Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

MNI coordinates of all the vertices of fsaverage
by Yolanda Vives 20 Jun '12

20 Jun '12

Dear Freesurfer experts, How could I know the MNI coordinates of the 163.842 vertices of the left hemisphere of fsaverage? Best regards, Yolanda

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mris_label2annot mislabeling
by Arno Klein 20 Jun '12

20 Jun '12

hello! i have saved a couple of .label files and am trying to convert them to a .annot file with: mris_label2annot --h lh --s MMRR-21-1 --l lh.superiorfrontal.label --l lh.superiorparietal.label --ctab FreeSurferColorLUT.txt --a output the stdout is: ColorTable atlas_colortable.txt AnnotName output nlables 2 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/MMRR-21-1/surf/lh.orig 1 11829830 Left-Cerebral-Exterior 2 16119285 Left-Cerebral-White-Matter Mapping unhit to unknown ... clearly the anatomical names assigned are incorrect, and when i view the output with tksurfer, the labeled patches are in the right places but are assigned these same incorrect anatomical names. i have tried renaming the .label files to no avail. what am i doing wrong? cheers, @rno

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Editing Putamen Segmentation
by Kristin Javaras 20 Jun '12

20 Jun '12

Dear all, For a number of my participants, Freesurfer's automated segmentation of the putamen appears to include brain matter that isn't putamen - this problem persists across 5-6 slices, on average. I was wondering what people would recommend - should I edit the aseg? Thank you in advance for any advice, Kristin Javaras _______________________________ Kristin N. Javaras, PhD Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Telephone : +1 (608) 890-1407

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Re: [Freesurfer] -inter error
by Anastasia Yendiki 20 Jun '12

20 Jun '12

Oops, that's a typo, meant "is unavailable". In any case something like this should show up early in the logs. On Wed, 20 Jun 2012, Bruce Fischl wrote: > "not unavailable"???? > > On Wed, 20 Jun 2012, Anastasia Yendiki wrote: > >> >> Hi Maria - Do you at any point get the following warning? >> "WARN: CVS template is not unavailable in the current version" >> >> Thanks, >> a.y >> >> On Wed, 20 Jun 2012, Maria Gemzicka wrote: >> >> > Hi, >> > I run -corr and -intra with no errors. -inter finishes without errors if >> > does not use doregcvs. >> > When I want to use cvs for registration, I get error: >> > >> > iterating >> > >> > done with candidates >> > >> > Active BCs = 91494 >> > >> > Total BCs = 548640 >> > >> > no-eqs = 245610 >> > >> > surf2vol(26656) malloc: *** mmap(size=295714816) failed (error code=12) >> > >> > *** error: can't allocate region >> > >> > *** set a breakpoint in malloc_error_break to debug >> > >> > [0]PETSC ERROR: --------------------- Error Message >> > ------------------------------------ >> > >> > [0]PETSC ERROR: Out of memory. This could be due to allocating >> > >> > [0]PETSC ERROR: too large an object or bleeding by not properly >> > >> > [0]PETSC ERROR: destroying unneeded objects. >> > >> > [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 >> > >> > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. >> > >> > [0]PETSC ERROR: Memory requested 295714444! >> > >> > >> > >> > trac-all.error in scripts: >> > >> > >> > ...... >> > >> > PROCESSOR x86_64 >> > >> > OS Darwin >> > >> > Darwin shemp.mri.yorku.ca 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr >> > 9 >> > 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 >> > >> > $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ >> > >> > /Users/Maria/Applications/freesurfer/bin/trac-preproc >> > >> > PWD /Users/Maria >> > >> > CMD mri_cvs_register --mov mgFS6 --template cvs_avg35 --outdir >> > /Users/maria/Desktop/mgFS/mgFS6/dmri/xfms/cvs >> > >> > >> > Thank you. >> > >> > >> >

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-inter error
by Maria Gemzicka 20 Jun '12

20 Jun '12

Hi, I run -corr and -intra with no errors. -inter finishes without errors if does not use doregcvs. When I want to use cvs for registration, I get error: iterating done with candidates Active BCs = 91494 Total BCs = 548640 no-eqs = 245610 surf2vol(26656) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 295714444! trac-all.error in scripts: ...... PROCESSOR x86_64 OS Darwin Darwin shemp.mri.yorku.ca 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ /Users/Maria/Applications/freesurfer/bin/trac-preproc PWD /Users/Maria CMD mri_cvs_register --mov mgFS6 --template cvs_avg35 --outdir /Users/maria/Desktop/mgFS/mgFS6/dmri/xfms/cvs Thank you.

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qdec
by Jenny Liu 20 Jun '12

20 Jun '12

Hello I am using the Qdec Analysis.The long and base directories are created already, and I am at the first stage of post-processing. For the long_mri_slopes command, there seems to be some difficulty for Qdec to find the appropriate folder. As background, in my qdec table, I have the fsid and the fsid-base (along with other variables) (see attached too) ie. fsid fsid-base group age painUnp tp WB101_1 WB101_template MNP 65.72 11.7 0 The first command that the instructions tell me to do is: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time tp --qcache fsaverage However, the error comes up as: ERROR: /study/NCCAM/Data/MRI/processed/structural/freesurfer/WB101_1.long.WB101_template/label/lh.cortex.label does not exist! To check this error, I search the directory of freesurfer, and there are several folders for WB101. One is labeled "WB101_1.long.WB101_template"; another is labeled "WB101_template". The "WB101_1.long.WB101_template" directory does not contain the file "/label/lh.cortex.label" or the file "/surf/lh.thickness", but the "WB101_template" directory does. How do I change the commands of the long_mri_slopes so that it reads the "WB101_template" directory to find these two files, instead of the "WB101_1.long.WB101_template" directory? Or is the error due to another issue? Thanks, Jen

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ROI labels
by Cat Chong 19 Jun '12

19 Jun '12

Dear Freesurfers, I would like to show several ROI labels that we created on top of an an average brain which demonstrates the group results of cortical thinning with advancing age. In qdec, when I go into File>Load Label, I can only view one label at a time. Is there a way to show several labels together on an average brain, just for visualization purposes? cheers, Cat

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ICV calculation error?
by Gabor Perlaki 19 Jun '12

19 Jun '12

Hi all, We use freesurfer 5.1.0 and we ran the recon-all on 100 subjects. We checked the talairach transform, skull strip the pial surfaces and the segmentations as suggested on Freesurfer Wiki. Everything seems to be fine, however, the ICV values from the stats/aseg.stats seem to be incorrect. The average value of ICV's is 1280 cc for men and 1108 cc for women, which seems pretty low. In 21 subjects from the 100 the ICV was even smaller than the supratentorial volume. The talairach transforms seems to be fine by visual inspection. 1. I think the wrong estimation of ICV value (because of the talairach transformation is not the best, although it seems right by visual inspection) won't affect the cortical/subcortical segmentations. Is it right? 2. What volumes should I sum to get an ICV, which is not estimated from the talairach transformation? 3. Is it a volume (other than ICV) reported by freesurfer, which can be used for correcting for overall head size? I'd appreciate an early reply. Thanks, Gabor

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position open
by Gennan Chen 18 Jun '12

18 Jun '12

Hi! We have an algorithm developer position open. Below is the job description. Although it stats in a very general term, the person will spend most of time working on freesurfer related algorithms and services. Experience in PhD or Post doc did count as long as it is related to algorithm development. Please send resume to me directly. Thanks Gennan Chen (gennan.chen(a)synarc.com) Engineering Manager, Engineering Department, CCBR-Synarc (www.synarc.com) Algorithm Development Engineer Analyzes, prototype, designs, programs, debugs, and modifies medical imaging processing algorithms used in clinical trials settings. Responsibilities: * Prototype, Design, develop, unit test and release medical imaging processing algorithms to support Synarc's business. * Work with end users to understand requirements. * Write and contribute to design specifications, installation guides and other technical documentation in accordance with Synarc best practices. * Work with other technical staff to support system installations, upgrades, and configurations of software. * Assist in training of users and creation of user manuals. * Ensure that systems are released in accordance with regulatory and Synarc standards. * Work with end users, other developers, software QA, product managers and software project managers to deliver applications, bug fixes and enhancements. * Use professional experience to provide creative, effective solutions to complex problems. Qualifications: Education: PhD in biomedical engineering, physics or computer science Experience: 4+ years of design and implement complex medical imaging algorithms in related fields such as registration and segmentation. Expert in Matlab and extending Matlab in C/C++ Experience in Freesurfer and related processing stream. Experience with DICOM standard Experience with cloud, cluster and other high performance computation environment. Experience with Java enterprise application development stack Experience with SQL and relational database Skills: Good problem solving, technical troubleshooting, organizational, interpersonal and team skills. Good written and verbal communication skills. ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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map ROI-based measures back to surface
by Leon 18 Jun '12

18 Jun '12

Hi, FreeSurfer experts I used mri_make_surface_parcellation and parcellated the brain into 200 ROIs. Then some measures were derived based on the ROIs and now I have 200*1 matrix with each ROI having a value. What I want to do is to map the ROI-based measures back to the surface files and show the intensity differences between these 200 ROIs on surfaces. Could someone tell me what is the best way to realize that? Forgive me if this question has bee asked before, but I really do not know how to input best keywords for the question to search in the archive. Many thanks in advance! Leon

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Freesurfer June 2012