Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30078 discussions

read_curv
by Reza Rajimehr 03 Mar '08

03 Mar '08

Hi, Using "read_curv", I load the curvature file into Matlab. How can I get the corresponding vertex indices for these curvature values? Thanks, Reza ************************************ Reza Rajimehr, MD Postdoctoral Research Fellow NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th Street Charlestown, MA 02129 Phone: 617-669-0930 Email: reza(a)nmr.mgh.harvard.edu ************************************

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Re: [Freesurfer] Editing annotations
by Graham Wideman 01 Mar '08

01 Mar '08

Ronald: There are a couple of articles on this subject on the FS wiki, including one I just posted: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_5flabeledit Graham At 2/26/2008 06:55 AM, you wrote: >Forgive me if this has been covered before, but I was unable to find an >answer after searching for a bit. I have been considering editing the final >surface parcellation for those scans that have problems in certain areas. >Can these corrections then be used to correct the surface registration for >the input into Qdec? > >Also, to test out the editing process I have been simply importing the annot >file, editing the labels, then exporting it. Is this the correct thing to >do, and is there a tutorial anywhere about this kind of editing? > >Thanks, > >Ronald Pierson > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: annotation binary files into ascii format
by Teddy Youn 01 Mar '08

01 Mar '08

Hi everyone, Thanks again for your help from my previous query. I had a question about how to convert the binary format of the annotation file to ascii format, similar to using mris_convert to surface files from binary to ascii. Is there an equivalent program that does the same thing for annotation files? Thanks very much, -Teddy Youn Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

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question about moving from freesurfer to afni and keeping registration
by Jena B. Hales 29 Feb '08

29 Feb '08

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Qdec "map label to subjects" error
by nels5614＠umn.edu 29 Feb '08

29 Feb '08

Hello, I have a question in regards to the "map label to subjects" feature in Qdec. Basically, I draw and save a label, and then try to map the label to all of the subjects in my SUBJECTS_DIR, but while running mri_label2label, I get this error: > ERROR: there is a vertex in the label that cannot be matched to the > surface. This usually occurs when the label and surface are from > different subjects or hemispheres or the surface has been changed since > the label was created. Label point 7: vno = 166358, max = 163842 command > failed: mri_label2label --srclabel > /home/bfs-raid1/ryanm/FREESURFER/142_FAE2_blade/v4/freesurfer-from-blade/qdec/lh.parahippocampal_cp --srcsubject fsaverage --trgsubject 18208 --trglabel /home/bfs-raid1/ryanm/FREESURFER/142_FAE2_blade/v4/freesurfer-from-blade/qdec/lh.parahippocampal_cp --regmethod surface --hemi lh I have three groups I am trying to compare, 2 proband groups, and 1 control group. So, I constructed separate .dat files and label files for each- one comparing controls vs. group1, and the other comparing controls vs. group2. I seem to be able to run analyses fine on the data, I am just having problems with the "map label to subjects" feature. The order in my .dat files does differ from the order of datasets in my SUBJECTS_DIR, I don't know if this has anything to do with my error. Any advice/suggestions would be greatly appreciated. Thanks! Miranda Nelson

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RE: [Freesurfer] statistics in aparc.stats
by Pedro Paulo Oliveira Jr 29 Feb '08

29 Feb '08

Aaron, My opinion is that you are right, but maybe the folding index should be taken into account. When we reach a conclusion about this I think is a good question to put in the faq. best regards, Pedro Paulo on E61 -- mens. original -- Assunto: [Freesurfer] statistics in aparc.stats De: "Goldman, Aaron (NIH/NIMH) [C]" <aarong(a)mail.nih.gov> Data: 28/02/2008 22:23 Hi, I just had a question regarding the statistics in ?h.aparc.stats. I'm interested in calculating average thicknesses for several labels combined, and wanted to verify how to do that correctly. The way the stat files are calculated, would it be valid to simply take an average of the listed average thicknesses, weighted by the listed surface areas? Thanks, -Aaron- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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help with freesurfer error
by joel bruss 28 Feb '08

28 Feb '08

I was trying to run a single sujbect through recon-all and got the following error: Thu Feb 28 16:34:57 CST 2008 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Feb 28 16:34:58 CST 2008 /fmri/studies/retinotopic/new_retinotopic/3362/3362_resampled.dir/freesurfer_pipeline.dir/sub1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux dendrite 2.6.22.16-0.1-default #1 SMP 2008/01/23 14:28:52 UTC i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Feb 28 16:34:58 CST 2008 I don't speak FreeSurfer and don't understand this error. Please help. -Joel

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qdec error...
by Cameron B. Ellis 28 Feb '08

28 Feb '08

Hi, I pasted an error that I am receiving in qdec below. SUBJECTS_DIR is /space/lightning/2/users/NEAA-freesurfer. If you need any more information from me I will be happy to provide it. Any help is much appreciated. Thanks, troy:cameo[87] ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 48 Checking inputs nframestot = 48 Allocing output Writing to /autofs/space/lightning_002/users/NEAA-freesurfer/qdec/NEA A-freesurfer/y.mgh gdfReadHeader: reading /autofs/space/lightning_002/users/NEAA-freesur fer/qdec/NEAA-freesurfer/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 txt-untxt 1.01875 Class Means of each Continuous Variable 1 groupPH-gendermale 2.8400 2 groupPL-gendermale 0.5333 3 groupVH-gendermale 0.6000 4 groupVL-gendermale -0.4667 5 groupPH-genderfemale 1.0857 6 groupPL-genderfemale 0.0833 7 groupVH-genderfemale 3.1167 8 groupVL-genderfemale 0.6500 INFO: gd2mtx_method is dods Reading source surface /autofs/space/lightning_002/users/NEAA-freesur fer/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /autofs/space/lightning_002/users/NEAA-freesu rfer/fsaverage/surf/lh.white.avg.area.mgh ERROR: no contrasts specified Error in Analyze: command failed: mri_glmfit --y /autofs/space/lightn ing_002/users/NEAA-freesurfer/qdec/NEAA-freesurfer/y.mgh --fsgd /auto fs/space/lightning_002/users/NEAA-freesurfer/qdec/NEAA-freesurfer/qde c.fsgd --glmdir /autofs/space/lightning_002/users/NEAA-freesurfer/qde c/NEAA-freesurfer --surf fsaverage lh --label /autofs/space/lightning _002/users/NEAA-freesurfer/fsaverage/label/lh.cortex.label

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Freesurfer Citation in Paper
by Pedro Paulo Oliveira Jr 28 Feb '08

28 Feb '08

Is correct the statement below? FreeSurfer implementation of cortical surface-based analysis is distinct from other surface-based algorithms and conventional volume based morphometry with atlas mapping, as it does not necessarily depend on smoothing or matching to an atlas. Thanks in advance, Pedro Paulo Jr

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Error loading lh.curv
by SHRIKANTH KULASHEKHAR 27 Feb '08

27 Feb '08

Hi, When I try loading curvature files on to inflated brains of the same subject, Freesurfer closes abruptly with the following error. % alloc: invalid block: 0xaec980: 0 0 68 Abort I am using Freesufer version stable4 on an Linux workstaion running on an AMD64 version of Debian 4.0, with kernel 2.6.24.2. Could anyone advice on how I could proceed ? Thanks in advance. Shriks 5, 50, 500, 5000 - Store N number of mails in your inbox. Go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html

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