[Freesurfer] Writing annotations

Alex -- Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email:af...@cam.ac.uk Phone:+44 (0) 1223 764670 Fax:+44 (0) 1223 336581 Australian Details: Melb

[Freesurfer] Dense annotations

this to something else? Thanks for your help, Alex -- Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email:af...@cam.ac.uk Phone:+44 (0) 1223 764670 Fax:+44 (0) 1223 3

Re: [Freesurfer] Dense annotations

uniform) parcellations of > the surface. > > cheers, > Bruce > On Thu, 9 Apr 2009, Alex Fornito wrote: > >> Hi, >> We're trying to create some customized annotations in matlab, and then write >> them out to an .annot file. >> >> Some of these an

[Freesurfer] Anatomical stats for fsaverage

Hi, I'm playing around with different ways of generating custom annotation files using the fsaverage surface, and would like to estimate the surface area of each ROI. I tried running mris_anatomical stats, but it seems to required wm.mgz, which is not contained in the fsaverage directories (please

Re: [Freesurfer] Anatomical stats for fsaverage

s you can use if you want, I think mris_info will print it out. > > cheers > Bruce > > > On Fri, 5 Jun 2009, Alex Fornito wrote: > >> Hi, >> I'm playing around with different ways of generating custom annotation files >> using the fsaverage surfac

Re: [Freesurfer] Anatomical stats for fsaverage

r something, or you could run mri_annotation2label and run > label_area on the individual labels. > > Do you really want the surface area on the average subject? > > On Sat, 6 Jun 2009, Alex Fornito wrote: > >> Thanks, >> I did as you suggested, but got a different error t

Re: [Freesurfer] Anatomical stats for fsaverage

No, sorry. What is the error? On 09/06/2009 17:31, "Douglas N Greve" wrote: > Does this workaround account for the error in the raw area unavoidable > on an average surface? If not, are you aware of it and is it important > for your analysis? > > doug > > A

[Freesurfer] surf2surf for annots

Hi all, I have a custom annot in fsaverage space that I would like to map to the surface of each of my subjects. I have 2 questions about how mri_surf2surf does this: 1 - Does it use the surface-based registration performed in autorecon2, or is it a volume-based registration? 2 - If it is a volume

[Freesurfer] Mri_label2vol memory error

Hi all, I've tried running mri_label2vol on a few different computers now and keep encountering the same memory error. Can anyone provide suggestions as to how to get around this problem? I've included the output from a run using linux on a dual 3.05 GHz Xeon with 8GB ram below. Thanks for your hel

Re: [Freesurfer] Mri_label2vol memory error

o specify a different annot-table to > match your labels. > > doug > > Alex Fornito wrote: >> Hi all, >> I've tried running mri_label2vol on a few different computers now and keep >> encountering the same memory error. Can anyone provide suggestions as to how >&g

Re: [Freesurfer] Mri_label2vol memory error

On 20/10/2009 18:11, "Douglas N Greve" wrote: > > I just created a ribbon.mgz (link below). Copy this into fsaverage/mri > and see if it works. > > doug > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ribbon.mgz > > Alex Fornito wrote:

Re: [Freesurfer] Mri_label2vol memory error

again, Alex On 21/10/2009 12:27, "Alex Fornito" wrote: > Hi again, > After running the command, the output image seems to have the left hemi cortex > parcellated, but the right is all assigned one intensity (2000). Is there > something I'm missing? Outp

[Freesurfer] Problems converting annots

Hi all, Sorry to keep pressing this issue, but I am really stuck and need to sort this out before I can progress. I have been generating some customised annotation files, generally with 500 or more ROIs. The parcellation is done on a per hemi basis, meaning that there will not always be the same nu

[Freesurfer] FW: MINC Startup

Hi, We've just installed version 3.05 for Mac and get the error below when running -autorecon1. I've noticed this error has been posted to the list a few times, but it always seems to have been resolved internally. Any help is much appreciated. Thanks, Alex Can't locate MNI/Startup.pm in @INC (

[Freesurfer] Volumes for labels

returns. Is the mris_anatomical_stats volume estimate calculated on a vertex-by-vertex basis? Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre National Neuroscience Facility The University of Melbourne Levels 2 & 3, 161 Barry St Carlton South

[Freesurfer] Cluster thresholding

oup_lh_thk-0001.label Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia Ph:

Re: [Freesurfer] Cluster thresholding

-ocp <*.mgh> the output file *.sum can be opened in text editor and *.mgh can be seen using tksurfer. Check the link above link for more details (i just followed that link when i did last month). let me know if you get into more problems. pratap On 11/28/2007 07:43 PM, Alex Fornito

[Freesurfer] Qdec on leopard

Hi, I've just installed version 4.0.3 for leopard and can't open qdec. I get the error below. Any help is appreciated. Alex qdec & [1] 956 [pspc83:MRI_data/freesurfer/subjects_cann] alexfornito% X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of