Freesurfer March 2011

freesurfer@nmr.mgh.harvard.edu

111 participants
170 discussions

way to binarize MGH file
by Ritobrato Datta 07 Mar '11

07 Mar '11

Hi All, I am looking for a way to binarize MGH files. I took a mask I made in volumetric space to surface space, and I want to binarize it so it doesnt contain decimal values. What is the command? Will mri_binarize work on mgh files ? I need to manipulate MGH files, with the same output type. Please let me know. Thx Ri

2 1

mri_convert FS_v5 Cannot allocate memory
by Ben Hamida Cammoun Leila Faiza 06 Mar '11

06 Mar '11

Hello, Since upgrading to the Version5 of FS, I cannot use the mri_convert I saw in the FS mailing a similar problem but in recon-all. Do you have any suggestion for mri_convert command? This is my command and error, and I added in also the reference of the mail I talked about. Thanks in Advance for your help. ps: I am working on MacPro4,1 with 6GB Leila bash-3.2$ mri_convert -vs 1 1 1 $CMT_SUBJECTS_DIR/$MY_SUBJECT/raw_diffusion/${MY_SUBJECT}.nii $CMT_SUBJECTS_DIR/$MY_SUBJECT/raw_diffusion/${MY_SUBJECT}_b0_resampled.nii.gz mri_convert -vs 1 1 1 /Users/leila/cmt/subjects//chuv_ayse_1_tp3/raw_diffusion/chuv_ayse_1_tp3.nii /Users/leila/cmt/subjects//chuv_ayse_1_tp3/raw_diffusion/chuv_ayse_1_tp3_b0_resampled.nii.gz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Users/leila/cmt/subjects//chuv_ayse_1_tp3/raw_diffusion/chuv_ayse_1_tp3.nii... INFO: using NIfTI-1 qform TR=6100.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) Reslicing using trilinear interpolation mri_convert(18893) malloc: *** mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(212, 212, 102): could not allocate 89888 bytes for 36156th slice Cannot allocate memory Re: [Freesurfer] Memory allocation problem with mri_robust_template Mahen Fri, 11 Feb 2011 09:16:27 –0800

2 1

Freesurfer Tutorial and Workshop April 16-18 in Sao Paulo, Brazil
by Pedro Paulo de Magalhães Oliveira Junior 06 Mar '11

06 Mar '11

The Freesurfer group and the Hospital das Clinicas from São Paulo University will be offering a three-day Freesurfer Tutorial and Workshop April 16-18 at the Radiology Institute in Sao Paulo, SP, Brazil. A description of the course and a list of the topics covered can be found soon at http://www.neuroimagem.com but it's based on the description of http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription The course will take three days this year and will be in English. The registration fee is 400 BRL. If you want to apply for a spot send an e-mail to ppj at netfilter.com.brwith your details. We'll have a form in the website soon. There is room for only 40 participants and registration is on a first-come, first-serve basis. If you are not one of the first 40, you will be put on a waiting list and will be notified if a spot becomes available. If you need any information about arranging payment for the course, accommodations,course location, as well traveling issues please contact me in the e-mail above. Regards, Pedro Paulo Oliveira Jr. --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

1 0

aparc+aseg.mgz and aparc.a2009s+aseg.mgz
by Pedro Paulo de Magalhães Oliveira Junior 06 Mar '11

06 Mar '11

I was checking the values at both aparc.a2009s+aseg.mgz and aparc+aseg.mgz and comparing it with the labels in FreeSurferColorLUT.txt I have noticed some problems: 1) There are values out of the range specified in FreeSurferColorLUT.txt (in bert dataset there are 353528 voxels with values above 14999) 2) There are many areas in FreeSurferColorLUT.txt that don't appear neither in aparc+aseg nor in aparc.a2009s+aseg My main concern is with the out of range values, which structure they map to? thanks --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

2 1

qdec
by wangguihong 05 Mar '11

05 Mar '11

I am a new user of freesurfer 5.0 to find the thickness differences between con and pat,and I have processed the data all right with recon-all.But I have several questions about qdec.I hope someone can help me. I just input the data in qdec.table.dat ,with others options just as the default,but the thickness output from the Find Clusters and Goto Max is difference from the data displayed on the teminal before qdec's analysis, why? And also,can somebody explain the function of the buttons in the qdec's third step (display),such as Set using FDR in the False Discovery Rate ,Monte Carlo Null-Z simulation.In detail, in my research, I just want to find the thickness differences between con and pat in the 33 ROI per hemisphere,if I just let these buttons as the default ,is it right ? Last, what does the "MAX" and "VtxMAX" and "NVtxs"mean just as follows,which is output from the teminal. Generating cluster stats using min threshold of 2... Found 5 clusters Contrast: 'rh-Diff-Yes-No-Intercept-thickness', 10fwhm, DOF: 21 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -3.4159 8928 51.50 31.9 -34.9 46.8 146 postcentral 2 -2.6111 120796 42.30 30.5 -6.5 -32.9 79 entorhinal 3 -2.5302 122287 22.28 35.4 -68.1 43.1 41 inferiorparietal 4 2.3762 145773 21.24 40.3 22.6 20.6 46 parsopercularis 5 2.1491 24852 19.94 4.8 -40.1 71.5 55 paracentral ============================================================ Thanks in advance! guihong

1 0

BBRegister mincost and B0 Masking
by Michael Waskom 04 Mar '11

04 Mar '11

Hey Doug, When using the bbregister feature to mask areas with b0 distortion, I find noticeably lower registration cost values (as revealed by the first number in the .mincost file that gets generated). When this number is calculated, does it take into account the registration in the areas affected by the mask? In other words, are the lower numbers evidence that masking distorted regions is significantly improving the registration accuracy, or just an artifact of masking out regions where the is bad registration from the cost calculation? Thanks! Mike

1 0

Re: [Freesurfer] Counting Gyri
by Bruce Fischl 04 Mar '11

04 Mar '11

mris_curvature -max -w <path>/lh.white will write out the max curvature at each vertex to a file named lh.white.max. Load this into tksurfer as a using the file->load curvature menu. You can then create a path in tksurfer by clicking on two end points, and type plot_curv 0 at the tcl (%) prompt. This will create a file named surfer_curv.dat, which has one row/vertex in the path with each column being: vno x y z distance curv val val2 stat amp the "curv" field will give you the max curvature at each point cheers Bruce On Fri, 4 Mar 2011, Allie Rosen wrote: > Hi Bruce, > > I managed to draw and save a curve over my area of interest. I am not quite > sure what to do next. While in the subject folder, I tried typing: > > mris_curvature -w [the name of my path] > > to no avail. Any thoughts? > > Thanks, > Allison > > > > > On Fri, Mar 4, 2011 at 11:36 AM, Allie Rosen <rosen.allie(a)gmail.com> wrote: > >> Hi Bruce, >> >> Thanks for your response - I'll try this out and see how it goes! >> >> Allison >> >> >> >> On Thu, Mar 3, 2011 at 6:16 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: >> >>> Hi Allison >>> >>> I guess you could draw a curve on the surface and count the # of local >>> maxima in the first principal curvature (which can be generates using >>> mris_curvature -w...) >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 3 Mar 2011, Allie Rosen wrote: >>> >>> Hello everyone, >>>> >>>> I am interested in counting the number of gyri in a specific region of >>>> the >>>> brain. I am aware of the Local Gyrification Index feature, but am hoping >>>> to >>>> get precise numbers of gyri. Is there any way to do this? (By the way, I >>>> do >>>> not have Matlab) >>>> >>>> Thank you for your help, >>>> >>>> Allison Rosen, MSc >>>> Graduate Student, Department of Neurosurgery >>>> Toronto Western Hospital 14-327 >>>> 399 Bathurst St. >>>> University of Toronto >>>> >>>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> >

1 0

Counting Gyri
by Allie Rosen 03 Mar '11

03 Mar '11

Hello everyone, I am interested in counting the number of gyri in a specific region of the brain. I am aware of the Local Gyrification Index feature, but am hoping to get precise numbers of gyri. Is there any way to do this? (By the way, I do not have Matlab) Thank you for your help, Allison Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

2 1

Re: [Freesurfer] label to volume
by leemon albert 03 Mar '11

03 Mar '11

Hey, I found the results (volume of V1) with mri_label2vol in FS 4.5 is different the one in BA.stats from FS 5.o? Do they use the same method or not? Which one is more reliable? Thanks. All the best Meng Date: Wed, 02 Mar 2011 15:28:44 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] label to volume To: Adil Javed <ajcns(a)yahoo.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4D6EA87C.9090706(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Adil, try using mri_label2vol. Run it with --help to get docs doug

2 1

general info about FS
by Roberto Sghedoni 03 Mar '11

03 Mar '11

Hi, I'm at the very beginning with FreeSurfer. I found it when I was looking for software for brain segmentation and volume evaluation. I'm reading the tutorial and I tried to run a couple of patients. Someone told me that Freesurfer has not to do with volume based morphometry, but I don't understand exactly why (is it based on a different techniques but it has the same aim?). By the way I have two questions: - can this software be applied to single patient cases if I have some reference for different structures (for example hyppicampus)? - has freesurfer some relation to a similar commercial software called Neuroquant ? (I saw it at RSNA a couple of years ago and it looked like very similar). Thanks

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 March 2011