Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

missing stats files
by Rajagopalan, Venkateswaran 27 Apr '10

27 Apr '10

Hi All, In some of our subjects in stats folder i don't see lh and rh .curv.stats files (so only 6 stats files in total whereas in others i have 8 stats files in total) why is that. Recon-all finishes without any error what am i doing wrong. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

1 0

Re: [Freesurfer] nu-correct parameters
by Nick Schmansky 27 Apr '10

27 Apr '10

for 3T scans, try this modification to the nu_correct usage in recon-all. first, create a file called 'xopts' with this one line: mri_nu_correct.mni --proto-iters 1000 --distance 50 then, run recon-all with these params: recon-all -s subjid \ -nuintensitycor \ -nuiterations 1 \ -expert <path>/<to>/xopts the new flags being '-nuiterations 1 -expert ./xopts'. these params are taken from a new paper: http://web.mysites.ntu.edu.sg/zvitali/publications/documents/N3_NI.pdf also, mri_nu_correct.mni --help provides help info. n. On Mon, 2010-04-26 at 21:48 +0200, Leonardo Chesi wrote: > Dear all, > > I’m Leonardo, a student of the University of Pisa. We study AD’s > patients by MRI. In the last days I had have many problems with the > segmentation because of the B0 inhomogeneity with a 8 channel phased > array coil on a 3.0 T General Electric machine. In some articles I > have found the nu_correct command that provide to normalize the image. > I’m writing to you to ask if some of you know the optimal parameters > to give input to nu_correct to normalize as well as it possible the > image. I’ve try with the default parameters and my segmentation is > already better than the previous. > > Moreover I’d like to know if there is a manual of this command because > on the FreeSurfer Wiki I can’t find detailed information. > > I’m waiting for your corteous help. > > Greetings > > Leonardo > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

question about clustering simulation
by Anthony Dick 27 Apr '10

27 Apr '10

Hello all, I am interested in using the mri_glmfit simulation to control for multiple comparisons in data I have run on the surface in AFNI. Before doing this, I have a few questions: 1. What does the simulation with the mc-z flag do, exactly? It claims to be comparable to AFNI's AlphaSim, but it takes a maximum cluster area for each iteration, which is not exactly what AlphaSim does. Here is my guess: Given a surface, a given smoothness of the data, and a given per-vertex threshold, for each iteration the simulation populates that surface with random data taken from a normal distribution, thresholds the data, and applies the smoothness of the actual data (supplied as an input parameter). It then computes the maximum cluster size in area for that "image". Doing this n iterations gives a distribution of maximum cluster sizes that occur for random data of a given smoothness, and taking cluster sizes above a certain percentile rank controls for the FWE at a level equal to that percentile rank (e.g., 95th% controls for FWE = .05). AlphaSim does something similar, although instead of taking maximum cluster sizes at each iteration it computes all given cluster sizes. AlphaSim also allows for different cluster connectivity radius, but it seems Freesurfer computes only for neighboring vertices. All in all, if this is correct, it seems like a good implementation. 2. It is my understanding that one could bypass running the glm in Freesurfer and only compute the simulation, as the simulation only needs information about the surface, and the smoothness of the data (which are supplied by the user). To do so, you have to "fake out" Freesurfer to bypass glm, but that turns out to be pretty painless. 3. In a future distribution, is it possible to modify this procedure to also output maximum cluster sizes in terms of number of nodes, rather than area? Can you please let me know if I am mistaken in any of these assumptions? Thanks in advance. Anthony -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Web: http://home.uchicago.edu/~adick/

3 3

FOV error
by Antoine Leflon 27 Apr '10

27 Apr '10

Hi all , I have got a problem with the field of view which is told to be 300 (instead of 240 ou 256) and when running tkmedit it's impossible to have good views ... Can someone tell me the error I did ? Because with other data everything is working . thanks

2 4

Talairach to vertex index: selec_talairach_point?
by Arslan, Ali 26 Apr '10

26 Apr '10

Hi, I'm trying to go over a long list of talairach coordinates and to find their vertex indices. I did a bit of research and saw a previous question on the same topic: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12550.html So I went on to write a tcl script in order to write the corresponding vertex indices to a file. But the problem is, the function selec_talairach_point gives 4 successive outputs, therefore I can't parse the vertex number because it gets overwritten. such as these: % select_talairach_point 66.18 -14.56 39.06 surfer: vertex 68342: dist = 0.002702 % surfer: dmin=0.0027, vno=68342, x=43.6843, y=-11.1042, z=35.8562 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % 0 (0 0 0) My questions are: 1) is there an easier way of doing this besides writing a tcl script? 2) how can I access the function "selec_talairach_point" to modify it temporarily (so that it outputs ONLY vertex indices and not anything else) 3) is there a way to parse the output of this function in tcl? Ali B. Arslan Graduate Student in Cognitive & Linguistic Sciences

3 2

talairach registration-problem
by Rajagopalan, Venkateswaran 26 Apr '10

26 Apr '10

Dear All, In two of my subjects talairach registeration is giving me wrong results in the sense instead of taking my input image to talairach space the talairach image is registered to my input image. This happens just only in two subjects out of 14 subjects. Can anyone please tell me how to fix this or am i doing something wrong.I am running the autorecon1 the same way as i am running in other subjects. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

1 0

nu-correct parameters
by Leonardo Chesi 26 Apr '10

26 Apr '10

Dear all, I'm Leonardo, a student of the University of Pisa. We study AD's patients by MRI. In the last days I had have many problems with the segmentation because of the B0 inhomogeneity with a 8 channel phased array coil on a 3.0 T General Electric machine. In some articles I have found the nu_correct command that provide to normalize the image. I'm writing to you to ask if some of you know the optimal parameters to give input to nu_correct to normalize as well as it possible the image. I've try with the default parameters and my segmentation is already better than the previous. Moreover I'd like to know if there is a manual of this command because on the FreeSurfer Wiki I can't find detailed information. I'm waiting for your corteous help. Greetings Leonardo

1 0

Best color/overlay settings for viewing retinotopy data in tksurfer?
by Dickinson, Annelise (NIH/NIMH) [F] 26 Apr '10

26 Apr '10

Hi all, Just wondering if any retinotopy people have a favorite color scale/overlay setting that they use to display the data in tksurfer? Please let me know! Thanks! -Elise ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

1 0

hippocampal subregions
by Hui Jing Yu 26 Apr '10

26 Apr '10

Dear Freesurfer Experts, I am wondering if there is a way to further segment the hippocampal regions (CA1, CA2, etc.) using Freesurfer. If not included in FS by default, if there is any atlas for those subregions. Thank you in advance.

1 0

Re: [Freesurfer] Segmentation fault
by De La Llave Teddy 26 Apr '10

26 Apr '10

The recon-all.log was in the included files of the mail. I resent it for you 2010/4/26 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > and the recon-all.log? Also, can you post these to the list so others can > help? > > On Mon, 26 Apr 2010, De La Llave Teddy wrote: > > Hi Bruce, >> >> here is the output of bugr: >> >> Cut-and-paste the following info into your FreeSurfer problem report: >> -------------------------------------------------------------- >> >> FREESURFER_HOME: /usr/local/freesurfer >> >> Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 >> >> Debian version: 5.0 >> >> Kernel info: Linux 2.6.28-18-genric i686 >> >> -------------------------------------------------------------- >> Additional information >> >> 1) subject name: >> test >> >> 2) the entire command-line executed: >> recon-all -s test -i /usr/local/freesurfer/subjects/ELMA0016.img >> -autorecon-all >> >> 3) the error message generated: >> >> Segmentation fault >> ERROR: mri_ca_register with non-zero status 139 >> but continuing despite the error >> #----------------------------------------- >> #@# CA Reg Inv Mon Apr 26 06:17:14 CEST 2010 >> /usr/local/freesurfer/subjects/test/mri >> >> mri_ca_register -invert-and-save transforms/talairach.m3z >> >> Loading, Inverting, Saving, Exiting ... >> Reading transforms/talairach.m3z >> ERROR: cannot find or read transforms/talairach.m3z >> ERROR: mri_ca_register with non-zero status 0 >> Linux freesurfer-virtual 2.6.28-18-generic #60-Ubuntu SMP Fri Mar 12 >> 04:40:52 UTC 2010 i686 GNU/Linux >> >> recon-all exited with ERRORS at Mon Apr 26 06:17:15 CEST 2010 >> >> >> Please find the recon-all.log included in this mail. >> >> cheers, >> Teddy >> >> >> 2010/4/26 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> >> Hi Teddy, >>> >>> we need more info than this. Can you send us the recon-all.log and the >>> output of bugr. >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Mon, 26 Apr 2010, De La Llave Teddy wrote: >>> >>> Hi all, >>> >>>> >>>> I am running recon-all as follows: >>>> >>>> recon-all -subjid subjectTest -all >>>> >>>> and get this error: >>>> >>>> Segmentation fault >>>> ERROR: mri_ca_register with non-zero status 139 >>>> >>>> I can't continue the rest of the process because the file >>>> talairach.m3z not exist. >>>> >>>> I saw that others have the same problem but there are no solutions? >>>> >>>> freesurfer runs on the virtualbox available in the website. It run >>>> with 1,4Go of RAM. >>>> >>>> >>>> Thanks for your help, >>>> >>>> >>>> Teddy >>>> >>>> >>>> >>>> >>> 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. >>> >>> >>> >> >> >> -- Teddy De La Llave Ingénieur développement R&D teddy(a)eye-brain.com e(ye)BRAIN www.eye-brain.com

1 0

← Newer
1
2
3
4
5
6
7
...
15
Older →

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 April 2010