Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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

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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

2 1

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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bbregister and surface overlay on EPI
by Praneeth Namburi 25 Jul '09

25 Jul '09

Hello Dr. Greve, I used the bbregister tool to register a BOLD EPI volume to the surface with the --init-fsl option. The result looks good in tkregister2. Using the resulting .dat file, I am trying to express the vertex coordinates of the surface in EPI voxel space (EPI volume: 128 x 128 x 36 matrix, limits: -64 to 64, -64 to 64 and -18 to 18). Given the following 4x4 matrices, vox2ras_epi : vox2ras transformation matrix from the EPI volume header bbregMat : transformation matrix from the .dat file created from bbregister command Given the vertices of the subject's surface (nVert x 4) : srfVert I used the following transformation to express the surface in EPI voxel coordinates: srf_epiVox = srfVert * inv(bbregMat) * inv(vox2ras_epi) When I view the results of this transformation in MATLAB, I can see that the above expression is incorrect. I used imagesc to show one slice of EPI and scatter to plot of all the vertices in that slice. Can you please let me know what the mistake is? Am I applying the transformation in an incorrect coordinate space? Am I missing any transformations? Looking forward for your reply. Thank you. Yours Sincerely, Praneeth

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clusterwise correction for multiple comparison
by Rosa Steimke 24 Jul '09

24 Jul '09

HI! i have a question regarding multiple comparion correction in qdec. can i use a clusterwise correction? i found the following script for glm: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite but i dont understand how i should apply it in qdec. what shoudl i use as input directory? rosa -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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qdec question
by Prapti Gautam 24 Jul '09

24 Jul '09

Dear Freesurfers, I just have some quick questions regarding qdec: 1. How many covariates does the latest version of qdec allow you to select? I am using FS version 4.3.0 and I cannot select more than 2 continuous variables. I am just wondering if a newer version allows you to select more covariates. 2. Does qdec allow you to choose between study designs DOSS and DODS? I currently do not see this option and I think my current version of qdec defaults to the DODS option. Thank you for your time, Prapti

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