Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Glmfit subtraction between 2 individuals
by Adam Nitenson 29 Jun '12

29 Jun '12

Hi all, I am trying to visualize the surface map showing the Post Treatment - Pre Treatment cortical thickness in a single subject. The Post and Pre scans are processed like 2 separate subjects. I used the commands: mris_preproc --f /cluster/roffman/users/Stable5_PerRun/Subject_Files/FB12_Pairs/FB0011040 --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/THICKNESS-MAP-LH.mgh and mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/THICKNESS-MAP-LH.mgh --fsgd /cluster/roffman/users/fsgd/FB12_Pairs/FB0011040.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/Post_Minus_Pre/LH --surf fsaverage lh --fwhm 4.6 The subject and fsgd lists only have 2 subjects (the post and the pre) and the contrast is the 1 -1, same as the group.diff.mtx on the Wiki. I receive the error DOF = 0, which is likely because each group only has 1 subject. Usually I have multiple subjects in each group. Is there an alterate way to generate this difference map when only using 2 subjects?? Best, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

3 2

lh.pial question
by Borzello, Mia 29 Jun '12

29 Jun '12

Hi all, Is there a way to edit the pial files (e.g. lh.pial)? I want to delete a few vertices we think are causing errors for a 3D printing we are trying to do. Thanks, m

2 3

surface vertex pairs; voxel coloring for tkmedit
by John Papaioannou 29 Jun '12

29 Jun '12

Hi, In regard to the surface files, is it correct to say that the wm and pial vertices correspond to each other (e.g., wm vertex # 12345 corresponds to pial vertex # 12345 as the minimum distance between the two surfaces), and so have the same number of vertices? Also, I would like to "colorize" voxels, but not for segmentation. Instead, colored voxels would represent various metric "anomalies". It's rather easy with curv files for 3D display (positive or negative values at vertex), but I want to show this on tkmedit in 2D. Could you explain what is the easiest way to do this? Thanks, John ___ John Papaioannou Medical Imaging Sciences Digital Mammography, CAD Mammography Department of Radiology Biological Sciences Division The University of Chicago 5841 South Maryland Avenue Chicago, Illinois 60637 773.834.5104 voice 773.702.0371 fax

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Freeview scripting reference
by Inge Kasbohm Amlien 29 Jun '12

29 Jun '12

Hi list, I am looking for a complete reference to scriptable commands for Freeview, comparable to what exists for tksurfer (e.g. http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScripting/Tk…) Does this exist? Thanks! ___________________________________ Inge Kasbohm Amlien E-mail: inge.amlien(a)psykologi.uio.no Phone: +47 97106525 Psychologist // Ph.D candidate Centre for the Study of Human Cognition Department of Psychology, University of Oslo

2 1

ROI from left to right hemi - cortical thickness
by Irene Altarelli 29 Jun '12

29 Jun '12

Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23

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mri_robust_template- Segmentation Fault
by Usman Khan 28 Jun '12

28 Jun '12

Hi there Freesurfer, I am running into a seg fault while running mri_robust_template on freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on a Centos6.2 build. Thinking that this may perhaps be an OS-related issue, I tried to download FS binaries from http://www.freesurfer.net/pub/dist/freesurfer/misc/linux-centos6_x86_64/ but the link is dead Any help would be appreciated Usman $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --satit: Will estimate SAT iteratively! --mov: Using 191_0001.nii.gz as movable/source volume. --mov: Using 192_0001.nii.gz as movable/source volume. Total: 2 input volumes --template: Using test.nii.gz as template output volume. reading source '191_0001.nii.gz'... reading source '192_0001.nii.gz'... Segmentation fault (core dumped)

2 1

Pial and WM boundary edits
by Skyler Gabriel Shollenbarger 28 Jun '12

28 Jun '12

To whom it may concern, After running autorecon2 (recon-all -subjid xxxxxxxx -autorecon2) there were areas that required correcting for both the pial and WM boundaries. I added control points to correct the WM boundaries and saved them using File > Save Control Points. I also used the select voxels tool to extend the boundaries in areas where the pial surface was not generous enough resulting in excluded GM and saved them using File > Save Volume. After adding these voxels and control points I ran (recon-all -autorecon-pial -subjid xxxxxxxx) however received an error that '-autorecon-pial' was not recognized. Then, in attempt to regenerate the boundaries with the new voxels and control points saved, I ran (recon-all -subjid xxxxxxxx -autorecon2-cp). When reloading the image to inspect the new boundaries using command (tkmedit xxxxxxxx brainmask.mgz -surfs -segmentation wm.mgz $FREESURFER_HOME/ASegStatsLUT.txt), I found that the errors were not fixed. If anyone has insight into what I'm doing incorrectly it would be much appreciated! Skyler -- Skyler G. Shollenbarger Graduate Student Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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TRACULA question: pathstats.overall.txt
by Minjie Wu 28 Jun '12

28 Jun '12

Dear TRACULA Developer & User, I am wondering if it is possible to add other DTI measurements to the pathstats.overall.txt along with those DTI parameters already included (FA, MD, AD, RD)? Thank you very much. Minjie

2 4

Building ROI from SPM5 MNI results
by Kairys, Anson 28 Jun '12

28 Jun '12

Hi Everyone, I would like to "import" an ROI into a FS analysis and extract thickness measures form within this region. Is this at all possible? Thanks Anson K, ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Recent paper on FreeSurfer reliability
by Ed Gronenschild 28 Jun '12

28 Jun '12

Dear Bruce, Doug, Nick, and other co-workers, As authors of the recent paper “The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements” we would like to take the opportunity to respond to the numerous e-mails and reactions written on mailings lists and websites. We have never expected that our paper would have such an adverse impact. We have noticed that several so-called “journalists” have misinterpreted and erroneously extrapolated our conclusions. Even though this is not in our hands, we want to express our disappointment of these events and that we feel very uncomfortable with the created harassment. We want to stress that it has never been our intention to put FreeSurfer in a bad light or to blame its developers, rather we wanted to quantify the effects that you frequently warned the users about. The results of our study confirm your recommendations and increase the awareness of such effects to (novice) users. It is of course unavoidable that modifications to algorithms will produce different results; we, nevertheless, must admit that we were surprised that some effects were rather large. We are using FreeSurfer frequently for our MRI data and we definitely intend to do so in the future. We are impressed by the efforts of your team to improve the algorithms and to extend the capabilities of FreeSurfer. We are most grateful to you and the other developers because these continuing efforts enabled and will enable us to perform our research in a valid and proper manner. Unfortunately, the media attention gave the impression that our conclusions would only be directed to FreeSurfer. We have written in our discussion section that some of the conclusions may apply to other packages in the field of neuroimaging as well. We hope that you can acknowledge our sincere intention to examine and increase awareness of uncontrolled variation in MRI data analyses in general and not to pinpoint Freesurfer. Therefore, we have informed also the users and developers of FSL about possible similar effects. Ed Gronenschild, Petra Habets, Heidi Jacobs, Ron Mengelers, Nico Rozendaal, Jim van Os, Machteld Marcelis

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Freesurfer June 2012