Re: [Freesurfer] ROIs of BV not coinciding with FS

hi Barnali- a good place to start is here: http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles at least 2 things need to be corrected: 1.the first value in each row of the label file must be a vertex number from the FS surface (yours look like line numbers). I don't know if the v

Re: [Freesurfer] finding closest vertex in matlab

hi Corey- There's many ways to do this, but here's how I would: 1.transform the talairach coordinates to RAS (using some transform you have already determined), that's what the surface vertices are in. You probably want to use the pial surface. [vert_coords]=read_surf(SURFFILE); 2.for each elect

Re: [Freesurfer] is there any more documentation for mri_segment?

in mm (default=4) -v verbose -pset % threshold (default=0.80) -x extract options from filename -w set wsize (default=11) -u usage good luck, -- brian t. quinn On Thu, 25 Mar 2004, Tamara Knutsen

Re: [Freesurfer] updated tkmedit won't run..

can get the surface drawn, and a blank tksurfer tools window. the output informed me it it found tk8.4 but needs tk8.3. if i compile the tk8.3 libraries, will this solve my problem(for tkmedit too)? thanks, brian t. quinn Brian T. Quinn MGH/MIT/HMS Athinoula A. Martinos Center for Biomedica

Re: [Freesurfer] New Segmentation

the steps for drawing a new segmentation are: 1. File->New Segmentation 2. define your colortable in the dialog box 3. Tools->Edit Segmentation 4. Tools->Configure Segmentation Brush good luck, Brian T. Quinn MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13

Re: [Freesurfer] Freesurfer & tkmedit

hi Xavier- i've encountered this problem before. we had to compile tk8.3, and that seemed to fix everything. also, we had to put the path to the tk8.3 in the beginning of the path variable. there may be an easier way i'm unaware of, but this worked for sure. good luck, Brian T. Qui

Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer

hi Rob- load the y values into tksurfer to see scatter plots. this file is generated during the estimation step of mris_glm (--y y.name_000.bfloat). to load in tksurfer: File->Load Group Descriptor File select the file with .fsgd that is associated with your sigt file(s). for the name i used a

Re: [Freesurfer] new segmentation error

i believe you have to create the directory first. Brian T. Quinn MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 On Wed, 14 Jul 2004, Chekema Nayasha Prince wrote: I used the new segmentation in tkmedit to draw labels in the

Re: [Freesurfer] could you please tell me how to use mris_anatomical_stats?

for even more detail with the annotations: mris_anatomical_stats -b -a $SUBJECTS_DIR/bert/label/rh.aparc.annot bert rh will output that statistics for each area in tabular format. use the '>' character to output to a file. -- brian t. quinn On Tue, 12 Oct 2004, Bruce Fischl wr

Re: [Freesurfer] tkmedit question

mri_label_volume -s -l will output to the logfile the volumes for each of the labelvalue(s) you list. example: mri_label_volume -s s126 -l s126hipps.log $SUBJECTS_DIR/s126/mri/aseg 17 53 will output the hippocampal volumes for subject s126. -- brian t. quinn On Tue, 28 Sep 2004, George

Re: [Freesurfer] Parcellation

and your CSURF_DIR is probably wrong. try this: setenv CSURF_DIR $FREESURFER_HOME (it should not be the subject's id) good luck, brian t. quinn On Mon, 18 Oct 2004, Bruce Fischl wrote: > Hi Massimiliano, > > it looks like your SUBJECTS_DIR isn't set properly. It

Re: [Freesurfer] help - mri_fill seed points

--- specify the points you select in the wm volume on the command line: recon-all -stage2 -cc-xyz -pons-xyz -subjid -------- good luck, brian t. quinn On Tue, 2 Nov 2004 [EMAIL PROTECTED] wrote: Hello,    I am new to the world of free surfer and just started processi

Re: [Freesurfer] mri_fill

n? Massimiliano ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] loading curvature

$systemTime+2] > [clock seconds]} {set foo 0} SetOrientation 0 SetZoomLevel 2 UnloadVolumeDisplayTransform 0 DoVolumeColorScaleInfoDlog DoBrushInfoDlog set gbDisplayFlag(flag_OriginalSurface) 0 SendDisplayFlagValue flag_OriginalSurface -- brian t. quinn On Wed, 12 Jan 2005, Goldman, Aaron (NIH/NIM

Re: [Freesurfer] parcellation

hi Wan- setenv $CSURF_DIR $FREESURFER_HOME parcellate_suject bert -- brian t. quinn On Thu, 13 Jan 2005, Wan Park wrote: Hi, I am want to parcellate my brains, but when I put "parcellate_subject" alone, I receive the following message; tcsh: CSURF_DIR: Undefined variable What should I

Re: [Freesurfer] parcellation

typos. that should be: setenv CSURF_DIR $FREESURFER_HOME (not $CSURF_DIR) and: parcellate_subject bert On Thu, 13 Jan 2005, Brian T. Quinn wrote: hi Wan- setenv $CSURF_DIR $FREESURFER_HOME parcellate_suject bert -- brian t. quinn On Thu, 13 Jan 2005, Wan Park wrote: Hi, I am want to parcellate my

Re: [Freesurfer] Parcellation 2

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] manual editting not implemented

an "create surface", but nothing is changed. What could have been wrong? Comments are appreciated. Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

Re: [Freesurfer] manual editting not implemented

ian On Fri, 14 Jan 2005, Joongnam Yang wrote: Thanks Brian, Does that mean csurf interface is useless for "creating surfaces" to implement the editting of major topological defects? Nam. "Brian T. Quinn" <[EMAIL PROTECTED]> 01/14/05 3:22 PM >>> hi Nam- please refr

Re: [Freesurfer] how to visualize the parcellation

ems to have finished without problems. now, how can i visualize the different areas? thanks, wan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t.

Re: [Freesurfer] how to seed points 2

select the CC and pons points. if you don't have talairach coords or you just can't seem to get a good transform for you data, then use the RAS(but remove the talairach.xfm file and xform line in COR-.info). -- brian t. quinn On Wed, 26 Jan 2005, Wan Park wrote: Hello, Because I had proble

Re: [Freesurfer] averaging brains over two sessions

@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn

Re: [Freesurfer] Skull Stripping Problem

in and aux, respectively. select edit voxels tool, then Tools->Configure Volume Brush. in the dialog box, select 'Clone' under the Mode section, and 'Aux Volume' under the Clone Source section. now when you make edits to the main volume, it will fill in with the values from t

Re: [Freesurfer] spherical surface problem

fer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Parcellation II

another brain but this time i obtained this which looks much better: -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fsfast tkmedit-sess problem

hi Mike- in response to your 2nd question, the manual was created a few years ago and the binaries have changed since then, so the images won't look exactly the same, but should not be drastically different. thanks, brian t. quinn On Tue, 12 Apr 2005, Mike Angstadt wrote: Hi, I've ju

Re: [Freesurfer] -notalairach option not working

creating a transform during this step? Thanks, Margaret ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer

RE: [Freesurfer] Missing libraries?

hi Alex- this is not a problem. you can safely ignore it. thanks, brian On Tue, 7 Jun 2005, Fornito, Alexander wrote: Hi, We've managed to get it working. Your help is very much appeciated!! However, when I run recon-all -stage1, things work fine until it calls nu_correct. I then get a recur

Re: [Freesurfer] Vertex number

hi Sarah- you can you the matlab code in $FREESURFER/matlab to do this. use read_surf.m for this. -- brian On Fri, 15 Jul 2005, Sarah Rugheimer wrote: Hello, Does anybody know if there is a file with or a way to obtain a mapping of the vertex number with say the RAS coordinate system. I k

Re: [Freesurfer] Vertex number

m 1-> nverts+1 One more quick question. Do I have to read in the hemisphere's separately or is there a surface file that has both of them together (either the orig surface or the smoothwm surface)? each hemisphere separately Thanks so much for you help! Sarah thank you, brian Bri

Re: [Freesurfer] difficultly generating talairach.m3z

! Thanks Eliz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn

Re: [Freesurfer] difficultly generating talairach.m3z

i just wanted to point it out. keep it in mind in the future. On Fri, 29 Jul 2005, Elizabeth Fenstermacher wrote: Thanks Brian, Jenni actually already helped me. Eliz On Fri, 29 Jul 2005, Brian T. Quinn wrote: refer to: https

Re: [Freesurfer] anatomical_stats

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] Scripts in TkSurfer

or: http://www.msen.com/~clif/TclTutor.html you define the .tcl script for tksurfer on the command line foreach s ($SUBJECTS) foreach h (rh lh) tksurfer $s $h inflated -tcl load_ovrly_and_snaps.tcl tksurfer $s $h pial -tcl load_ovrly_and_snaps.tcl end end i hope this helps. good luck, -- brian t

Re: [Freesurfer] talairach transform issues

14-935-5019 [EMAIL PROTECTED] -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] unload segmentation?

urfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] mri_vol2surf help

if the borders are jagged you could dialate then erode the label on the surface in tksurfer. Tools->Labels->Dialate Selected Label Tools->Labels->Erode Selected Label this will also close any holes in the label. -- brian On Thu, 11 Aug 2005, Fornito, Alexander wrote: That worked thanks. Wand

Re: [Freesurfer] process volume again

-normalization -usenuintensitycor -skullstrip -segmentation stage one will take you a bit further down the FS stream, but will produce the wm volume. as for the -COR and -mgz flags, use whatever is appropriate. thanks, brian t. quinn On Fri, 19 Aug 2005, David Soscia wrote: hey guys, N

Re: [Freesurfer] auto segmentation editing

man/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harva

Re: [Freesurfer] auto segmentation editing

-0826 C- (518)-469-8317 [EMAIL PROTECTED] "Brian T. Quinn" <[EMAIL PROTECTED]> 08/23/05 2:08 PM >>> mri_edit_wm_with_aseg or recon-all -edit_wm_with_aseg (if it's in your version of recon-all -> grep for it.) On Tue, 23 Aug 2005, David Soscia wrote: thats

Re: [Freesurfer] global thickness

Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.

Re: [Freesurfer] regarding talairach & nuintensitycor

the talairach2 script to use the brain volume. Thanks in advance, You're welcome, brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] regarding talairach & nuintensitycor

this line: fast -t1 -c 3 brain.img seg_3.img should be: fast -t1 -c 3 brain.img -od seg_3 again, you may have to play with the -c value (3-6 have some success). thanks, -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Editing pial surface

ailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] A problem occurred while running recon-all in the new dev version

Sep 21 09:51:01 EDT 2005 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Group analysis

ormation is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian

Re: [Freesurfer] help with mris_ca_label

.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer