Freesurfer

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30132 discussions

pial surface editing
by Francesco Siciliano 28 Aug '13

28 Aug '13

Hello, I am having a few issues with editing the pial surface in freeview. It appears as though the edits I make to the brainmask are not being taken into account when I re-run recon-all. I work on a MacBook Pro and have been using "shift+click" to delete voxels at a brush value of 1 and then saving the brainmask.mgz back into the mri folder. When making edits to the brainmask I have the brainmask highlighted. Upon clicking save, the mri folder contains both brainmask.mgz and brainmask.mgz~ (The version with a ~ seems to indicate the older version of the file based on modification time). Additionally, the edits that I make to brain.finalsurfs.manedit.mgz for pial surface that has extended into the cerebellum seems to not be taken into account when I re-run recon-all. I have been making a copy of brain.finalsurfs.mgz, pasting it into the mri folder, and renaming it brain.finalsurfs.manedit.mgz. I then load this volume and make edits to it according to the same specifications as the brainmask.mgz. Shouldn't I be able to see changes made to the pial surface in the brainmask.mgz from edits I make to the brain.finalsurfs.manedit.mgz after running recon-all? Neither the brainmask.mgz nor the brain.finalsurfs.mgz take into account the edits I've made on brain.finalsurfs.manedit.mgz. I'm not sure if I'm deleting voxels incorrectly or saving incorrectly. I've tried to troubleshoot several times and keep encountering similar issues. The version of FreeSurfer that I am working from is: freesurfer-i686-apple-darwin9.8.0-stable5-20110525 My editing interface looks slightly different from the current version explained on the freesurfer wiki. I do not have an option to select recon-editing. Adding control points, however, has been successful. I have been using the command recon-all -autorecon2 -autorecon3 -s subj001 Any help getting to the bottom of this would be greatly appreciated! Thanks, Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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license error with FS5.3
by S.V.Shepherd [work] 28 Aug '13

28 Aug '13

I see some reports of license failures, and seem to be having a similar problem. Our installations of 4.5 and 5.1 work normally, but with 5.3 I had a mysterious error in unpacksdcmdir that ultimately traced to a license error in mri_convert. I can reproduce the error like so: *mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz* mri_convert /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/subjects/bert/mri/T1.mgz T1.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/subjects/bert/mri/T1.mgz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/.license -------------------------------------------------------------------------- *bugr* FREESURFER_HOME: /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 5.9 (Tikanga) Kernel info: Linux 2.6.18-308.4.1.el5 x86_64 *cat $FREESURFER_HOME/.license* ppo...(a)mail.rockefeller.edu 9148 *C7cx5HQ1V7ws (This is the same license we use successfully with v4.5 and v5.1) Thanks! (Also, please advise and accept my apologies if I'm using the list wrong -- just getting started here.) best, stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620

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matrix ill-conditioned....
by Jacobs H (NP) 28 Aug '13

28 Aug '13

Hi Doug, I divided everything by 10, but the problem remains. I have been searching a bit more. Could it be that the problem is that the range in cognitive scores in the control group is very small? When I run the groups separately, the patients are not a problem (the range in cognition is very large), but the controls are still the problem. Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================ ________________________________________ Van: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Verzonden: vrijdag 23 augustus 2013 17:31 Aan: Jacobs H (NP) CC: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test The values in the interaction column are probably much larger than the values in the other columns (thus they are "badly scaled"). You can divide them by a number to bring their scale down to that of the other columns without changing the p-values. Version 5.x does this automatically. On 08/23/2013 11:25 AM, Jacobs H (NP) wrote: > I am using version 4.5, as all the old analyses were also done with this version. > What do you mean with rescale? > THanks > Heidi > ________________________________________ > Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Verzonden: vrijdag 23 augustus 2013 17:23 > Aan: freesurfer(a)nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test > > what version of FS are you using? It may be that you just need to > rescale that column (if the scale is much more than the other columns) > > On 08/23/2013 11:12 AM, Jacobs H (NP) wrote: >> Hi again! >> >> I am trying to run these contrasts but FreeSurfer tells me that "ERROR: matrix is ill-conditioned or badly scaled, condno = 101380 >> Possible problem with experimental design: >> Check for duplicate entries and/or lack of range of >> continuous variables within a class." >> >> Could this be due to the fact that there is a high correlation between cognition, education and cognition x education? (the product is correlated with the factors of that product) >> Or is something else going on? >> How can I solve this? >> >> Thanks >> Heidi >> >> ________________________________________ >> Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Verzonden: donderdag 22 augustus 2013 17:52 >> Aan: freesurfer(a)nmr.mgh.harvard.edu >> Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test >> >> both of those contrasts are correct >> doug >> >> On 08/22/2013 10:51 AM, Jacobs H (NP) wrote: >>> Arrghh, again wrong email, sorry.... >>> >>> Thanks. I think I understand the rational behind it. >>> Just to be sure, would this be correct: >>> >>> For each group separately >>> 0 0 0 1 0 0 (group - cognition - education - cognition x education - age - ICV) >>> >>> For the F-test (same order) >>> 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 >>> 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 >>> >>> Heidi >>> >>> >>> ________________________________________ >>> Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>> Verzonden: donderdag 22 augustus 2013 16:46 >>> Aan: freesurfer(a)nmr.mgh.harvard.edu >>> Onderwerp: Re: [Freesurfer] FW: Contrast and F-test >>> >>> you need to have all 3. If you want to examine the interaction, then you >>> need a new contrast to test the interaction. Set all to 0 except for the >>> interaction term >>> doug >>> >>> >>> On 08/22/2013 10:42 AM, Jacobs H (NP) wrote: >>>> Dear Doug, >>>> Thank you for the information. Sorry for not sending this to the list. >>>> Do you mean that I then have to include the three variables (covariate 1, covariate 2, product of these two) or only the product in the fsgd file? >>>> If I need to include all three of them, can you advise me on the contrasts? >>>> If it is only the product, I think I can use the same contrasts as before, right? >>>> >>>> Thanks >>>> Heidi >>>> ================================================ >>>> Dr. Heidi Jacobs >>>> Postdoc researcher >>>> Faculty of Health, Medicine and Life Sciences >>>> School for Mental Health and Neurosciences >>>> Division Cognitive Neuropsychiatry and Clinical Neurosciences >>>> Alzheimer Center Limburg >>>> h.jacobs(a)maastrichtuniversity.nl >>>> www.maastrichtuniversity.nl >>>> www.heidijacobs.nl >>>> >>>> Dr. Tanslaan 12, 6229 ET Maastricht >>>> P.O. Box 616, 6200 MD Maastricht, The Netherlands >>>> T +31 43 38 84 090 F +31 43 38 84 092 >>>> ================================================ >>>> ________________________________________ >>>> Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>>> Verzonden: donderdag 22 augustus 2013 16:34 >>>> Aan: freesurfer(a)nmr.mgh.harvard.edu >>>> Onderwerp: Re: [Freesurfer] Contrast and F-test >>>> >>>> If you want to test for an interaction between continuous variables, >>>> then you should create a new regressor by multiplying them together then >>>> test that regressor >>>> doug >>>> >>>> >>>> On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: >>>>> Hi all, >>>>> >>>>> I my manuscript, I examined the association between cognition and cortical thickness. I first did this in three groups separately and then ran a F-test. >>>>> One of the reviewers, now wants me to examine the interaction between cognition and education (all continuous). >>>>> >>>>> Would this be the correct contrast for each group separately (last two zeros are for covariates, also continuous) >>>>> >>>>> 0 1 -1 0 0 >>>>> >>>>> Would this be the correct way for the F-test: >>>>> >>>>> 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0 >>>>> 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0 >>>>> >>>>> Thanks! >>>>> >>>>> Heidi >>>>> >>>>> ================================================ >>>>> Dr. Heidi Jacobs >>>>> Postdoc researcher >>>>> Faculty of Health, Medicine and Life Sciences >>>>> School for Mental Health and Neurosciences >>>>> Division Cognitive Neuropsychiatry and Clinical Neurosciences >>>>> Alzheimer Center Limburg >>>>> h.jacobs(a)maastrichtuniversity.nl >>>>> www.maastrichtuniversity.nl >>>>> www.heidijacobs.nl >>>>> >>>>> Dr. Tanslaan 12, 6229 ET Maastricht >>>>> P.O. Box 616, 6200 MD Maastricht, The Netherlands >>>>> T +31 43 38 84 090 F +31 43 38 84 092 >>>>> ================================================ >>>>> _______________________________________________ >>>>> 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 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> 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. >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> 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 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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recon-all: 'segmentation fault'
by Mark Plantz 28 Aug '13

28 Aug '13

Hello all, I recently created a .gca atlas for a set of special subjects. After running recon-all for one of these subjects, I was left with the following error during the 'Subcortical Segmentation' section: *searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)* *final transformation (x=0.0, yr=90.000, zr=-0.000):* *-0.000 0.000 1.000 128.000;* *-0.000 1.000 -0.000 128.000;* *-1.000 0.000 0.000 128.000;* * 0.000 0.000 0.000 1.000;* *Segmentation fault* * * I also attached a copy of the .gca atlas, the labels.mgz file, and the LUT I am using. Right now I have two probable causes of the problem: 1.) Since I did not include all of the regions as the normal .gca atlas, recon-all may be exiting with error. [I only included the following regions for labels: caudate, white matter, gray matter, cortex, thalamus, hippocampus, parahippocampus, putamen, pallidum, and amygdala]. 2.) I used a different look-up table [LUT] with different segmentation values for the previously listed regions. Do you think that either of these could be the reason for the segmentation fault? Any ideas on how to get around it? Thanks in advance. Best, MP atlas.gca<https://docs.google.com/a/u.northwestern.edu/file/d/0BzKLhN7P9kNQR0JYZTV6dG…>

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recon-all issue (CSF seg as gray matter)
by Alexandre Gramfort 28 Aug '13

28 Aug '13

Hi, after running recon-all on many datasets without any manual intervention, it looks like I finally have to. As you can see in : https://dl.dropboxusercontent.com/u/2140486/Screen%20Shot%202013-08-28%20at… the CSF is segmented as gray matter while white+gray matters are merged. what's my best option to fix this? thanks Alex

2 1

apply a label to an overlay in tksurfer
by Sarah Madsen 27 Aug '13

27 Aug '13

Hello, Is there a way to apply a label to a mgh file? I would like to show a gray brain with values from an mgh shown only in the significant areas (ie only within my label). Is there a way to do this? I have a set of mgh files with beta values from a regression. I also have a set of labels for the significant areas. Both sets of files were created in matlab and are in fsaverage space. I can open the two files together in tksurfer and see the entire beta map, along with the label for the significant regions. Is there a way to zero-out all of values in the mgh overlay which fall outside of my label? A command line option would be preferable, since I have several maps. Thank you very much!

2 1

Freesurfer dependencies
by ye tian 27 Aug '13

27 Aug '13

Dear Freesurfers, Where may I find a list of freesurfer dependent libraries? Thank you very much! Sincerely, Ye

2 2

Otto: update freesurfer to latest version?
by Otto Muzik 27 Aug '13

27 Aug '13

Dear All, I would like to upgrade my freesurfer distribution to the latest version - Is there an automated procedure to do this? My current version is linux-gnu-stable5-20110522 Many thanks! Otto

1 0

tutorial subject not found
by leila nasehy 27 Aug '13

27 Aug '13

Dear Supporter I am new to freesurfer and have started to download tutorial data for tracula.There is an error saying: "hostname: Host name lookup failure" what shall I do? Regards Leyla

1 0

pb reading .annot in matlab/python
by Alexandre Gramfort 27 Aug '13

27 Aug '13

hi, when trying to read the following .annot file: https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig… using the following matlab code: -- [vertices, label, colortable] = read_annotation('left_mc-z.negative.sig.ocn.annot'); unique(label) unique(colortable.table(:, end)) setdiff(colortable.table(:, end), unique(label)) -- there seem to be a discrepancy between the "label" and the last column of colortable "colortable.table(:, end)" the script outputs: -- Reading from version 2 colortable with 7 entries read (originally none) ans = 0 2244856 3987639 5840816 11298645 13698134 16665710 ans = 2244856 3834223 3987639 5840816 11298645 13698134 16665710 ans = 3834223 -- in other words 0 is in label but not in the colortable. Should I conclude that 0 is 3834223? If so what's the proper way of figuring this out? thanks Alex

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