Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Peirhinal cortex thickness
by Gomar, Jesus 29 Aug '13

29 Aug '13

Dear all, I am interested on getting thickness measures of the perirhinal cortex. I am using version 5.3 and I am aware that a label for the perirhinal cortex has been created in version 5.2. However, when I run recon-all I don't get thickness measures of the perirhinal cortex (just as I do for instance for entorhinal cortex of middle temporal cortex) In summary, my questions are: 1. Is the calculation of perirhinal cortex thickness automated in version 5.3? 2. If not, Can I get some info on how to proceed to obtain this measure? Thanks in advance for any advice! Jesus J. Gomar The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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generating new surface
by Ian Charest 29 Aug '13

29 Aug '13

Dear Freesurfers, I need to generate a surface which lies halfway between the wm/gm border and the pial surface so that I can then import it in matlab using read_surf.m to get the vertex coordinates and faces for the surface that, as I said, would not be the pial surface, but defined at half cortical thickness. I looked at mri_vol2surf --help, and its option --projfrac 0.5 seemed to be what I wanted, but I don't know how to call mri_vol2surf for the specific needs I have. Also, mri_vol2surf produces an overlay mappable onto a surface and not a surface per se, so maybe what I am looking for lies elsewhere. Any help would be highly appreciated!! ian

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Re: [Freesurfer] Thickness vertex by vertex
by Giusy Chinnici 28 Aug '13

28 Aug '13

Thanks all, I did it :) Cheers Giusy Inviato da iPhone Il giorno 28/ago/2013, alle ore 18:40, Avram Holmes <holmes(a)wjh.harvard.edu> ha scritto: > check the .vol values I think they should match those from read_curv. > > Avram > > > On Wed, Aug 28, 2013 at 11:37 AM, Giusy Chinnici <giusy.chinnici(a)gmail.com> wrote: >> Thanks all, >> >> I opened the file subj/surf/?h.thickness with MATLAB using the function read_curv(subj/surf/lh.thickness). I obtained a vector with dimensions nverticesX1, but I need also the vertex IDs. Are vertex IDs in the thickness file ordered from 0 to n? Is there some other way to obtain a table with vertex IDs and the corresponding thickness values? >> >> @avram:as you suggested, I tryed to use MRIread('subj/surf/lh.thickness.mgh'), it doesn't return the desired values. You can find the result in the attachment . >> >> thanks >> Giusy >> >> >> 2013/8/28 Avram Holmes <holmes(a)wjh.harvard.edu> >>> Giusy, >>> >>> You can access vertex level info in Matlab with MRIread('SUBJECT.FILENAME'). >>> >>> Avram >>> >>> >>> On Wed, Aug 28, 2013 at 8:42 AM, Giusy Chinnici <giusy.chinnici(a)gmail.com> wrote: >>>> Dear all, >>>> >>>> Is there available a function that, given a certain ROI, returns per vertex thickness (not the average thickness)? >>>> >>>> Thanks >>>> Cheers >>>> >>>> Giusy Chinnici >>>> _______________________________________________ >>>> 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. >>> >>> >>> >>> -- >>> Avram Holmes PhD >>> Instructor in Psychiatry, Harvard Medical School >>> Assistant in Research, Massachusetts General Hospital >> >> >> >> -- >> Giusy Chinnici > > > > -- > Avram Holmes PhD > Instructor in Psychiatry, Harvard Medical School > Assistant in Research, Massachusetts General Hospital

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Brainhack 2013 Invitation and Registration Link
by MCLAREN, Donald 28 Aug '13

28 Aug '13

Dear colleagues, I wanted to draw your attention on the upcoming Brainhack 2013, which is being held from October 23-26 at the Centre International d'Études Pédagogiques, Sèvres, France (just outside of Paris). Brainhack 2013 is a unique workshop with the goals of fostering interdisciplinary collaboration and open neuroscience. The structure builds from the concepts of an unconference and hackathon: The term “unconference” refers to the fact that most of the content will be dynamically created by the participants — a "hackathon" is an event where participants collaborate intensively on projects. Participants interested in neuroimaging from any discipline are welcome. Ideal participants span in range from graduate students to professors across any disciplines willing to contribute (e.g., mathematics, computer science, engineering, neuroscience, psychology, psychiatry, neurology, medicine, art, etc…). The primary requirement is a desire to work in close collaborations with people outside of your specialization in order to address neuroscience questions that are beyond the expertise of a single discipline. One should come to brainhack ready to engage into collaborative projects, and with some material (slides, ideas, data, tools) ready to start a project or a discussion panel. Brainhack will build on the successful techniques used in other unconferences to keep the meeting focused and productive. It is possible to start a project and build a team as early as today. Please have a look at the website for information on the conference and a sample of projects (from Brainhack 2012): http://www.brainhack.org The Preliminary Schedule for Brainhack 2013 is available online: http://www.brainhack.org/?page_id=27753 ***NEW*** We will be accepting and publishing Brainhack 2013 abstracts. Abstracts should be submitted when you register. Registration is now open: http://www.brainhack.org/?page_id=27743 Please share this with your friends and colleagues. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Thickness vertex by vertex
by Giusy Chinnici 28 Aug '13

28 Aug '13

Dear all, Is there available a function that, given a certain ROI, returns per vertex thickness (not the average thickness)? Thanks Cheers Giusy Chinnici

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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

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