Freesurfer January 2006

freesurfer@nmr.mgh.harvard.edu

32 participants
47 discussions

mri_mask bug
by Yuhong Jiang 27 Jan '06

27 Jan '06

Hi, We were running free-surfer (freesurfer-Linux-rh9-dev20051003-full.tar.gz) on RedHat 9 and encountered a problem with the command mri_mask. It is not at all working. Here is what we entered as input: mri_mask input.mgz mask.mgz output.mgz No matter what we put as the mask, the input.mgz and output.mgz are always identical. Is there a bug with this command? (The command says "writing masked volume to output.mgz..." then about 10 seconds later it's done - although nothing is done). Thanks. --Yuhong ============================================================================= Yuhong Jiang yuhong(a)MIT.EDU 617-876-2054 http://web.mit.edu/yuhong/www =============================================================================

5 8

label to mask
by Roger Alvaredo 27 Jan '06

27 Jan '06

Hello! I am a new user of Freesurfer. I have done the parcellation of a subject and it seems correctly. Now, I would like to know how to do this: 1. How could I assemble some labels in one and export this to a binary mask?? Thanks!

2 1

making cutsom .tcl files
by Goldman, Aaron (NIH/NIMH) [C] 26 Jan '06

26 Jan '06

Hi, can someone recommend a good help or reference site for making tksurfer/tkmedit .tcl files? Thanks, -Aaron- Aaron L. Goldman Kelly Contractor Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov

2 1

nu_correct
by N.M. van Strien 26 Jan '06

26 Jan '06

Hi, I am having a problem with running the recon-all script. As soon as I get to intensity normalization, the script stops and gives an error for nu_correct (see output below). The MNI tools seem to be set up correctly however. The environment is set up as such that: MINC_BIN_DIR /usr/local/freesurfer/lib/mni/bin and this is where nu_correct does live. Any idea how to overcome this problem? I am running Fedora Core 3 and both the RH9 dev release as well as the CentOS4_x64 dev release show this problem. Thank you for your help, Niels van Strien Nu Intensity Correction Thu Jan 26 16:42:22 CET 2006 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc nu_correct: Command not found. ERROR: nu_correct Linux VUMC 2.6.12-1.1381_FC3smp #1 SMP Fri Oct 21 04:22:48 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with errors at Thu Jan 26 16:42:30 CET 2006 Niels M. van Strien (MSc) Dept. of Anatomy Vrije Universiteit University Medical Center Room MF-G130 Van der Boechorststraat 7 1081 BT Amsterdam The Netherlands tel: +31 20 44 48047 fax: + 31 84 222 7040 e-mail: n.vanstrien(a)vumc.nl http://anatomie.med.vu.nl/afdeling/persons/vanstrien.html

2 1

4T data converting
by Du, Antao 25 Jan '06

25 Jan '06

Hi, I am trying convert the data from our 4T (Siemens) to mgz. But there is error message of "Floating exception": [antao@freesurfer fad131]$ mri_convert MR_16_100_2005_10_24_16_30_48_78125_49238781.IMA ../FAD131/mri/orig mri_convert MR_16_100_2005_10_24_16_30_48_78125_49238781.IMA ../FAD131/mri/orig reading from MR_16_100_2005_10_24_16_30_48_78125_49238781.IMA... Floating exception [antao@freesurfer fad131]$ Can someone help me solve this problem? Thanks, Antao

2 2

FW: [Freesurfer] overlay thickness maps
by Kirk, Gregory 23 Jan '06

23 Jan '06

-----Original Message----- From: Kirk, Gregory Sent: Monday, January 23, 2006 4:25 PM To: 'Kevin Teich' Subject: RE: [Freesurfer] overlay thickness maps Yes Kevin, im still a dum dum sometimes, as your comment I Looked it in shell window, and saw all was not well. In response to Load-Overlay-> load lh.thickness from the subject surf/ Directory get errors % surfer: needs at least 2 marked vertices % surfer: needs at least 2 marked vertices % surfer: needs at least 2 marked vertices % mri_read(): couldn't determine type of file /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/THORNTONH/sur f/lh.thickness surfer: couldn't load /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/THORNTONH/sur f/lh.thickness sclv_read_from_volume: error in MRIreadInfo. The overlays that are loaded in the buckner are .mgz files and it does not seem happy with these Doug Greve is the winner in our best suggestion category with Another method is to use mri_surf2surf to to convert the curv file into an mgh file (run it with --help to see how to use it). Then just load the mgh file as an overlay (with "compute identity"). Which when applied with- and the output is- [gkirk@Nuit surf]$ mri_surf2surf --hemi lh --srcsubject MASONO --srcsurfval thickness --src_type curv --trgsubject MASONO --trgsurfval lh.thickness.mgz --trg_type mgz srcsubject = MASONO srcval = thickness srctype = curv trgsubject = MASONO trgval = lh.thickness.mgz trgtype = mgz surfreg = sphere.reg hemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/MASONO/surf/l h.sphere.reg Loading source data Reading curvature file /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/MASONO/surf/l h.thickness INFO: trgsubject = srcsubject Saving target data Reshaping 2 (nvertices = 107662) Gives .mgz files that surfer is happy to use as an overlay, and produces what looks like good Thickness maps. Thanks all Greg. -----Original Message----- From: Kevin Teich [mailto:kteich@nmr.mgh.harvard.edu] Sent: Friday, December 23, 2005 5:33 PM To: Kirk, Gregory Cc: Freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] overlay thickness maps There are a couple things that could be wrong. Make sure that calculating an identity registration is the proper thing to be doing here. Doug can probably tell you more about this. Next, is the file actually loading? Make sure that the output to the shell doesn't have any errors, and that there's a new line in the label/value area with the overlay's name on it. Make sure that there are actually values in that line as you move the mouse aroudn over the surface. If there are, do View->Configure->Overlay and see if you can set the threshold so that it encompasses the values, as the default threshold might be incorrect. On Fri, Dec 23, 2005 at 03:42:31PM -0500, Kirk, Gregory wrote: > > I would like to overlay lh.thickness, rh.thickness on inflated for > single subject, not the glm results, how to do that is well documented > from the tutorial/tutorial group study > > > tried tksurfer subject lh inflated - got the gray surface > > next file->load overlay -> $SUBJECTS_DIR/subject/surf choose > lh.thickness > * calculate identity map > > it redraws the surface but there is no colormap of the thickness -- Kevin Teich

1 0

notes on Jan 2006 release
by Sasha Wolosin 23 Jan '06

23 Jan '06

Dear all, In the notes on the Jan 2006 release it was mentioned that the subcortical atlas is built from the Siemens scans, and thus might not be reliable for GE scans. How might this subcortical atlas handle data aqcuired on a Philips scanner? thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

2 3

cannot configure overlay in tksurfer
by Eric Feczko 23 Jan '06

23 Jan '06

Hi all, I'm trying to overlay some cortical thickness correlation maps onto a freesurfer surface, and when I select configure->overlay from the toolbar, an error message pops up stating: bad window path name ".wwConfigOverlayDisplayDlog.fwFlags.cbwReverse" bad window path name ".wwConfigOverlayDisplayDlog.fwFlags.cbwReverse" while executing "grid $cbwReverse -column 2 -row 1 -stick w" (procedure "DoConfigOverlayDisplayDlog" line 126) invoked from within "DoConfigOverlayDisplayDlog" invoked from within ".w.fwMenuBar.mbwView.mw.cmw5 invoke active" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke active]" (procedure "tk::MenuInvoke" line 47) invoked from within "tk::MenuInvoke .w.fwMenuBar.mbwView.mw.cmw5 1" (command bound to event) I'm using banzai and am working in the dev environment. If anyone can help me out, that would be great, thanks! -Eric

1 0

mri_convert ascii
by Sasha Wolosin 19 Jan '06

19 Jan '06

Dear all, Is there a way to convert FreeSurfer surface files to ASCII? In the most recent listserve, it was mentioned that mri_convert can be used to convert FreeSurfer surface files to ASCII format, but I could not figure it out- I thought mri_convert could only handle volumes. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 3

RE: [Freesurfer] (no subject)
by Bagnato, Francesca (NIH/NINDS) [F] 19 Jan '06

19 Jan '06

I am trying to run mris_anatomical_stats -f <file name> for seeing the results get written into a file, but it says "unknown option" for -f. Thanks, francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, January 19, 2006 10:33 AM To: Bagnato, Francesca (NIH/NINDS) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) And your command-line is ...? Bagnato, Francesca (NIH/NINDS) [F] wrote: I am sorry: Mris_anatomical_stats.. Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, January 18, 2006 6:25 PM To: Bagnato, Francesca (NIH/NINDS) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) we don't have an mris_stats. What do you mean? Bagnato, Francesca (NIH/NINDS) [F] wrote: Dear Users: I would like to know which is the name of the file (and its location) where all he results end up after the mris_stats... Thanks, francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer January 2006