Re: [Freesurfer] process dying during longitudinal reconstruction

What happens if you restart it? The log terminates in an odd place that I've never seen before. Nick On Wed, 2009-10-14 at 22:36 +, Dana W. Moore wrote: > Hi everyone, > > I am trying to run the longitudinal stream on some images. I have 3 > timepoints, and 2 of them finished the stream ju

[Freesurfer] process dying during longitudinal reconstruction

Hi everyone, I am trying to run the longitudinal stream on some images.  I have 3 timepoints, and 2 of them finished the stream just fine, but a third quits during autorecon1 during the 3rd and final longitudinal step.  There is no error message or anything, it just stops.  The log file is atta

Re: [Freesurfer] isxconcat-sess

Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in

Re: [Freesurfer] a question about mri_label_volume -eTIV

see: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV also note that mri_segstats is easier to use for getting etiv. nick On Wed, 2009-10-14 at 14:22 -0500, Guang Zeng wrote: > Hi, there, > > From FS Wiki, eTIV - estimated Total Intracranial Volume, aka ICV, > > I read > > mri_label_volume re

[Freesurfer] a question about mri_label_volume -eTIV

Hi, there, >From FS Wiki, eTIV - estimated Total Intracranial Volume, aka ICV, I read mri_label_volume requires specifying the transform file to use, and the scale factor: mri_label_volume -eTIV \ $sdir/transforms/talairach.xfm 1948 \ $sdir/aseg.mgz 17 53where $sdir is the path to the sub

[Freesurfer] Any way to calculate overlap of labels to atlas regions quickly?

Hello, I'm interested in subdividing some of the standard atlas regions into anterior and posterior divisions. Besides creating individual labels for each of the labels, is it possible to create a generic anterior label for multiple subregions (encompassing an entire lobe at a time), then quick

[Freesurfer] index out of bounds

Hello FreeSurfers, I'm trying to analyze some BOLD data where the subject moves through a dozen or so states over the course of an hour. None of these repeat but they are the same for all subjects. I have a .par file that specifies the duration of each segment with an integer index for each one.

Re: [Freesurfer] Fwd: probabilistic segmentation of gray matter

Hi Giacomo, all the freesurfer commands are stored in the subject's recon-all.log file. You should be able to find the mri_ca_label command in there and modify it. cheers Bruce On Wed, 14 Oct 2009, Giacomo Mandruzzato wrote: > Thank you for the answer but sorry, I don't know how use mri_ca_lab

Re: [Freesurfer] [martinos-tech] surfcluster & simulations

so doug we ran them using qdec. can you expand? On Tue, Oct 13, 2009 at 6:00 PM, Douglas N Greve wrote: > >> >> >> It depends on which program you ran and how you ran it. >> >> >> Frida Polli wrote: >> > >> > >> > hey bruce, nick, doug >> > >> > when we use qdec to generate simulations to find CWP

Re: [Freesurfer] Fwd: probabilistic segmentation of gray matter

Thank you for the answer but sorry, I don't know how use mri_ca_label function! I have aparc+aseg.mgz volume segmentation and I would have a probabilistic segmentation of gray matter cortical in ctx.mgz file. How can I do? I am a beginner freesurfer user! best Giacomo 2009/10/14 Bruce Fischl >

Re: [Freesurfer] using freeview

yes, that looks right On Wed, 14 Oct 2009, Ahmed, F, Me wrote: > Hello, > > I had problems with the "sliver" problem with Tkmedit and tried all of the > possible solutions to try and correct it, to no avail. My last resort was > using freeview. I tried the example commands Nick wrote on the wi

Re: [Freesurfer] Fwd: probabilistic segmentation of gray matter

Hi Giacomo, we don't write out the probabilities by default. To get them you would need to add -write_probs to the mri_ca_label command line (you can find it in recon-all.log for each subject). cheers Bruce On Wed, 14 Oct 2009, Giacomo Mandruzzato wrote: > -- Forwarded message --

[Freesurfer] Fwd: probabilistic segmentation of gray matter

-- Forwarded message -- From: Giacomo Mandruzzato Date: 2009/10/14 Subject: probabilistic segmentation of gray matter To: freesurfer@nmr.mgh.harvard.edu Hi, I have a question about a probabilistic segmentation of gray matter with freesurfer. How can I do it? if I binarize like t

[Freesurfer] fwd: Re: Re: problem display tksurfer in vmware

-Msg original- De: Giacomo Mandruzzato Enviado: 14/10/2009 06:22:24 Assunto: Re: Re: [Freesurfer] problem display tksurfer in vmware Hi, I have a question about a probabilistic segmentation of gray matter with freesurfer. How can I do it? if I binarize like this: mri_binarize --i aparc+