 2012, at 7:48 PM, Johnson wrote: > there are two transformation matrices one in aseg and one in rawavg, how do I > use them ? > > On 04/11/2012 6:12 PM, Bruce Fischl wrote: >> yes >> On Wed, 11 Apr 2012, Johnson wrote: >> >>> great, so if

Re: [Freesurfer] Stylus Input for Cortical Edits

Wil, We've been using the Cintiq models with great success for the past several years, it really speeds up manually editing. Only Windows and OS X are 'officially' supported by Wacom, but there is a thriving community

Re: [Freesurfer] mri_label2vol

so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct? On 4/11/2012 8:12 PM, Bruce Fischl wrote: > Invert one and compose it with the other > > > > On Apr 11, 2012, at 7:48 PM, Johnson wr