RE: [Freesurfer] Intstallation problems on new dev?

Great. Sorry, I'm a but slow on the uptake sometimes :) Thanks for your help! -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 9/9/2005 9:46 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvar

[Freesurfer] Skull stripping

Hi all, Couple of questions re: failures of skull stripping" - If you edit the brain volume after autorecon1, do you need to re-run autorecon1 again, or van you just continue on to autorecon2? - Is it a major problem if the strip removes the cerebellum, since it's excluded by the cuttting planes

RE: [Freesurfer] Skull stripping

, but I'd prefer to edit that after the surfaces are created. Thanks again! Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Sat 9/10/2005 10:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer]

RE: [Freesurfer] subcortical segmentation

I thought the recent version, eg., freesurfer-Linux-rh7.3-dev20050912-full.tar.gz did the subcortical segmentation. I've run it on a couplde of brains so far and it seems to be ok. Are there still some bugs with it? -Original Message- From: Bruce Fischl [mailto:[EMAI

RE: [Freesurfer] subcortical segmentation

: Fornito, Alexander Cc: Bosky Ravindranath; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] subcortical segmentation Hi Alex, that was a prerelease version. The subcortical stuff seems fine, but we have fixed a couple of small bugs in other things, so we are going to recommend that

[Freesurfer] large radius

HI, I've got some 3T SPGR data (512 x 512 x 104, vox dim. 0.488 x 0.488 x 2). I seem to be able to convert them to .mgz ok, but when I run mri_watershed I get an error saying "main radius too high" (output below). Any ideas as to what's happening? Thanks, Alex mri_watershed 1001670.mgz 10016

RE: [Freesurfer] large radius

: Wed 14/09/2005 6:29 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] large radius Hi Alex, I think that mri_watershed is 'incorrectly' assuming 1*1*1mmm

RE: [Freesurfer] intensity normalization failure

Is it possible to obtain and intensity histogram of the wm voxels, or descriptive stats (eg., Mean, SD) as a quick check? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thursday, September 15, 2005 3:33 AM To: Tracy Wang Cc: freesurfer@nmr.mgh.harvard.edu Subject:

RE: [Freesurfer] intensity normalization failure

creating surfaces on one, and then re-run afdter manual edits on the other?) Thanks, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 9/15/2005 10:11 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu; Tracy Wang Subject:RE

[Freesurfer] anatomical stats

Hi, I'm using the 20050905 distribution and it seems like mris_anatomical_stats is trying to look for cor files, when I've run my analyses using mgz. Is there a way to change this, or have I got it wrong?. Here is the output mris_anatomical_stats 101 lh white reading volume /data/flanders/wo

RE: [Freesurfer] anatomical stats

From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 9/16/2005 9:51 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] anatomical stats p.s. the flags should always come before the mandatory command line args. On Fri, 16 Sep 2005, Fornito, Al

RE: [Freesurfer] anatomical stats

ginal Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Sat 9/17/2005 10:33 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] anatomical stats try -b On Sat, 17 Sep 2005, Fornito, Alexander wrote: > I can create a log file

[Freesurfer] Autorecon re-processing

HI, Just wanted to check a few things re: re-running autorecon. I'm guessing that re-running autorecon with the -pial flag re-runs make_final_surfaces, which takes about 4-6 hours (correct?). What is re-run when the -wm and -cp flags are used, and how long do they take? >From what I understand, -

RE: [Freesurfer] Autorecon re-processing

ty sulcus, only partially enters it. I was curious as to why the orig/white surface would not follow the surface of the wm volume, and if there is anyway to fix it? Thanks, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 9/20/2005 4:03 AM To: Fornito, Al

RE: [Freesurfer] anatomical stats

Yeah, that's what I meant. That's fine, just wanted to make sure I wasn't doing it wrong! -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 9/20/2005 5:22 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Sub

RE: [Freesurfer] Autorecon re-processing

2:19 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] Autorecon re-processing probably susceptibility problems. Try putting some control points in the wm, but there may not be enough g/w contrast to get good surfaces. On Tue, 20

[Freesurfer] mgz format

Hi, Just wandering if someone could tell me what converting to mgh or mgz actually does to the image. COR changed it to 256x256x256, 1mm3, what happens with mgz/mgh? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

[Freesurfer] old version

HI, I need to re-install an older version of freesurfer in order to finish a study I have been working on, but it seems that particular distribution is no longer on the website. I think it was the 20040218 distribution (or maybe that was that update for it, I'm not sure). The recon-all -version

[Freesurfer] anatomical stats

HI, I'm finishing a study I completed using an older version of freesurfer (20040218), and have noticed that I get different values for surface area and grey matter volume when using mris_anatomical_stats for my labels depending on whether I use the mris_anatomical_stats that it is part of this

[Freesurfer] Pial surface errors

Hi, I've been having some problems with some of my images where the pial surface misses some parts of some gyri. Just wandering what the best way to fix this is. I've experimented changing the intensities using the configure volume brush tool in tkmedit with some success, but was wandering if t

[Freesurfer] Keeping edits

HI, I've been running autorecon2-wm or -cp after making edits to the brain volume as well, but it seems that the brain edits are not retaned in the final output. Is there a flag I'm missing? Also, to confim, If I run autorecon2-cp with the -keepwmedits flag, this will retain any edits made to th

[Freesurfer] Subcortical questions

Hi, Just wandering if there are any options for improving the results of the subcortical segmentation. It seems to label to large an area for many structures (eg., white matter gets included in the thalamus label). Also, are the surfaces through the midline of the subcortex (ie., the portion lab

[Freesurfer] Surface edits

Hi, When editing the wm, is it better to fill sections (eg., when thickening temporal lobe strands) using a brush with intensity at 255, or 110? I've noticed that if I fill using 110 and run autorecon2-cp with -keepwmedits the fill is basically ignored when the wm is re-segmented. Just wandering

RE: [Freesurfer] Surface edits

] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 14/10/2005 9:13 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface edits you need to fill the wm with 255 so we know it's an edit. Bruce On Fri, 14 Oct 2005, Fornito, Alex

[Freesurfer] Keeping edits

Hi, Is there any way to run autorecon2-cp with an edited brain volume so that it concurrently adjusts the pial surface. Everytime I try to run it, it seems to erase my edits to the brain volume. Howeever, running autorecon2-wm or -pial, uses the brain edits. Some help on this would be much appre

[Freesurfer] PDs?

Hi, We're about to start a longitudinal study and are keen to get accurate measures of structural change. Currently we are planning to acquire a T1 and T2, and have some spare time for another acuqisition. I've noticed in a recent paper (Fischl, et al (2004) Neuroimage,23, S69-S84) you discuss

[Freesurfer] .sulc and .curv

Hi, I was just wanting to know more about the .curv and .sulc files. Specifically, I had three questions: 1 - What exactly does the value assigned to each vertex represent (eg., is it the curvature of the vertex in the .cuv file?) 2 - How are they derived/calculated? 3 - What do they mean neuroan

RE: [Freesurfer] .sulc and .curv

Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 25/10/2005 10:57 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] .sulc and .curv 1. This is the smoothed

RE: [Freesurfer] aseg

Hi Jenni, Does this command provide the partial-volume corrected volumes, or do you need to use mri_seg_stats for that? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -

RE: [Freesurfer] PDs?

(clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 24/10/2005 10:19 PM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Su

RE: [Freesurfer] PDs?

of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Greg Harris [mailto:[EMAIL PROTECTED] Sent: Sat 29/10/2005 9:32 AM To: Fornito, Alexander; Bruce Fischl Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PDs? Hi Bruce and Alex. We currently thin

RE: [Freesurfer] area file

Hi, I was just wandering what determines the area value assigned to a given vertex. Is it the average area of the faces of the triangles to which it is attached? If so, what determines the area of the traingle faces? Do the values in the ?.area file reflect regional variations in surface area? I'

[Freesurfer] Control points

Hi, I was just after some more pointers on using control points. Some gyri are missed in some of my images, and using control points recovers them, but it also tends to make the wm surface eat into the grey matter in some regions. Just wandering if there's anyway to prevent this from happening?

[Freesurfer] Control point problems

Hi, The orig (white matter) surface misses some spots in some of my images, particularly around the anterior temporal lobes. I've tried using control points, and although this segments the strands in the wm.mgz volume, the surface still does not capture the true grey/white interface. I've tried

[Freesurfer] labels in tksurfer

HI, Just wandering if there's any way to adjust the opacity of labels as displayed in tksurfer? I'd like to display a label on the inflate surface and still see the curvature underneath. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Departmen

RE: [Freesurfer] Normalization problem

Hi, I've encountered similar problems. Do you know if it's specific to the autorecon2 flag? I'm wondering if running each process separately and sequentially get around it, e.g, running recon-all -normalization2, then recon-all -segmentation, then recon-all -fill, etc... Thanks, Alex Alex F

RE: [Freesurfer] N3 in FreeSurfer

Hi, I've created some labels in tkmedit, but it seems that I can only load one at a time in tksurfer.I can load eithe individually, but if I try to load one label while another is already loaded, tksurfer closes automatically. The output is below. Thanks, Alex tksurfer 140 lh inflated sur

[Freesurfer] mri_label2vol

Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the

RE: [Freesurfer] mri_label2vol

PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mr

RE: [Freesurfer] mri_label2vol

ourne [EMAIL PROTECTED] From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 6/12/2005 6:10 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol >From --help on mri_label2vol: --proj type start stop delta Pro

RE: [Freesurfer] mri_label2vol

Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 6/12/2005 9:50 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol Hmmm, when yo

[Freesurfer] Custom parcellation atlas

Hi all, I would like to create my own custom parcellation atlas for the frontal lobes using labels that I have traced on the surfaces. From what I can gather from the mailing list, I need to use mris_ca_train to do this. The usage states indicates I need to specify a canonical surface and an ann

RE: [Freesurfer] Custom parcellation atlas

elbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Sun 11/12/2005 12:34 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Custom parcellation atlas you need 1 annot/training subjects. The canonical surface is the ?h.sphe

RE: [Freesurfer] autorecon2-wm

Hi Doug, I tried to download this but get a "No such file `recon-all-nmr'" message. Cheers, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL

RE: [Freesurfer] autorecon2-wm

To: Fornito, Alexander Cc: Freesurfer Mailing List; Marin Richardson; Sasha Wolosin Subject: RE: [Freesurfer] autorecon2-wm Alex, The file is actually called 'recon-all', so try: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all After that is copi

RE: [Freesurfer] Defining one's own atlas in FreeSurfer

Hi, I'm also trying to create my own custom atlas, but can't seem to create an annotation file. I load my files in tksurfer, than click the "Export annotation" option and save the file. When I then try to re-import the annotation, nothing appears, and I get the message: % surfer: WARNING: no l

RE: [Freesurfer] Defining one's own atlas in FreeSurfer

y The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 16/12/2005 11:34 AM To: Fornito, Alexander Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer -n

RE: [Freesurfer] Defining one's own atlas in FreeSurfer

ECTED] Sent: Fri 16/12/2005 12:25 PM To: Fornito, Alexander Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer yes, sulc represents large scale structure of the folding patterns and preferences deep folds over shallow ones, while

RE: [Freesurfer] Defining one's own atlas in FreeSurfer

2005 12:25 PM To: Fornito, Alexander Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer yes, sulc represents large scale structure of the folding patterns and preferences deep folds over shallow ones, while curv is a differential

[Freesurfer] Sulcal depth

Hi all, >From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex

RE: [Freesurfer] Sulcal depth

ginal Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm

RE: [Freesurfer] Sulcal depth

.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 10:36 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.e

RE: [Freesurfer] Sulcal depth

(clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 11:29 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu

RE: [Freesurfer] Sulcal depth

ssage- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 10:33 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth you might be able to use mri_segstats. Give it the thickness file as --in, and use the sulc as the

[Freesurfer] tksurfer script

Hi, Is there any way to load a colour look-up table through tksurfer scripting? I can't seem to see any options in the usage. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED]

RE: [Freesurfer] tksurfer script

PROTECTED] Sent: Wed 28/12/2005 11:40 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer script labl_load_color_table On Wed, Dec 28, 2005 at 04:06:08PM +1100, Fornito, Alexander wrote: > Is there any way to load a colour look-up table through tksur

[Freesurfer] mris_anatomical_stats on custom annot

Hi, I'm trying to run mris_anatomical_stats on a custom parcellation, but am having problems because I don't know what the flag to speficy the appropriate colour table is. If I run the -b option, I get output but with no labels. If I run -f, I get a message saying that no colour table is loaded.

RE: [Freesurfer] mris_anatomical_stats on custom annot

e University of Melbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Sat 31/12/2005 12:54 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomical_stats on custom annot Hi Alex, did you run mris_c

[Freesurfer] .sulc in tksurfer

Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter

RE: [Freesurfer] .sulc in tksurfer

red to green (or light gray to dark gray if using binary colors) On Wed, 4 Jan 2006, Fornito, Alexander wrote: > Hi, > Does the 'threshold midpoint' value in tksurfer's curvature display control > correspond to values in the .sulc file (assuming the .sulc file is loaded),

RE: [Freesurfer] .sulc in tksurfer

ECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/01/2006 12:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] .sulc in tksurfer yes, that makes sense. On Wed, 4 Jan 2006, Fornito, Alexander wrote: > Hi Bruce, > I'm t

[Freesurfer] rh and lh neighbour error

Hi, I've been getting the following error message when running autorecon2-wm with some of my images.Any idea as to what might be causing this? Thanks, Alex Fill Fri Jan 6 14:15:18 EST 2006 Using transforms/talairach.lta mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -seg

[Freesurfer] Which white?

Hi, I've got a few reltively simple questions that I'm sure I've seen the answers to before but can't seem to find them again. What is the difference between ?h.orig, ?h.white, and ?h.smoothwm? Which one is automatically brought up in tkmedit when ?h.pial is loaded as a surface? Which is usd in t

[Freesurfer] Essential ingredients for labels

Hi, I'm trying to create some custom labels using matlab, but haven't had much luck. From what I've read on the FAQ page, the last two columnns are optional, so I've left them out. My label file therefore has 4 columns - vertex ID, and x y z, with the total number of vertices at the top. When I

RE: [Freesurfer] Essential ingredients for labels

:42 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Essential ingredients for labels Hi Alex, send us the label and we'll have a look. Bruce On Tue, 17 Jan 2006, Fornito, Alexander wrote: > Hi, > I'm trying to create some custom labels u

[Freesurfer] control points

Hi, I've generally been successful in using control points to get the white surfaces into darker areas, where the white matter appears similar to grey matter. I'm wandering if it's possible to use control points (or any other remedy) to get make the white matter segmentation less 'harsh', i.e.,

[Freesurfer] mri_convert orientation

Hi, I'm trying to reorient some analyze files using mri_convert. The files are in LAS format and I'd like to get them in LPI format. i run the command below, but get the message: mri_convert: unknown flag "--in-orientation" mri_convert -it analyze 101_lh_bound_gs -ot analyze ./101_lh_bou

[Freesurfer] RE: mri_convert orientation

.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Fornito, Alexander Sent: Tue 21/02/2006 9:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: mri_convert orientation Hi, I'm trying to reorient

[Freesurfer] tcl and annotations

Hi, Is there any way to 'automatically' save the labels in an annotation file using a -tcl script (or some other way) for a set of subjects? Thanks Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EM

[Freesurfer] MNI coords

Hi, I need to manually specify a seed point for the corpus callosum cutting plane on some of my images, although some of them don't seem to have the MNI coordiates available through clicking view >information in tkmedit. Not sure why this is the case, since other images do have this info. Specif

RE: [Freesurfer] MNI coords

8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 3/30/2006 11:41 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MNI coords Hi Alex, try "volume scanner coords

RE: [Freesurfer] MNI coords

30/2006 11:41 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MNI coords Hi Alex, try "volume scanner coords" for the subjects that don't have the MNI coords. Sorry, I know this is more confusing than it needs to be. In the new version you j

RE: [Freesurfer] MNI coords

, Bruce On Thu, 6 Apr 2006, Fornito, Alexander wrote: > Hi Bruce, > I tried using the volume scanner coords (which were identical to the RAS > coords), but this didn't seem to do the trick; the cutting plane was still > skewed away from the true midline. > After re-running some o

RE: [Freesurfer] MNI coords

els 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 4/6/2006 11:03 PM To: Fornito, Alexander Cc: f

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