Freesurfer

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30132 discussions

Partial brain scanning and registeration
by SHAHIN NASR 20 Sep '11

20 Sep '11

Hi I want to know if there is any limit for the automatic registration of functional scans on structural ones when we are scanning activity just in a specific part of the brain (e.g. occipital cortex).

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Optseq2 Null Events between every Event
by Anita Cservenka 20 Sep '11

20 Sep '11

Hi, I was wondering if it is possible to use optseq2 to get null events (e.g. fixation) between each event type. I would like to see the optimal sequence of trials for a design that involves two event types (each 0.5 sec), 60 TRs for one event, 26 TRs for the other, and a 2sec TR. I would like to have an intertrial interval lasting between 2-10 seconds (jittered) between each of the 0.5 sec long events. I can’t seem to find an option for optseq2 that would allow me to set a null event between each 0.5 sec event. Is this possible and if so what options should I use? Thanks! Anita

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Patch file to ascii issues
by Michael Waskom 20 Sep '11

20 Sep '11

Hi, Two issues related to patch files. Issue number 1: If I generate an ascii flat patch file like so: $ bin_patch=fsaverage/surf/lh.cortex.patch.flat $ mris_convert -p $bin_patch lh.cortex.patch.flat.asc And then inspect the file that gets created: $ head lh.cortex.patch.flat.asc #!ascii version of patch fsaverage/surf/lh.orig. The 1st index is not a vertex number 149297 296943 1 vno=0 -60.013611 4.446770 0.000000 2 vno=1 -56.163204 88.759064 0.000000 3 vno=2 -112.137077 -18.977211 0.000000 4 vno=3 -34.436668 -72.297958 0.000000 This is sort of annoying if I want to read it into Matlab, etc. (actually Python) using routines that expect an array of numbers. Is there any way to suppress the intercoordinate output? Issue number 2: Even if I get around the text file formatting issues, I run into some problems when I try and generate meshes with the resulting data. It seems like the triangles component of the surface makes references to vertex ids that don't exist anymore. In other words, the triangles array contains values that are larger than the number of rows in the vertices array. Obviously I'm doing things that aren't officially supported by Freesurfer there, but does that jive with your knowledge of how the patch files are written? Thanks! Michael

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How can I include 3 covariates in my GLM model
by Dalwani, Manish 20 Sep '11

20 Sep '11

Hello Freesurfer's, I am using QDEC and I have created and FSGD descriptor file with 2 groups (pts and ctrls) and three continuous variables: age, IQ and mean thickness. I have 2 questions: 1. I can only choose 2 covariates at one time? How can I choose all three covariates in one model in my design? 2. I tried group and 2 covariates combinations to check if it runs ok and found that when I select age and IQ, it runs...when I select IQ and mean thickness it runs but it fails when I try running with age and mean thickness in the model? The error in the terminal says matrix not correct, check duplicates..., etc.. What I am doing wrong? Thanks, Manish Dalwani

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please help, unsupported slice timing
by Gregory Kirk 20 Sep '11

20 Sep '11

i am trying to run tracula on a large number of subjects, tracula dies quicklyin -prep stage when mri_convert tries to copy/rename the diffusion data, the error actually comes from the data read function. the data is already in .nii format the error is 'unsupported slice timing pattern 5' this is diffusion data that is already in .nii format so the slice timing information is irrelevant, no slice timing correction is done on diffusion data, but the info was obviously encoded in the nifti header. what do i need to do to get this data to load, go edit the .nii header and 'remove' this info. i tried with the fsledithd function and just setting the 5 to 0 does not work, then i just get a 'read error' with no other information. this data is from a 1.5T siemens mobile scanner so the snr will be a little lower and the bval = 800 is lower so it is just the data that could use the helping hand of the spatial priors to find the tracts. i can run 500 of these if i can get this fixed, incarcerated psychopaths so an important data set. thank you Greg

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Re: [Freesurfer] FW: flipped orientation in tksurfer and tkmedit
by Ilana Hairston 20 Sep '11

20 Sep '11

Hi Doug, No, we had the lh loaded in tksurfer, and when saving a point it showed up on the *left* in tkmedit (i.e., the right side). thanks ilana On Tue, Sep 20, 2011 at 11:34 AM, weiland, Barbara <bweiland(a)med.umich.edu>wrote: > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto: > freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, September 14, 2011 6:10 PM > To: Ilana Hairston > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] flipped orientation in tksurfer and tkmedit > > When you say on the "right hemi in tkmedit" do you mean on the right side > of the image (which is the left side of the brain)? > doug > > Ilana Hairston wrote: > > Hi there, > > We recently had a problem that tksurfer and tkmedit were flipped > > relative to each other. Basically, when saving a point in the left > > hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit. > > Any ideas how this could have happened? > > Thanks > > ilana > > > > > > > > -- > >> ****************************** > >> Ilana Hairston ,PhD > >> Research Assistant Professor > >> 4250 Plymouth Rd. (rm 2439) > >> Psychiatry Department, Addiction Research Center University of > >> Michigan, Ann Arbor MI 48109-2700 > >> Tel: 734-232-0232; Mobile: 650-906-8449 > >> > >> ******************** > >> Reminder: Women do 66% of the work worldwide, earn 10% of the income, > >> and own 1% of the world's property > > > > > > > > ---------------------------------------------------------------------- > > -- > > > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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. > > -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

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Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
by Lauge Emil Borch Laurs S0rensen 20 Sep '11

20 Sep '11

On Mon, Sep 19, 2011 at 15:20, R Edgar <freesurfer.rge(a)gmail.com> wrote: > Are you sure that there aren't per process limits which are set lower > than those? > > Richard I just checked, and no, there is no per process memory limit. Is there any way to get more information out from mri_ca_register than what is written in the logs? Lauge

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mris_calc problem
by Dabbs (Kevin) 19 Sep '11

19 Sep '11

I have ran into a problem with mris_calc using Freesurfer 5.1 on Mac OS Leopard. When running long_mris_slopes I am getting this error; ERROR 1 : mris_calc compute sym. pct. change (spc) problem? It seems to running properly until it hits; mris_calc -o /Volumes/larry/cluster_results/1007base3/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-1007base3_lh_thickness_PENQ8v/beta1.mgh div ./tmp-1007base3_lh_thickness_PENQ8v/beta0.mgh The ./tmp files do exist whern mris_calc is called. I have seen on the Wiki that a fixed version of mris_calc is available for Centos. If you think I could be running into the same problem, is a fix available for Leopard? Thanks, Kevin Department of Neurology University of Wisconsin-Madison

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Is this normal when importing the annotations in tksurfer?
by Chen, Xu 19 Sep '11

19 Sep '11

Hi, Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04 LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer installation. Everything seems OK when running "tkmedit". However, a msg shown below pops up when I was trying to view cortical parcellation labels in tksurfer as instructed in the webpage of "testingfreesurfer". "...... Found embedded color table in annotation. 8600 vertices did not have an annotation!" What does this message implicate? Could it be attributed to the data problem (e.g. the inconsistency of vertices between the annotation & surface ) or my computer system? Is it normal to get it? Thanks a lot Jerry ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Re: [Freesurfer] ICV differences from version 5.0 to 5.1
by Ed Gronenschild 19 Sep '11

19 Sep '11

Jon, The reason is that already in one step earlier in the pipeline, the nu-correct stage, a difference arises. See thread on "Differences in nu.mgz between v5.0.0 and v5.1.0" Cheers, Ed > Hi, > > We have noticed differences in Talairach registration (and > therefore ICV estimates) in some of our subjects from version 5.0 > to version 5.1. Please see the attached document. There are 4 > subjects, each row represents the same subject, same input images, > same recon-all options (-all) between versions. The bottom of the > second page has a table with the ICV values for these subjects > across versions. > > Have there been any changes to the Talairach registration step from > 5.0 to 5.1 that would account for these differences? > > Thanks, > Jon

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