Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Questions about Qdec
by Paola Valsasina 06 Jun '11

06 Jun '11

Dear FS list, I have a couple of questions about QDEC toolbox. 1) If I perform a multiple regression model and I obtain a significant cluster of correlation, is it possible to extract the corresponding regression coefficient, in order to report the strength of this correlation at that point? 2) Is it possible to perform some kind of masking? (e.g., to quantify correlation with a metric only within cortical areas that are different between groups?) 3) Is it correct that it is not possible to overlay the results of different qdec models on the same brain within qdec toolbox, but that we have to use a different tool (e.g. freeview?) to overlay multiple sig.mgh images at the same time? Thank you for any help Kind regards, Paola ----------------------------------------------------------------- Dai il tuo 5XMILLE al San Raffaele. Basta una firma. Se firmi per la ricerca sanitaria del San Raffaele di Milano, firmi per tutti. C.F. 03 06 42 80 153. INFO: 5xmille(a)hsr.it - www.5xmille.org

2 1

Commands missing in freesurfer directory
by ANN40＠pitt.edu 06 Jun '11

06 Jun '11

Hi all, I recently downloaded and installed freesurfer for a Mac PowerPC. I tried running recon-all on my data and an error message came up saying command not found for talairach_avi and many other commands. I looked in my /Applications/freesurfer/bin directory and that file wasn't there. All the commands that had worked such as mri_convert were. Does anyone know what could be causing this problem? Thanks, Ashley

1 0

Wm segmentation problem
by Irene Altarelli 06 Jun '11

06 Jun '11

Dear Freesurfers, we are processing a dataset of children through recon-all, applying manual corrections when needed. For one subject, after manual correction and running autorecon2-cp, we observe errors in wm segmentation, bilaterally, with portions of gm included in wm - as can be seen in the attached picture. This concerns most of the coronal slices. We have been checking that control points were not misplaced and they look ok to us. What do you think is happening there and is there anything we can try before manually correcting these errors? Thanks very much in advance, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23

3 3

freesurfer license
by carolina.mr 05 Jun '11

05 Jun '11

2 1

How to refine the recon-all results from old version?
by Xinian Zuo 04 Jun '11

04 Jun '11

Hi, FSers We have lots of data run based on a previous version (see 5.0). Is there any way to refine them using the FS5.1 pipeline but not to re-run all steps of recon-all? Many thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

2 2

GUI analysis
by Carolina Valencia 03 Jun '11

03 Jun '11

Dear freesurfer users I want to know where I can find the GUI that assist in the management and analysis of groups of data not shown in the FreeSurfer Analysis Pipeline Overview Thanks, Carolina

2 1

surface appear dark in Freeview, inverted normals?
by Reza Farivar 03 Jun '11

03 Jun '11

Good morning, I've constructed some monkey surfaces that actually look quite accurate, but appear dark in Freeview (they render normal in tksurfer). It really looks like the normals are inverted. Could that be the case? If so, how do I invert them? I know of non-freesurfer tools that can do this, but I thought there might be some simple freesurfer command for that. Thanks, Reza

2 1

a question about fsaverage
by Dai Dai 03 Jun '11

03 Jun '11

Hi, everyone The freesurfer v5 i downloaded do not have fsaverage3 ~ fsaverage7, where can i find them? 2011-06-03 Dai Dai

2 1

WM edits with tkmedit make no difference
by Joel Bruss 03 Jun '11

03 Jun '11

I have a subject run through recon-all that has gross errors in GM/WM surfaces. I did my best to follow the ControlPoints tutorial on: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints My first try had >300 control points with no difference in the WM.mgz file. I stumbled upon the freesrufer.failure_modes.ppt and it states: "Don’t edit too much! This will reduce reliability and is almost never needed. Usually this means you need to start over as you’ve done something wrong (e.g. put control points in the wrong place)." I deleted my control points .dat file and tried again with only 12 control points, somewhat logically spaced throughout the whole brain. Still no improvement. Attached is a coronal image, typical of the error. So, what to do? Much of the normalized volume has values of 110 and it's my understanding that adding control points to values <110, that are known WM, will bring down the average value/tissue intensities. Here's a part of the stdout as I ran recon-all -autorecon2-cp -autorecon3 -subjid "subject": preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.1 +- 6.4 [80.0 --> 125.0] GM (74.0) : 72.4 +- 9.9 [30.0 --> 96.0] setting bottom of white matter range to 82.3 setting top of gray matter range to 92.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... My control points fall withing the WM range, as does much of the "110" labeled voxels, but the surface/WM.mgz file isn't improving. What am I doing wrong and what can I try next? Thank you in advance for any/all responses. -Joel

2 1

Problem in func2roi-sess
by John Richey 03 Jun '11

03 Jun '11

Dear freesurfer experts, I am having a problem in extracting ROI data using func2roi-sess, and any help would be most appreciated. I wish to evaluate functional data in two ROIs that I created using mri_cor2label (left and right amygdala). Here is the command line: func2roi-sess -roidef 54 -analysis autreg_analysis_vol -anatlabel 54 -s 20110519_12925 -maskthresh 1.3 Below, I pasted the relevant portion of the logfile produced by func2roi-sess. To the best of my understanding, at least part of the problem seems to be due to the fact that a file called COR-.info can't be found, nor can a file called "bold/001//../transforms/talairach.xfm". I've also tried it with the flag -labelspace tal (and native), but no luck. Should these have been produced by selxavg3-sess , or perhaps I am missing a step somewhere along the way? Many thanks, J Richey ... INFO: label2mask_linear: there were 2141 label hits voxsize = 60.8, rszthresh = 1e-07, thresh = 6.08e-06 INFO: label2mask_linear: there were 75 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 75 Done averging over ROI (nhits = 75) ------------------------------------------- /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925 mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg bold/register.dat --label /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label --talxfm talairach.xfm --finalmskvol bold/autreg_analysis_vol/54/mask --roiavgtxt bold/autreg_analysis_vol/54/-001.txt ------------------------------------------- corRead(): can't open file bold/001/COR-.info -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925 mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg bold/register.dat --label /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label --talxfm talairach.xfm --finalmskvol bold/autreg_analysis_vol/54/mask --roiavgtxt bold/autreg_analysis_vol/54/-001.txt version $Id: mri_vol2roi.c,v 1.32 2011/03/02 00:04:25 nicks Exp $ -------------------------------------------------------- roifile = bold/autreg_analysis_vol/54/-001 roitxtfile = bold/autreg_analysis_vol/54/-001.txt oldtxtstyle = 0 srcvol = bold/001/ srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/001/ ...can't find talairach file 'bold/001//../transforms/talairach.xfm'

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