[Freesurfer] Version compatability

Hi, Is it a problem combining results from data processed using versions 3.03, 3.04, and 3.05? I have some data processed on 3.03 but I'm updating other machines and I'd like to install 3.05. Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department

[Freesurfer] mri_convert orientation

Hi, I'm trying to convert a series of siemens dicom mosaic format files to analyze format, while reorienting at the same time. Running the command below converts and reorients only the filename specified in the command line (which is the first file in the series), whereas leaving out the

RE: [Freesurfer] Converting DICOMs

, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 10/4/2006 2:03 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Converting DICOMs On Wed, 4 Oct 2006, Fornito, Alexander wrote: Hi, I'm new to fMR and am using

[Freesurfer] Converting DICOMs

Hi, I'm new to fMR and am using mri_convert to convert from siemens dicom to analyze/spm format.I ran the command below and had a couple of questions: 1 - Why does the first INFO: line say that 807 files were found when only 805 were input? 2 - Why were only 800 of 805 files converted? 3 - As

RE: [Freesurfer] ROI Curvature

0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 10:21 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature p.s. sorry, the mean and Gaussian curvatures displayed

[Freesurfer] ROI Curvature

Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a

RE: [Freesurfer] 3T problems

0469 email: [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 4/28/2006 1:35 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3T problems did you check the talairach? On Fri, 28 Apr 2006, Fornito, Alexander

RE: [Freesurfer] Repeated-measures in mris_glm

8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 4/13/2006 1:45 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm Try using

RE: [Freesurfer] Repeated-measures in mris_glm

PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 4/12/2006 2:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm How did you create the average subject? Is there a T1.mgz in the mri

[Freesurfer] Repeated-measures in mris_glm

Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers

RE: [Freesurfer] Repeated-measures in mris_glm

] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 9:31 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm There are two ways to do it: 1. You can use DOSS, making each subject it's own class

RE: [Freesurfer] Repeated-measures in mris_glm

/11/2006 11:43 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Repeated-measures in mris_glm Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander

RE: [Freesurfer] MNI coords

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: freesurfer

[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.

RE: [Freesurfer] MNI coords

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

[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

[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

[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.,

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 using matlab

[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

[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

[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

RE: [Freesurfer] .sulc in tksurfer

] 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 trying to extract

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 filename 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

RE: [Freesurfer] Sulcal depth

: [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 mask and use

[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

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

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.edu Subject: RE: [Freesurfer] Sulcal

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] Defining one's own atlas in FreeSurfer

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 measure (mean

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

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 2 tells

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

] 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 curv

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 copied to your

RE: [Freesurfer] Custom parcellation atlas

] 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.sphere.reg. The annots can

RE: [Freesurfer] mri_label2vol

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 you say it looks splotch

[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

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

[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

[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

[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?

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?

[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

RE: [Freesurfer] .sulc and .curv

and 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

[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] 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, Alexander

[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

[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

[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

[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

RE: [Freesurfer] anatomical stats

[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, Alexander wrote: Hi

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

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] 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 isotropic

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

[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

[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] Skull

RE: [Freesurfer] Intstallation problems on new dev?

Do you mean you're not sure if it will work? -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 9/9/2005 9:28 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer

RE: [Freesurfer] Intstallation problems on new dev?

To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intstallation problems on new dev? we just have to test it. We've run the equivalent process many times, just not in the recon-all env yet

[Freesurfer] Intstallation problems on new dev?

Hi, We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz distribution on our systems, which run Debian 3.1. I noticed that unpacking the distribution did not place the perl5 directory in $FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then downloaded the

[Freesurfer] Lib prob?

Hi, We've recently installed the freesurfer-Linux-rh9-dev20050729.tar.gz distribution along with fs_supportlibs.tar.gz. csurf works ok, but if i try to run tksurfer, I get the error message below. We'd appreciate any help as we've been stuck for a while. Thanks! tksurfer 127 rh

[Freesurfer] Label colours

Hi, Can labels be loaded in different colours in tkmedit? Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___

RE: [Freesurfer] Editing labels

to label... -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Fri 8/12/2005 7:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] Editing labels The internal representation of the label format is treated differently

RE: [Freesurfer] Editing labels

the surface (?). -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Thu 8/11/2005 5:18 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] Editing labels I've been trying to edit some labels in tkmedit and have noticed

[Freesurfer] mri_vol2surf help

Hi, I'm trying to resample a volume (representing a subregion of the subjects T1) onto the surface using mri_vol2surf. When I try to load the output as an overlay in tksurfer, nothing appears. The output is below. Any help would be appreciated (note, I;ve also tried to output in analyze format

RE: [Freesurfer] mri_vol2surf help

PROTECTED] Sent: Thu 8/11/2005 1:42 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] mri_vol2surf help Definitely do not use cor as the output. Use paint format (also known as .w). See the examples. doug On Thu, 11 Aug 2005, Fornito, Alexander

RE: [Freesurfer] anatomical_stats

. Quinn [mailto:[EMAIL PROTECTED] Sent: Sat 7/30/2005 4:27 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] anatomical_stats sure: cd $SUBJECTS_DIR mris_anatomical_stats -f file.txt -b -a subjid/label/hemi.aparc.annot subjid hemi On Sat, 30

[Freesurfer] Editing labels

Hi, I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing

RE: [Freesurfer] stage1

Hi, The new version of recon-all certainly sounds exciting. Any dates for Linux release planned? I'm looking at starting processing on a large set of images and wouldn't want to begin and then re-do some of the processing because a superior method came out. Regards, Alex -Original

[Freesurfer] Skull stripping

Hi, recon-all stage1 overstrips some of my images during the skull-stripping stage. I've played with the different options, but they don't seem to make any difference at all. Any suggestions? I've tried feeding in a pre-stripped brain (stripped using BET), but the intensity normalization

RE: [Freesurfer] mri_vol2surf

) = 1.00548 +/- 0.427572 avg vertex radius (mm) = 61.0534 +/- 17.1529 -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 7/5/2005 1:40 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu Subject:RE

RE: [Freesurfer] mri_vol2surf

again, A. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 7/4/2005 11:25 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] mri_vol2surf Hi Alex, no, label files are text files with the extension

RE: [Freesurfer] mri_vol2surf

to apply the image as an ROI to the surface to get regional anatomical info. Thanks, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 7/4/2005 11:25 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer

[Freesurfer] mri_vol2surf

Hi, I'm trying apply ROI masks that I've manually traced in volume space to the same image's surface using mri_vol2surf. mri_vol2surf seems to requires a register.dat file, and I'm unsure what needs to be registered, since the volume that I traced the masks on is exactly the same as the one

RE: [Freesurfer] mri_vol2surf

macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro} -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 7/1/2005 12:47 PM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu

RE: [Freesurfer] mris_glm

-- recon-all exited with errors at Tue Jun 28 14:41:03 EST 2005 -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Wed 6/29/2005 2:26 AM To: Fornito, Alexander Cc: Itamar Kahn; Freesurfer Mailing List Subject:RE: [Freesurfer] mris_glm Alex

RE: [Freesurfer] mris_glm

... The following must be revisited** Segmentation fault -Original Message- From: Itamar Kahn [mailto:[EMAIL PROTECTED] Sent: Tue 6/28/2005 9:51 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject:Re: [Freesurfer] mris_glm

[Freesurfer] mris_make_average_surface

subject name for each subject? Why does it avarege the orig, and not final surfaces? Could you please give me an example of a command line? Thanks, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 6/22/2005 10:02 PM To: Fornito, Alexander Cc

[Freesurfer] vertex correspondance

Hi again, So many questions!! Is there some sort of correspondence between vertices on the inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner surface, is there a point on the outer surface, and if so, does Freesurfer retain this information in any of the files?

RE: [Freesurfer] vertex correspondance

between the points on each surface. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 6/22/2005 9:20 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex correspondance

[Freesurfer] mris_glm

Hi, I was seeking some clarification re: the relationship between the fsgdf and design matrix file for use with mris_glm. It seems to me that the two contain very similar info, the examples in the help dont use the fsdf at all. Is it necessary to create one, or can you just run an

[Freesurfer] Problems in pial surface?

Hi, I've been using freesurfer with only one run (image) pers subject and have generally been obtaining good results. I've just noticed a few quirks in the estimation of the pial surface that I was seeking some clarification. 1 - the algorithm consistently misses portions of grey matter in the

RE: [Freesurfer] recon-all stage3

To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] recon-all stage3 then you should just run the rest of the analysis I guess and see if it works. In general all the surfaces of a hemisphere should have the same # of edges/faces/vertices *except

[Freesurfer] recon-all stage3

Hi, I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? Thanks, alex writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere spherical transformation took 0.91 hours navgs=32

[Freesurfer] Strip and register check

Hi, A couple of questions; 1 - The skull stripping feature has overstripped some of my brains, and using -wsmore doesn't completely fix the problem. Are there any other options? 2 - I'd like to check my registrations by mapping labels from the average back onto the individual's brain. What's

RE: [Freesurfer] recon-all-nmr -disable-autoseg

6/9/2005 1:10 AM To: Bruce Fischl Cc: Fornito, Alexander; Elizabeth Fenstermacher; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg I think it looks in the average7 directory for a few labels (central

[Freesurfer] recon-all stage4b error

Hi all, I've created my the fional surface for some people and am trying to register them using recon-all -stage4b.However, I get an error message saying that I needed to do average labels (see output below). I've noticed that I get the same message if I try to morph_subject, except

RE: [Freesurfer] recon-all-nmr -disable-autoseg

That worked, thanks, Doug. To expand on the labels issue, from my understanding, the labels are used to check that the registration worked, and that these are automatically created. I don't have any files in my labels directory. Do you need to run parcellate_subject to get them? Is there any

RE: [Freesurfer] Missing libraries?

mm size and 256 voxels for all directions writing to nu... -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Sat 6/4/2005 7:41 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject:Re: [Freesurfer] Missing libraries? Alex

RE: [Freesurfer] Missing libraries?

Thanks Nick, We'll give it a try and keep you posted. A. -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Sat 6/4/2005 7:41 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Missing

[Freesurfer] skull stripping

Hi all, The page about using FSL with freesurfer on the FSL website recommends using BET to skull strip the images before feeding them into freeusrfer. I've had a bit of play with this, and have noticed some marginal improvements. Would you generally recommed this practice? Are there any

[Freesurfer] morph_subject error

Hi, I've come across some problems when I run morph_subject. It seems to work fine until near the end. I've included the final bit of the log below. The problem seems to occur after it calls MNI programs. I've been having trouble using the MNI tools through freesurfer, so I created the

[Freesurfer] Missing libraries?

Hi, We're really stuck on this one... We are running a linux kernel 2.4.26 debian 3.0 (woody). We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. We can't get the MNI tools to work through freesurfer, and only

[Freesurfer] Talairach help!!

Hi all, Sorry to labour this point, but I'm stuck with the MNI tools and am having trouble progressing through my freesurfer analyses. I can't create the talairach.xfm and was hoping for some help. If I run mri_convert in the command line, I get the following: mri_convert -it spm

[Freesurfer] MNI problems

Hi, I've been having some problems with the MNI tools (I can't create the talairach.xfm) and was hoping for some help. If I run mri_convert in the command line, I get the following: mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ mri_convert -it spm

RE: [Freesurfer] WMFilll and talairach coordinates

5/18/2005 10:55 AM To: Fornito, Alexander Cc: peggy christidis; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates 1. to report talairach coords. 2. To get cutting planes to separate the hemispheres

RE: [Freesurfer] WMFilll and talairach coordinates

Wouldn't that occur by using the MNI tools anyway? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 9:39 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll

RE: [Freesurfer] WMFilll and talairach coordinates

-Original Message- From: Fornito, Alexander Sent: Thu 5/19/2005 10:27 AM To: Bruce Fischl Cc: Subject: RE: [Freesurfer] WMFilll and talairach coordinates Now I understand. And this information has

RE: [Freesurfer] Segmentation error

Great. Thanks!! -Original Message- From: florent segonne [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 1:22 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation error

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