Re: [Freesurfer] Freesurfer vertex wise area reference

Dear Mahinda, For the mris_preproc, I think Doug posted already explaining how it works - it uses a jacobian correction in a way that makes it mass-conservative. You may want to search the archives. For the ROIs, the standard method is to add up the areas of their constituent vertices, so it shoul

[Freesurfer] Merging .annot files

Hello all, I posted this question on the cmtk users google group, but no takers, and perhaps this is the more appropriate venue anyways. I've been successfully using cmtk within iPython. After running connectomemapper parcellate() to get the Lausanne parcellation scheme, I get six .annot fil

Re: [Freesurfer] problem with AutoReco3 mapping

Hi Jon can you send us an image, perhaps with an arrow in it showing us what you mean? cheers Bruce On Thu, 17 Jan 2013, jonwie...@netzero.net wrote: > I did an AutoRecon3 on a brain and when i viewed the results. it failed to > classify some the tgray and white matter in the left hemisphere.

Re: [Freesurfer] nu_correct problem (fwd)

Hallo, now I use cc... Actually I gave you wrong info - I DID rename file patient.mgz to 001.mgz and not orig.mgz as I wrote before, sorry. I attach recon-all.log file with errors from my last run. It is about nu_ correct. Thanks for help, Petr      -- Původní zpráva --

[Freesurfer] problem with AutoReco3 mapping

I did an AutoRecon3 on a brain and when i viewed the results. it failed to classify some the tgray and white matter in the left hemisphere. the area misses is on the extreme left side of the brain, within 10 mm of the left side of the hemisphere. are there some arguments i change change to fix t

[Freesurfer] edit or not to edit?

Hi FreeSurfer folks, we are about to process about 120 images with FS v5.1 and stand in front of a decision whether to do manual intervention or use the results from fully-automated FS run. We intend to use the volume, thickness, area, curvature measures of subcortical and cortical regions an

[Freesurfer] long_mris_slopes / mris_calc problem

Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to pr

Re: [Freesurfer] pial not computing

Hi Mia this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated) cheers

Re: [Freesurfer] WM of lobes

You will need to create an annotation of the lobes (use mri_annotation2label --lobesStrict, or define your own). Then run mri_aparc2aseg with the --labelwm option. You can look in a recon-all.log for the other command options doug On 01/17/2013 07:54 AM, Gabriel Gonzalez Escamilla wrote: > D

Re: [Freesurfer] pial not computing

Hi Mia we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote: > Hi Freesurfers, > > I just ran a recon, and it seems that only the lh.pial computed, but not the > rh.pial. What would be the cause of this? > Thanks, > m > > __

[Freesurfer] pial not computing

Hi Freesurfers, I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

Re: [Freesurfer] nu_correct problem (fwd)

Hi Petr, Try renaming /subject/patient/mri/orig/orig.mgz to /subject/patient/mri/orig/001.mgz and rerunning recon-all. The orig.mgz file is created later on in the recon-all stream. -Louis On Thu, 17 Jan 2013, Louis Nicholas Vinke wrote: Please remember to cc the list. -- Forwarded

Re: [Freesurfer] nu_correct problem (fwd)

Please remember to cc the list. -- Forwarded message -- Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET) From: zach.p...@post.cz To: Louis Nicholas Vinke Subject: Re: Re: [Freesurfer] nu_correct problem Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer web pa

[Freesurfer] WM of lobes

Dear freesurfersI'm trying to get the WM parcellation by lobes, I have read some previous FS archives regarding a similar topic, but they only want the volume value, and I'm interested in a WM lobes parcellation in mgz format (like aseg.mgz ), and I'm also interested in knowing if is possible to ob