Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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

Segmentation fault
by De La Llave Teddy 26 Apr '10

26 Apr '10

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 -- Teddy De La Llave Ingénieur développement R&D teddy(a)eye-brain.com e(ye)BRAIN www.eye-brain.com

2 1

Cluster size
by johanna feiler 26 Apr '10

26 Apr '10

Hello, I got the same concern as miranda with trying to determine the number of vertices in my significant regions. I tried the 'Map Label to Subjects' options way, but I'm not sure where I can find the information Nick is mentioning (the text that says 'Found 389 points in source label.'). What do you mean with options? Is it in the subjects' individual label files? What if I want this information for the group and not for the individual subjects? Thanks for your help! Johanna Feiler >>>>>>>>>>> Miranda, I'll assume for now that what you mean by 'cluster' is not a cluster in the sense of clusters produced by a cluster-based correction for multiple comparisons, which was only very recently introduced to qdec (actually, just a script generator is produced). But rather, I think you mean the areas of significance that remain after you have either manually adjusted the threshold or just left the thresholds at their defaults. If this is what you mean by cluster-size, there is no way now in qdec to get the size of this 'cluster', outside of drawing a label around it, and then click on the 'Map Label to Subjects' options, and looking for the text that says 'Found 389 points in source label.' (where in this example, the label had 389 points/vertices). If you want a bit more exact way, you can use tksurfer: tksurfer fsaverage lh inflated -overlay /path/to/qdec/sig.mgh to load the sig.mgh file (from your qdec contrast dir of interest), then adjust the thresholds (View->Configure->Overlay), then click on the 'cluster' you want (the blob), then click the 'Custom Fill' icon (a paint bucket), then click 'Up to functional values below threshold', click Fill, and it will fill that 'cluster' and the terminal window will show you the number of vertices filled. I'm hoping to add this 'fill' feature to qdec at some point, to give a label creation option other than drawing. Nick On Tue, 2009-01-13 at 16:43 -0600, nels5...(a)umn.edu wrote: > Hello, > > I am wondering if there is an easy way to determine the size of a cluster > of significant voxels resulting from a QDEC analysis? I have created a > label and mapped the label to all of the subjects, but didn't know if there > was a way to extract information about cluster size. > > Thanks, > > Miranda ___________________________________________________________ GRATIS: Movie-Flat mit über 300 Top-Videos. Für WEB.DE Nutzer dauerhaft kostenlos! Jetzt freischalten unter http://movieflat.web.de

1 0

WM segmentation error...
by Gonzalo Rojas Costa 23 Apr '10

23 Apr '10

Hi: I got a WM segmentation error such as that I show in the attached image... The segmentation error include many coronal slices in size (more than 15)... How can I correct it ?... Could that WM segmentation error produce a very big mesh defect (vertices=21320, convex hull=9913)... If you want, I could send you more additional files... Sincerely, Gonzalo Rojas Costa

2 1

7T MPRAGE
by Jose Luis Cantero Lorente 23 Apr '10

23 Apr '10

Dear Freesurfers, we are acquiring human T1-MPRAGE images (0.5 mm resolution) in a 7T siemen scanner (32-channel head coil). Unfortunately, 7T MPRAGE acquisitions typically present inhomogeneities leading to a broad range of segmentation failures in Freesurfer. Has anyone run automatic segmentation of 7T MPRAGE sequences by using Freesurfer successfully? If so, I would be highly interested to knowing specific parameters of 7T MPRAGE sequences to avoid these problems with Freesurfer. Thanks a lot in advance. Best, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

1 0

Reconstructing surfaces of post-resection brains
by Jed Singer 23 Apr '10

23 Apr '10

Hello! I've been using Freesurfer to build maps of the cortical surfaces of surgical epilepsy patients who have volunteered to participate as research subjects. It works great, except when these patients have had previous resections. In these cases, recon-all fails; I know there are ways that people get around this when working with brains that have lesions (manually filling in white matter, e.g.) but is it possible to get a reconstruction of the brain as it actually is? For example, in the case of someone who has previously had an anterior temporal lobectomy, I would love to end up with a model that does not have an anterior temporal lobe. I'm sorry if this is an obvious question - I've been digging through the archives of this list and furiously Googling and I've only found descriptions of how to manually fill in holes (due to lesions or caused by bad segmentations) in intact brains. Thanks in advance for any pointers, Jed

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