Re: [Freesurfer] 4.5 and 4.4 longitudinal base creation error from mri_concatenate_lta

Hi Matt Looks like there is something wrong with the lta mapping tp1 to the base. Can you send the full log? Thanks Martin On Oct 30, 2009, at 23:32, Matt Erhart wrote: Hello everyone, %% After running this command with v4.5 and v4.4: recon-all -base FREESURFERRECON_TEST_005_S_ 0221BASE45

[Freesurfer] 4.5 and 4.4 longitudinal base creation error from mri_concatenate_lta

Hello everyone, %% After running this command with v4.5 and v4.4: recon-all -base FREESURFERRECON_TEST_005_S_ 0221BASE45 -tp FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1 -tp FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1 -all -force %% I get this error: %% mri_concatenate_

Re: [Freesurfer] editing grey matter or white matter

Hi Karl, it looks like some type of darkening in the gray and white is going on there. If you put a couple of control points in the white matter where the intensity is less than 110 and rerun with autorecon2-cp it should fix this problem cheers, Bruce On Sat, 31 Oct 2009, karlkarl wrote:

Re: [Freesurfer] transverse gyrus and intermediate sulcus

Thanks Nick, This does seem to work. best wishes, Narly. On Tue, 20 Oct 2009, Nick Schmansky wrote: > Narly, > > v3.0 uses the aparc.a2005s atlas. > > to use the a2002s atlas in v3.0, edit the recon-all script and replace > instances of '2005' with '2002', which only appear in the cortparc2 >

Re: [Freesurfer] about the thalamus volume

yes, you should use Left-Thalamus-Proper and right On Fri, 30 Oct 2009, zhenxt03 wrote: > Hi, > > I found Left-Thalamus-Proper volume and Right-Thalamus-Proper volume in the > aseg.stats file. Do they have some difference between Left-Thalamus-Proper > volume and Left thalamus volume? If not, c

[Freesurfer] about the thalamus volume

Hi, I found Left-Thalamus-Proper volume and Right-Thalamus-Proper volume in the aseg.stats file. Do they have some difference between Left-Thalamus-Proper volume and Left thalamus volume? If not, can I use left or right thalamus proper volumes to do some statistics analysis between two groups

Re: [Freesurfer] structural morphometric analyses for 50 subjects

Hi Rito we have a very nice new longitudinal stream you can use for this. Martin Reuter can fill you in on it. cheers, Bruce On Fri, 30 Oct 2009, Ritobrato Datta wrote: > Hello All, > > I have processed about 100 datasets with recon-all (autorecon1, 2and 3) > > There are 50 subjects, each subjec

[Freesurfer] structural morphometric analyses for 50 subjects

Hello All, I have processed about 100 datasets with recon-all (autorecon1, 2and 3) There are 50 subjects, each subject is scanned twice, 19 months apart. So each subject acts as their own control. We only have structural data for these subjects only MPRAGES, one per each scan. No functional dat

Re: [Freesurfer] Fwd: FreeSurfer Error: bits = 0 not supported.

Hi Jordi, does this happen if you run it on a local machine? Is it repeatable? Where did you get the dicom from? cheers Bruce On Fri, 30 Oct 2009, Jordi Delgado wrote: > -- Forwarded message -- > From: Jordi Delgado > Date: 2009/10/30 > Subject: FreeSurfer Error: bits = 0 not

[Freesurfer] Fwd: FreeSurfer Error: bits = 0 not supported.

-- Forwarded message -- From: Jordi Delgado Date: 2009/10/30 Subject: FreeSurfer Error: bits = 0 not supported. To: freesurfer@nmr.mgh.harvard.edu Hello*, * My name is Jordi Delgado, I work with FreeSurfer on a cluster of machines. Yesterday I sent some subjects to process and fo