Freesurfer

freesurfer@nmr.mgh.harvard.edu

7 participants
30057 discussions

Determining r and p values from GLM
by rhaynes＠neuro.gatech.edu 10 Feb '06

10 Feb '06

In Figure 4 of your recent paper "Thickness of ventromedial prefrontal cortex in humans...", the graphs display r and p values which are defined at a "peak vertex" in the paper. In tksurfer, if you compute statistics over a defined ROI you get similar graphs, but how do you find the peak vertex in this set of vertices and how do you obtain r and p? And is there a way to get statistics (r and p) for all the vertices in the region (summary statistics, upper/lower bounds, etc)? Thanks. Ryan Haynes Research Assistant Children's Healthcare of Atlanta

1 0

DICOM file conversion problem
by Kerr, Catherine E. 10 Feb '06

10 Feb '06

I have what appear to be dicom files. The root directory of the CD ROM contains a file called dicomdir. The files are in a directory and named with non-consecutive 8-digit numbers. The directory is named with an 8 digit number as well. After converting the files to mgz format, running recon-all, and viewing the image, I see that the slices are not oriented correctly. In the coronal view, the image looks like a thin, incoherent stripe. In the sagital view there are several sagital slices and several coronal slices and most of the slices have no image on them. What is going on here?

2 1

mri_label2vol
by marc ruiz 10 Feb '06

10 Feb '06

2 1

RE: [Freesurfer] feat2surf
by Strien, N van 10 Feb '06

10 Feb '06

I sent this e-mail before, but it seems that it arrived nowhere. I hope you can have a look at it still - thanks. Niels Hi Doug, Thank you for your reply. Just to make sure, you linked a file called mri_surf2surf instead of mri_vol2surf. Is this what you intended? It seems as if the feat2surf script has some errors still - at least for me. The script as you made it searches for .img and .nii files. However when I run the script, the script stops when not finding any .img files. Or to be more precise: 1) it does not seem to look for any .nii files 2) it sets srcvol = mblok1+.feat/stats/*.img which will lead to errors later on in the script So the imglist variable is not filled with .nii images. When I run the script with set imglist = ($statsdir/*.nii), it finds my zstat*.nii images and properly sets e.g. srcvol = mblok1+.feat/stats/zsat1.nii etc Also, the script complains that the mkdir command receives too few arguments. This results in my case that the output of the mrui_vol2_surf command is stored in the $HOME dir. When using the mri_vol2surf manually I did manage to overlay the stats output. (only when using the mri_vol2surf of the previous (november) dev release). I would be grateful if you could send me the updated mri_vol2_surf. Thanks again for your help. The next step for me is a functional mri analysis in spherical space... so I might knock on your door again with that if I may. Niels

1 0

mri_surf2surf
by Don Hagler 09 Feb '06

09 Feb '06

Hi guys, There seems to be a minor bug in mri_surf2surf when trg_type = w. If trgsurfval is given as a relative path name (e.g. no directory sepcified with intention to create in current working directory), the output file name can be prefixed by" lh." or "rh." and it can be put in the subjects surf directory. Being put in that directory only happens when trgsubject is not ico. Don

2 2

rh.sphere.reg not running?
by Steve Smith 09 Feb '06

09 Feb '06

Hi - sorry if this is a stupid question, but when I use the latest recon-all I get the lh.sphere.reg fine but not the rh - the final listing is: ..... -rw-rw-r-- 1 steve analysis 563291 Feb 8 09:31 lh.thickness -rw-rw-r-- 1 steve analysis 5070714 Feb 8 09:31 lh.smoothwm -rw-rw-r-- 1 steve analysis 563291 Feb 8 09:34 lh.sulc -rw-rw-r-- 1 steve analysis 5071028 Feb 8 09:34 lh.inflated -rw-rw-r-- 1 steve analysis 5071339 Feb 8 11:42 lh.sphere -rw-rw-r-- 1 steve analysis 5071734 Feb 8 12:54 lh.sphere.reg -rw-rw-r-- 1 steve analysis 5071746 Feb 8 14:02 lh.rh.sphere.reg -rw-rw-r-- 1 steve analysis 563291 Feb 8 14:02 lh.avg_curv -rw-rw-r-- 1 steve analysis 3485297 Feb 8 14:09 rh.orig.nofix -rw-rw-r-- 1 steve analysis 2614948 Feb 8 14:10 rh.smoothwm.nofix -rw-rw-r-- 1 steve analysis 2615288 Feb 8 14:13 rh.inflated.nofix -rw-rw-r-- 1 steve analysis 2615615 Feb 8 14:37 rh.qsphere.nofix -rw-rw-r-- 1 steve analysis 580459 Feb 8 14:39 rh.defect_labels -rw-rw-r-- 1 steve analysis 580459 Feb 8 14:39 rh.defect_chull -rw-rw-r-- 1 steve analysis 580459 Feb 8 14:39 rh.defect_borders -rw-rw-r-- 1 steve analysis 5055170 Feb 8 20:54 rh.orig -rw-rw-r-- 1 steve analysis 121 Feb 8 20:54 mris_make_surfaces.rh.mrisurf.c.version -rw-rw-r-- 1 steve analysis 5055491 Feb 8 22:07 rh.white -rw-rw-r-- 1 steve analysis 561635 Feb 8 22:08 rh.curv -rw-rw-r-- 1 steve analysis 561635 Feb 8 22:08 rh.area -rw-rw-r-- 1 steve analysis 5055491 Feb 8 22:53 rh.pial -rw-rw-r-- 1 steve analysis 561635 Feb 8 22:53 rh.curv.pial -rw-rw-r-- 1 steve analysis 561635 Feb 8 22:53 rh.area.pial -rw-rw-r-- 1 steve analysis 561635 Feb 8 23:01 rh.thickness -rw-rw-r-- 1 steve analysis 5055810 Feb 8 23:01 rh.smoothwm -rw-rw-r-- 1 steve analysis 561635 Feb 8 23:04 rh.sulc -rw-rw-r-- 1 steve analysis 5056124 Feb 8 23:04 rh.inflated -rw-rw-r-- 1 steve analysis 5056435 Feb 9 00:53 rh.sphere looking at the supplied bert it does look like rh.sphere.reg should be there - am I being dumb? Cheers, Steve. ------------------------------------------------------------------------ ------------------ Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve(a)fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ------------------

1 1

Newest stream
by Clifford A. Smith, PhD 08 Feb '06

08 Feb '06

With the most recent release, does the skullstripping take place with brainmask.auto.mgz and brainmask.mgz? After completing recon-all autorecon-all I checked brain.mgz. I had some frontal areas missing, so ran recon-all -skullstrip -wsthresh 30. Brainmask.mgz looks good. I believe that I know the answer, but to be safe, after running autorecon2 brain.mgz will reflect these edits? Thanks, Cliff ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

3 3

output problems
by Durastanti, Valentina (NIH/NINDS) [F] 07 Feb '06

07 Feb '06

-----Original Message----- Dear All: after launching the command: "mris_anatomical..." I have an output where all the results are written but the mean cortical thickness (where I get 0.0000+0.00) and surface area (where I get 0 as well). Thoughts? Thanks you! Valentina

2 1

Importing .8 and .5 scans into freesurfer
by Faden, Eric (NIH/NIMH) [F] 07 Feb '06

07 Feb '06

I have scans that are at .8 and .5 resolution as dicoms. Currently I am using to3d to rotate the images to the proper orientation. After that I have tried using 3drefit -xdel 1.0 -ydel 1.0 -zdel 1.0 to "resize" the image so that mri_convert doesn't resample the image, but this is also messing up the statistics for obvious reasons. Is it reasonable to just multiply the statistics by .512 (.8 ^ 3) and .125 (.5 ^ 3)? or how else can I prevent freesurfer from resampling my images to 1.0 resolution? -Eric

2 2

already skullstriped
by wuhappy＠seu.edu.cn 07 Feb '06

07 Feb '06

Hi, I already have the skullstriped brains data on the original image space. The skullstriped data is good. I want to know whether I can use the skullstripped data directly instead of starting from the original T1 images in FreeSurfer. Thank you very much! -Steven -- Ph.D. Laboratory of Image Science & Technology (LIST), Department of Biomedical Engineering, Southeast University, Nanjing, Jiangsu Province, P.R. of China,210096 Phone: +86-25-3794249 Fax: +86-26-3792698

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer