Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

rerunning recon-all
by Luke Bloy 11 Sep '13

11 Sep '13

I have a somewhat strange question and hopefully someone can help me out. I have a few hundred subjects that have all been run through recon-all, and have gone through some QA. In some of the cases control points have been added or brain masks have been modified etc, and recon-all has been rerun with the 'autorecon2-cp' and autorecon3 flags. My issue now is that my cluster is being upgraded to a different OS, and I'm planning on rerunning on my subjects on the new cluster, but with the same freesurfer version. So my question is how should I go about this. Should a just rerun 'recon-all' from the beginning. If I do this would I be losing the whatever edits I made during the QA procedure? Should I just do rerun with the 'autorecon2-cp' and 'autorecon3'? Am I being overly concerned with a change in computers? Thanks Luke

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mri_tesselate: max vertices 1000000 exceeded
by Martijn Steenwijk 11 Sep '13

11 Sep '13

Dear all, I'm trying to process some high res data using the approach Lusebrink proposed, but I'm getting the following error in mri_tessellate: mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ mri_tessellate: max vertices 1000000 exceeded It seems that max number of faces and vertices is hardly defined in the code. Would it be possible to provide another compiled version (centos6_x86_64-stable-pub-5.3.0) with these numbers doubled or so? Best regards, Martijn

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FS versions
by elisa veronese 11 Sep '13

11 Sep '13

Dear FS team, I'm using the web portal Neugrid (https://neugrid4you.eu/it) for the analysis of my T1w MRI data with FreeSurfer. In particular, I'm using the *reconall -all*. My question is about possible problems arising from different FS versions. The version provided by Neugrid is the Freesurfer version *5.1.0 *Linux CentOS4 x86_64 When I perform the subsequent manual correction on my workstation, I use Freesurfer version *5.3.0* Linux CentOS4 x86_64 Is this correct? Should I downgrade to the 5.1.0 version also in my workstation? Thank you in advance. Regards, Elisa -- Elisa Veronese - PhD * Research Unit on Brain Imaging and Neuropsychology (RUBIN) * * Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php *

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mri_annotation2annotation?
by Yang, Daniel 11 Sep '13

11 Sep '13

Hi all, I know I can use mri_label2label and then mris_anatomical_stats -l to obtain the label-based cortical thickness for each individual subject. I also know that there is a tool called mri_annotation2label. But is there a way to convert annotation to each individual subject, so that I can use mris_anatomical_stats -a to obtain the annotation-based cortical thickness for each individual subject? Many thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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ASeg Stats is done twice?
by Peter Wendorff 11 Sep '13

11 Sep '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I try to get information about the progress of my subjects out of the log files, writing a script that reports about the progress and sends progress messages. For that I try to get the individual stages as progress indicator from the recon-all.log. Usually lines like this indicate the start of a stage: #@# ASeg Stats Tue Sep 10 11:12:13 CEST 2013 the date of course is variable and indicates the current date. My problem now is exactly that Stage ASeg Stats, as it occurs twice. the first occurrence is after inflate2 (smooth2, inflate2, aseg stats), the second one is, as documented after cortribbon (parc stats 2, cortical ribbon mask, aseg stats, aparc-to-aseg). But [1] lists only the second occurrence. Is that wanted? is it due to my strategy to run autorecon1, autorecon2 and autorecon3 individually instead of autorecon-all -all? regards and thanks for your help Peter [1] http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlIwONQACgkQi8ffXNvWmYQ5yACgiD/sgP/PR+xsuZJWtGoeFKlL LcYAniH2Q+SSHzPLAc2aTphUyoTm0bv2 =JLDM -----END PGP SIGNATURE-----

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Number of independent vertices and Bonferroni correction
by Damien MARIE 10 Sep '13

10 Sep '13

Hello everyone, I'm using freesurfer for regression analyses and group analysis of cortical thickness, surface area, curvature and sulcal depth. I started to made illustrations and tables using the p < 0.05 FDR correction. However I have some p-value reaching 10^-32 and I would apply a Bonferroni correction. How determinate the number of independent vertices? Thanks a lot, best regards, Damien Damien Marie - Doctorant / PhD student E-mail: damien.marie(a)u-bordeaux2.fr Phone: +33 (0)5 57 82 09 39 Homepage: www.gin.cnrs.fr/spip.php?article23&lang=en Researchgate: www.researchgate.net/profile/Damien_Marie/ _______________________________________________ GIN (Groupe d'Imagerie Neurofonctionnelle) UMR 5296 - Université Bordeaux II Ségalen - CNRS - CEA 146, rue Léo Saignat - Case 71 33076 Bordeaux cedex _______________________________________________

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Editing WM
by Francesco Siciliano 10 Sep '13

10 Sep '13

Hi, I've noticed that occasionally when I manually edit recons, the white matter surface will be drawn to include a portion of the volume where no white matter pixels are present. Therefore, when I go to correct the incorrectly drawn surface, there are no pixels to delete under the white matter mask. It is almost as if I have deleted the pixels already yet I have not and the white matter surface is still drawn to include an area where there are no white matter pixels. Why could this be happening? Does it matter as long as there are no pixels in the incorrect area? Thank you, Francesco 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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z-scores age
by olof lindberg 10 Sep '13

10 Sep '13

Dear Douglas, no I did not run in GLM-fit - I run in qdec The conversion into z-scores was done in a statistical program (statistica) and was calculated on basis of all subjects (both groups) - the thing that confuses me is that - if I understand it correctly from previous discussions on the mailing list - it should not be needed to demean age in order to correct for it? So in qdec I get completely different results if i use z-scores - than if I use the original raw age data. If I look at the plot of the z-scores versus raw age in qdec the distribution on the plot is exactly the same. So I would expect that no matter using raw age or z-scores would affect results the same? But the results look completely different (basically the raw-age corrected data looks wrong) Am I doing something wrong? thanks Olof

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convert .mgh to .label?
by Yang, Daniel 10 Sep '13

10 Sep '13

Dear all, Is there a way to convert .mgh to .label? My .mgh is a ROI file from qdec-based group analysis and I don't want to draw the ROIs manually. Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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statistically truncate negative values
by Maya Rosen 10 Sep '13

10 Sep '13

Hi All, I have two conditions of interest in my GLM analysis, Condition A and Condition B. I would like to make a contrast of Condition A and Condition B that includes only those vertices that are significantly positively activated when compared to the Passive Viewing baseline. In other words, I would like to mask anything that is Passive > Condition A or Passive > Condition B and only include Condition A > Passive and Condition B > Passive when contrasting Condition A and Condition B, so as to limit my contrast to changes in *activation *in the two conditions, not *deactivation *. I see that in an older version, when isxavg-re-sess was used, there was a flag --trunc that would allow you to set the negative values to 0. If there is a way to do this in the v 5.1.0, I could then perform a second level contrast of positively activated Condition A and Positively activated condition B. Is there a way to exclude the negatively activated voxels from the Condition A vs Passive and Condition B vs Passive contrasts when looking at Condition A vs Condition B? I would like to do this statistically, not just at the map level. Thank you for your help! Maya

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Freesurfer September 2013