Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

RES: Help In VBM processing.
by Pedro Paulo de Magalhaes Oliveira Jr 30 Jul '09

30 Jul '09

Gergo Take a look in the Tutorial section of the wiki. Probably you'll find out that you can do the whole study using FreeSurfer. Cheers PPJ Enviado do meu celular Nokia -----Msg original----- De: Orsi Gergely Enviada: 30/07/2009 05:53:47 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] Help In VBM processing. Dear All! First of all, I'm completely newbie to freesurfer. So far I only used FSL (mainly), rarely SPM and NordicICE. I need to do a VBM study to compare 2 groups each containing 50 subjects for GM density (already done with FSL), volumetry (not yet done), and cortical thickness and surface area. I'd like to do the last two with Freesurfer. Just a single Unpaired Two-Group difference, to answer the question: Is there a significant difference between the two groups in cortical thickness or surface area. My only problem, that I havent found any tutorials or guides (step-by-step, along with the commands) to do this. Could anyone help me in this? I'd really appreciate it. Best Regards: Gergely Orsi Diagnostic Center of Pecs Hungary _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Processing data with -noaseg flag
by Falk Lüsebrink 30 Jul '09

30 Jul '09

Hi FreeSurfers, As the subcortical segmentation fails fairly often on my high resolution data I want to skip it by using the noaseg flag, but Im currently encountering another issue. 1.) During the fix stage of autorecon2 I receive following error during mris_euler_numbers (also if I want to view the lh.orig or rh.orig in tksurfer): rh.orig: face[233615].v[2] = 119048, but face 233615 not in vertex 119048 face list lh.orig: face[196300].v[1] = 100366, but face 196300 not in vertex 100366 face list 2.) Normally the subcortical segmentation is also used to cut both hemisphere and to remove the cerebellum. The cutting plane between the hemispheres is done very well, but I have never been able to remove the cerebellum. Do I need to remove it manually or are there some ways to remove it automatically? Is it required to be removed? 3.) Im interested in measuring cortical thickness only. But do I need to keep something else in mind while not using the subcortical segmentation to process my data? Thanks in advance, Regards, Falk

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mri_convert with old GE-LX data
by Chris Watson 29 Jul '09

29 Jul '09

Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matlab7@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm "image" mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matlab7@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm "image" mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matlab7@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm "image" mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file

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Surface Analysis of the Anterior Cingulate
by Stephen Tyree 29 Jul '09

29 Jul '09

One of the regions we are investigating using a surface-based analysis is the anterior cingulate. In some of our surface reconstructions, parts of this region are excluded from the ?h.cortex.label files. What are the criteria that Freesurfer uses to determine those boundaries? Could manual editing around the boundary reliably extend the usable surface in that area? Thanks. -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA

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Adding .mnc
by Jesse Bledsoe 29 Jul '09

29 Jul '09

Hello Everyone, I am attempting to add .mnc data but get the following error when trying to convert using: mri_convert subject.mnc subject/mri/orig/001.mgz I am following the tutorial reconstruction slides online. Here is the error: mri_convert EF0114.mnc EF0114/orig/001.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from EF0114.mnc... TR=0.00, 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) writing to EF0114/orig/001.mgz... sh: EF0114/orig/001.mgz: No such file or directory Broken pipe Thank you in advance for any suggestions, Jesse ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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Re: [Freesurfer] loading label in tksurfer
by Bruce Fischl 29 Jul '09

29 Jul '09

Hi Sharmili, this is not an error message. It is sampling the volume label coords onto the surface. What happens next? Does tksurfer display the label? cheers, Bruce On Wed, 29 Jul 2009, Sharmili 57 wrote: > > Hi ! > Thats all it says. The window with the inflated brain shuts down, as soon as i load the labe. But i don't get an error message. > > ssrithar@beo-01:/data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer $ t > ksurfer FASC rh inflated > surfer: current subjects dir: /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/ > Freesurfer > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer > surfer: Reading header info from /data/Psychiatrie/01_Projects_Folder/DA_Srithar > an/Freesurfer/FASC/mri/T1.mgz > surfer: vertices=147680, faces=295356 > Loading /apps/prod/i686/freesurfer-4.4.0/surface_labels.txt > surfer: ### redraw failed: no gl window open > surfer: single buffered window > surfer: tkoInitWindow(FASC) > surfer: using interface /apps/prod/i686/freesurfer-4.4.0/lib/tcl/tksurfer.tcl > Reading /apps/prod/i686/freesurfer-4.4.0/lib/tcl/tkm_common.tcl > Reading /apps/prod/i686/freesurfer-4.4.0/lib/tcl/tkm_wrappers.tcl > Reading /apps/prod/i686/freesurfer-4.4.0/lib/tcl/fsgdfPlot.tcl > Reading /apps/prod/i686/freesurfer-4.4.0/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > % /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer/FASC/label/tfusif > orm.rh.label /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer/FASC/l > abel/tfusiform.rh.label > ******************** 2107 nonzero vertices found ******************** > 2107 unassigned vertices in label - building spatial LUT... > assigning vertex numbers to label... > > > Thanks for your help > > Sharmili > >> Date: Wed, 29 Jul 2009 07:59:05 -0400 >> From: fischl(a)nmr.mgh.harvard.edu >> To: sharmili75(a)hotmail.com >> Subject: Re: loading label in tksurfer >> >> Hi Sharmali, >> >> can you just send us the text output in your email message instead of an >> image? That would be much more helpful. >> >> thanks >> Bruce >> On Wed, 29 Jul 2009, Sharmili 57 >> wrote: >> >>> >>> >>> >>> From: sharmili75(a)hotmail.com >>> To: freesurfer(a)nmr.mgh.harvard.edu >>> Date: Mon, 27 Jul 2009 22:54:21 +0000 >>> Subject: [Freesurfer] FW: loading label in tksurfer >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> Hi ! >>> >>> I've edited a label in tkmedit and now I want to open it with tksurfer, but I get the following error message. >>> >>> Could anyone help me? >>> >>> Best >>> Sharmili >>> >>> >>> >>> Neuigkeiten in Deinem Netzwerk? Findest Du hier! >>> Surfen Sie sicher ? die neue Version ist da. Internet Explorer 8! >>> _________________________________________________________________ >>> http://redirect.gimas.net/?n=M0907xIMDL >>> Den Nachfolger vom MSN Messenger findest Du hier! > > _________________________________________________________________ > http://redirect.gimas.net/?n=M0907xBing2 > Sparen Sie Zeit, Energie, Nerven. Bing?. Die Suche von Microsoft®

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FW: loading label in tksurfer
by Sharmili 57 28 Jul '09

28 Jul '09

Hi ! I've edited a label in tkmedit and now I want to open it with tksurfer, but I get the following error message. Could anyone help me? Best Sharmili Neuigkeiten in Deinem Netzwerk? Findest Du hier! _________________________________________________________________ http://redirect.gimas.net/?n=M0907xIE8_MSN3 Gratis Download – die neue Version des Internet Explorers ist da!

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Overlay surface onto EPI
by Praneeth Namburi 27 Jul '09

27 Jul '09

3 2

rerun auto-recon on error output
by Michael Scheel 27 Jul '09

27 Jul '09

Hi freesurfer-experts, I was running the recon-all script and did get some errors due to a missing vtk and x-windows libraries. The output that was created seems fine though, just some files are missing. I was wondering if there is way to rerun the analysis, but only the parts that exited with error? these programs exited with error mris_volmask mri_aparc2aseg (several times with different options) and a final mri_segstats Thanks, Michael

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continue from a specific stage of autorecon2
by Gonzalo Rojas Costa 27 Jul '09

27 Jul '09

Dear Pedro Paulo: I need to continue the freesurfer professing from a specific stage of autorecon2 (careginv; stage 4 of autorecon2 in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStableTablev4) Which is the command line to do it ?... Sincerely, Gonzalo Rojas Costa

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Freesurfer July 2009