Re: [Freesurfer] missing temporal lobes

Hi Kristina that shouldn't be needed. If you upload a dataset we will take a look cheers Bruce On Thu, 22 May 2014, Mayer Kristina wrote: Hi there, I tried to put more CP, so all the temporal lobe tissue is in the mask. This will end up in overestimation of white matter. So in a second step

[Freesurfer] Classifying thickness question

Hi Bruce, I had a few questions concerning the mris_classify_thickness algorithm that you wrote: 1) Are there any other options (i.e. other flags) that can be specified in the mris_classify_thickness -o [options] ... : ... commandline? Because in the description of th

Re: [Freesurfer] Classifying thickness question

Hi Panos that binary is as old as the hills and there are way, way newer and better things to use (you might check out RvoxM) cheers Bruce On Thu, 22 May 2014, pfot...@nmr.mgh.harvard.edu wrote: > Hi Bruce, > > I had a few questions concerning the mris_classify_thickness algorithm > that you w

[Freesurfer] R: Re: R: Re: R: Re: Problem of size

Hi FreeSurfer expert, after that I have used the command "recon-all" I would like to obtain wm-lh and wm-rh information ( for example wm-lh-bankssts,wm-lh-caudalanteriorcingulate,wm-lh-caudalmiddlefrontal, ...). I have read that mri_aparc2aseg command can help me, but when I use it I have two

[Freesurfer] wm and ctx labels - mri_aparc2aseg

Hi FreeSurfer expert, after that I have used the command "recon-all" I would like to obtain wm-lh and wm-rh information ( for example wm-lh-bankssts,wm-lh-caudalanteriorcingulate,wm-lh-caudalmiddlefrontal, ...). I have read that mri_aparc2aseg command can help me, but when I use it I have two

Re: [Freesurfer] mri_vol2vol memory error

Hi Ben, please post questions to the list and not to us personally. Thanks! I do not have an alternative. I think you are using Thomas Yeo's stream which we are not supporting. He just uses binaries from FS. doug On 05/22/2014 12:16 PM, Ben Mooneyham wrote: > Hi Douglas, > > Thank you for you

Re: [Freesurfer] Classifying thickness question

Hi Bruce, I see. Thanks for letting me know, I'll definitely check it out! Best, Panos > Hi Panos > > that binary is as old as the hills and there are way, way newer and > better things to use (you might check out RvoxM) > > cheers > Bruce > On Thu, 22 May 2014, > pfot...@nmr.mgh.harvard.edu wro

[Freesurfer] unpacking error

Hi, I am trying to unpack dicom files and convert them to nifti, but am running into an error. I ran the following command with no issue: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info however, when I try to run the next command to actually unpack the data: unpacksdc

Re: [Freesurfer] unpacking error

Remove the \<> On 05/22/2014 03:45 PM, Caroline Lewis wrote: > Hi, > > I am trying to unpack dicom files and convert them to nifti, but am > running into an error. I ran the following command with no issue: > unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info >

[Freesurfer] installation recon-all

Hi Freesurfers, I've downloaded and installed Freesurfer on in VirtualBox running Ubuntu 12.04 (on a Windows 7 host machine). In my shell, though, it's installed with CentOS4 (see below) I've been working through the page on testing the installation. Everything works nicely, until I get to the re

Re: [Freesurfer] mri_vol2vol memory error

Hi Ben, There should be a procsurffast flag called -volproj_lowmem which avoids this mri_vol2vol memory issue. -Louis On Wed, 21 May 2014, Douglas N Greve wrote: > > mri_vol2vol when used in this way does not manage memory very well. It > resamples the time series into a 256^3 volume of floats.

Re: [Freesurfer] Differing OS X version and recon-all

What was your previous version of OSX before the upgrade to Mavericks? I would expect, but I can not claim with absolute certainty, that the differences would be extremely negligible, if existent at all. We advertise that the same version of Freesurfer should be used for the entire processing s

Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal

Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. a.y On Thu, 22 May 2014, Yoonho Ch

Re: [Freesurfer] unpacking error

Thanks Douglas. Now I am running into other errors. I ran the command: unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast \ ? -run 8 bold nii 001.nii ERROR: reading 0008/11147SACC000.MR.RESEARCH_NEURO.8.1.2014.05.13.14.42.14.530.48877356.dcm tag 28 30 Also, some of the runs in the "scan.info"

Re: [Freesurfer] unpacking error

hmmm, if it does not have tag 28 30, then something is really wrong. This is a Siemens dicom, right? What scanner? doug On 05/22/2014 06:05 PM, Caroline Lewis wrote: > Thanks Douglas. Now I am running into other errors. I ran the command: > > unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast

[Freesurfer] mris_convert to GIFTI misaligned in freeview

Hi, I converted a surface to GIFTI e.g., mris_convert lh.white lh.white.gii lh.white and lh.white.gii align when they are both loaded in 'tkmedit'. However, they do not align when loaded simultaneously in 'freeview'. Of possible relevance: When I loaded lh.white.gii into 'freeview', I got