Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

controlling for age in qdec
by olof lindberg 10 Sep '13

10 Sep '13

Dear Freesufer experts. I am trying to run attached fsgd file in qdec or in GLM-fit. I just want to do a group comparison in which I compare cortical thickness between groups controlling for age. when I run the analysis with age as a raw score - the results seems very strange - if i on the other hand convert age to z-scores (with a mean of 0) then results seems to be as I would expect As I understand it - I do not need to centre Age in order to control for it? So what is then going wrong when I run the analysis? thanks Olof

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how does norm.mgz affect the behavior of mri_pretess?
by David Romano 10 Sep '13

10 Sep '13

Hi everyone, I was hoping that someone could clarify for me the role played by norm.mgz in the command mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz from the -tessellate step of the -autrecon2 section on the page http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. My understanding is that this command will (roughly) perform the following tasks for a given voxel v in filled.mgz with intensity 255: 1) Determine whether there are any other voxels of intensity 255 in the 3x3x3 cube centered at v. 2) If so, then further determine whether none of these share a face with v. 3) If so, then let S be the set of all such voxels, together with v itself, and identify an "optimal" collection of the remaining voxels in the 3x3x3 cube to add to S so that every voxel in S shares a a face with at least one other voxel in S, where "optimal" means that the added voxels should have intensities as close as possible to 255 in norm.mgz. Does this capture the role played by norm.mgz? Or am I way off? Thanks in advance for your help, David Romano

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recon-all for multiple subjects
by Anupa AV 10 Sep '13

10 Sep '13

Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working

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Issue running Longitudnal Analysis
by Ray, Siddharth 09 Sep '13

09 Sep '13

Hi all, I was trying to run freesurfer longitudinal analysis for my subjects at 2 time points and when I ran the pre_proc step it gave me an error that file 'lh/rh.thickness is missing'. Here is what I have done. 1) Run the Freesurfer till CA Normalize stage (till norm.mgz stage). 2) Created unbiased template - log file showed 'exited without error' (and it looks fine) 3) Run longitudinal processing - log file showed 'exited without error' , but when I closely looked at the file there was following error: #@# Talairach Failure Detection Wed Sep 4 14:22:01 CDT 2013 /work/02510/sray2/Free_Sub/FS_output/54062.long.54062_59467/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0124, pval=0.0000 < threshold=0.0050) Do you where is I am doing wrong. Why is the log file showing 'exited without error' if there was an error at Talairach Detection. Please let me know. Thanks, -Siddharth

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Recon-all ceases working after mri_nu_correct.mni ...
by Amy Bilderbeck 09 Sep '13

09 Sep '13

Dear FreeSurfer community, My recon-all commands have stopped working, when previously they (usually) completed just fine. I am not sure at what level the problem is at. I'm working off the Jalapeno cluster at FMRIB, where FreeSurfer is centrally installed. I run a configuration script to get started (. $FREESURFER_HOME/SetUpFreeSurfer.sh) and then define my subjects directory (SUBJECTS_DIR=~/scratch/my_fs_subjects). I then run recon-all commands e.g. fsl_sub -q verylong.q recon-all -s SubjectXXX -i T1_biascorr.nii.gz -all This previously worked. I now within minutes get a log file with no obvious error message, but which ends #-------------------------------------------- #@# Talairach Wed Aug 28 15:38:06 BST 2013 /home/fs0/amyb/scratch/Enigma_bipolar/FSURFER_OUTPUT/BF_subject10/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux jalapeno04.fmrib.ox.ac.uk 2.6.32-358.14.1.el6.x86_64 #1 SMP Mon Jun 17 15:54:20 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SubjectXXX exited with ERRORS at Wed Aug 28 15:38:13 BST 2013 We are using FreeSurfer version 5.3.0. After reading some of the archive I've checked that nu_correct is indeed stored in the freesurfer directory mni/bin/nu_correct. Any tips? Thanks and warm regards, Amy Dr. Amy Bilderbeck From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of ye tian Sent: 09 August 2013 21:05 To: Douglas N Greve Cc: Freesurfer Subject: Re: [Freesurfer] Qdec and one discrete variable Dear Doug, Thank you very much! Sincerely, Ye On Thu, Aug 8, 2013 at 4:46 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> wrote: Try adding a carriage return after TM doug On 08/08/2013 05:30 PM, ye tian wrote: Dear Doug, It is a mac. I made the meditation.levels file using emacs. emacs meditation.levels --> type "Normal" (level1) --> hit enter --> type "TM" (level2) --> save file Thank you very much! Sincerely, Ye On Thu, Aug 8, 2013 at 4:22 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>>> wrote: How did you create the levels file? Eg, did you use a windows computer? Or did you use msword or some other word processor. If not, can you send the levels file? On 08/08/2013 03:49 PM, ye tian wrote: > Dear freesurfers, > > I am experimenting qdec with one of my discrete variables. Besides > qdec.table.dat file, I do have a .levels file with the two levels of > the variable (say level1 and level2). However, I keep getting the > following error message: > > Reading discrete factor levels from config file > /$SUBJECTS_DIR/qdec/meditation.levels > level1 > done. > ERROR: /$SUBJECTS_DIR/qdec/meditation.levels is invalid. Must have at > least two levels. > Error loading the data table. > > Is there something that I have missed in the declaration of the variable? > > Thank you very much! > > Sincerely, > Ye > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@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<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358<tel:617-724-2358> <tel:617-724-2358<tel:617-724-2358>> Fax: 617-726-7422<tel:617-726-7422> <tel:617-726-7422<tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://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<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358<tel:617-724-2358> Fax: 617-726-7422<tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Segmentation edits
by krista kelly 09 Sep '13

09 Sep '13

Hi all, I am doing cortical thickness and surface area analyses and had a few questions regarding editing the borders. 1) Is it reasonable to edit every (big and small) error that I find? Basically, how much a difference would it make in terms of the surface area and cortical thickness values if I did not edit the smaller errors? 2) If the skull hasn't been completely stripped, but is not designated as either white or gray matter, do I need to adjust the thresholding for extracting the brain and re-extract? The only situation in which I feel this would be a problem is when doing whole brain analyses. 3) Would it make a difference to the data if I initially ran recon-all using freesurfer version 5.0 and then, after editing the segmentations/labels/skullstripping, reran autorecon 2,or 3 using freesurfer version 5.1? If anyone could answer any or all of these questions that would be great! Krista

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Tkmed in VirtualBox and wm parcelation
by Martin Kavec 09 Sep '13

09 Sep '13

Hi all, I have two questions: 1. Does tkmedit, or freeview work under VirtualBox 2. Is it possible to parcelate white matter in freesurfer? Thanks, Martin Sent from my iPad

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Cortical labels for WM seeding
by Sean Hatton 09 Sep '13

09 Sep '13

Hello FS Gurus, I would like to export FS labels as seed regions for deterministic tractography in TrackVis (probabilistic is not appropriate in this investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and grow the label into the WM and exclude GM. While I get a biologically plausible ROIs and plenty of good streamlines, I do get some stray streamlines that jump across the sulci into adjacent gyri which (I have read) is an artefact of seeding from GM. Have I got the right approach? Should I create an inverse intracranial volume mask as an exclusion mask? Something else? Kind regards, Sean Hatton Brain & Mind Research Institute University of Sydney, Australia.

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cluster threshold
by Yang, Daniel 09 Sep '13

09 Sep '13

Hi FreeSurfer Experts, On this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons) it says: "In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common thresholds." I am wondering how these thresholds were computed. In my own computation, I found z-value to be the following, but neither one-sided nor two-sided matches the thresholds of 1.3, …, 4 as shown above? one-sided: p-value=0.0500, z-value=1.6 p-value=0.0100, z-value=2.3 p-value=0.0050, z-value=2.6 p-value=0.0010, z-value=3.1 p-value=0.0005, z-value=3.3 p-value=0.0001, z-value=3.7 two-sided: p-value=0.0500, z-value=2.0 p-value=0.0100, z-value=2.6 p-value=0.0050, z-value=2.8 p-value=0.0010, z-value=3.3 p-value=0.0005, z-value=3.5 p-value=0.0001, z-value=3.9 Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Re: [Freesurfer] apply fnirt transformation on a surface
by Shani Ben Amitay 09 Sep '13

09 Sep '13

Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space? Thanks! Shani On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi <saad(a)fmrib.ox.ac.uk> wrote: > You need to convert your surface file into a format that workbench > understand (GIFTI): > > mris_convert lh.whiteinraw lh.whiteinraw.surf.gii > > Cheers > Saad > > > On 3 Sep 2013, at 10:57, Shani Ben Amitay <shani.holzer(a)gmail.com> wrote: > > Thank you! > Still somehow I haven't manage to make it work when I ran the suggested > command I get an error saying : > ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error > occurred while parsing element line number: 1 column number: 1. > Any advise? > > Thanks again > > Shani > > > > On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> thanks Matt >> Bruce >> On Mon, 2 Sep 2013, Glasser, Matthew wrote: >> >> > Hi Bruce, >> > >> > Connectome Workbench commandline utilities can do this with FSL warp >> > fields: >> > >> > wb_command -surface-apply-warpfield >> > >> > One needs to use the inverse warp as the <warpfield> argument and the >> > forward warp as the -fnirt <forward-warp>. >> > >> > Peace, >> > >> > Matt. >> > >> > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >> > >> >> A veritable game of telephone! Thanks Jesper. Matt? >> >> >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >> >> >>> Hi guys, >> >>> I didn't think we had any tools for doing that, and said so much on >> the >> >>> FSL >> >>> mailbase. But apparently the WashU people has something that does just >> >>> that >> >>> for you. I think the best person to contact about the details is Matt >> >>> Glasser. >> >>> >> >>> J >> >>> >> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> >> >>> wrote: >> >>> >> >>> Hi In Probtrackx, this is done internally. >> >>> If you just want to transform the vertex coordinates, then I think >> >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >> >>> knows better. >> >>> >> >>> Cheers, >> >>> Saad >> >>> >> >>> >> >>> >> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> >>> wrote: >> >>> >> >>> you might check on the FSL list. I think I've seen some >> >>> traffic indicating that there are some tools for doing >> >>> this. I'l cc Saad as he might know >> >>> >> >>> cheers >> >>> Bruce >> >>> >> >>> >> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >> >>> >> >>> Hi Shani, I don't think you can apply a FNIRT >> >>> transform to a surface. >> >>> doug >> >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >> >>> Dear freesurfer people, >> >>> Any idea whether I can apply transformation >> >>> that was calculated by fsl >> >>> fnirt on the white/pial surfaces calculated >> >>> using the freesurfer >> >>> stream? >> >>> Thanks! >> >>> Shani >> >>> _______________________________________________ >> >>> 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. >> >>> >> >>> >> >>> >> >>> -- >> >>> Saad Jbabdi >> >>> University of Oxford, FMRIB Centre >> >>> >> >>> JR Hospital, Headington, OX3 9DU, UK >> >>> (+44)1865-222466 (fax 717) >> >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >> >>> >> >>> >> >>> >> > >> > >> > ________________________________ >> > The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > >

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Freesurfer September 2013