Freesurfer

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30132 discussions

tumor volume segmentation...
by Gonzalo Rojas Costa 03 Aug '10

03 Aug '10

Hi: I segmented a T1 volume of a patient with a tumor... in the aparc+aseg and aparc.2009s segmentation,that tumor appears as "none"... How can I got the volume of the tumor ?... Sincerely, Gonzalo Rojas Costa

2 1

Vertex-wise thickness and mean thickness of clusters
by Joana Braga Pereira 03 Aug '10

03 Aug '10

Dear all, I would like to ask you whether there should be an exact correspondence between vertex-wise thickness and mean thickness of clusters. I'll explain you my problem. I did an analysis with 2 groups and 2 covariates. Then i run the mri_glmfit script and found clusters of greater thickness in controls compared to patients. When i extracted the mean thickness of these clusters and did a two sample t test i observed that the controls had greater thickness than patients, however not statistically significant, even after including in this analysis the 2 covariates. Is this normal? How does freesurfer uses the covariates when performing an analysis? Many thanks

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ROI-questions
by liyari5018 03 Aug '10

03 Aug '10

Hi All, I use QDEC to compare two groups differences, find some regions with significant differences. Considering this regions as ROI, i want to extract the mean thickness of ROIs for every subject, then compute the correlation between mean thickness and some scales . My questions is : should I extract mean thickness from the individual space or the common space? Any advice would be most appreciated LJ

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intracranial volume in qdec
by York, Philip 02 Aug '10

02 Aug '10

Hi experts, I was wondering it is possible to account for total intracranial volume in qdec statistical calculations, and if so, where do I find that under the 'general stats data tables' Thanks, Philip York UCDenver Radiology

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Re: [Freesurfer] .license file on Mac (Krish Subramaniam)
by sere f 02 Aug '10

02 Aug '10

Hi Krish, > thank you for your advice....now it works!!! Serena. > > > > > > > > ------------------------------ > > Message: 7 > Date: Mon, 2 Aug 2010 03:16:09 -0400 > From: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] .license file on Mac > To: sere f <serenaf33(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <2B627F31-D101-430F-B236-0EE5AACD59BE(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Serena > > It means you don't have write permissions in the directory. You should > invoke pico like > > sudo pico /Applications/freesurfer/.license > > ..it'll ask for your password and save successfully, provided you have > permissions. > > -Krish > > On Aug 1, 2010, at 8:32 AM, sere f wrote: > > > > > > > Hi All, > > > > I am new user of Freesurfer and i am getting trouble to install it. > > I want to install it on MacBook Pro and I have problem with the > > license file. > > I have tried to create it with: > > > > pico /Applications/freesurfer/.license > > > > and when I save it, I get this message: > > Error writing /Applications/freesurfer/.license: Permission denied > > and it is not saved. > > > > How can i do? any idea? > > Thanks. > > > > Serena. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 78, Issue 1 > ***************************************** > > > 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. > >

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Undefined Variable
by Carl Dambkowski 02 Aug '10

02 Aug '10

Hi! I may be missing something basic but when I enter: recon-all -s bert -autorecon1 I get: FREESURFER_HOME: Undefined variable. But I have already ran: setenv FREESURFER_HOME /Applications/freesurfer so that FREESURFER_HOME should be defined, right? I'm not sure if I'm missing something basic or something is completely wrong. I can access the already created files but it doesn't let me run a recon-all for some reason. Thanks for your help! Carl -- Carl Dambkowski, MS Research Assistant Cerebral Localization Laboratory Columbia University Medical Center (212) 342-3668

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Re: [Freesurfer] {Spam?} Re: preproc-sess error
by Douglas N Greve 02 Aug '10

02 Aug '10

you can setenv FSLDIR /usr/pubsw/packages/fsl/3.3.7 then re-source the stable3 environment. doug jkuster(a)PARTNERS.ORG wrote: > Hi Doug, > > Thanks for your messages. We have to keep using stable3 for the rest of this study. Does this mean we can just use a command to use the older version of fsl to fix the ispl error? > > Thanks, > Jake > ------Original Message------ > From: Douglas N Greve > To: swoodman(a)nmr.mgh.harvard.edu > Cc: freesurfer(a)nmr.mgh.harvard.edu > Cc: jkuster(a)partners.org > Subject: Re: [Freesurfer] preproc-sess error > Sent: Aug 2, 2010 1:54 PM > > If you're going to continue to use stable3 then you will need to have an > old version of FSL (the ip program is an FSL program from several > versions ago). Can you start using the new version of FSFAST? > > doug > > swoodman(a)nmr.mgh.harvard.edu wrote: > >> Additional info: >> >> FREESURFER_HOME: /usr/local/freesurfer/stable3 >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-v3.0.5-20070714 >> >> RedHat release: CentOS release 5.5 (Final) >> >> Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 >> >> NMR Center info (/space/freesurfer exists): >> >> Does this give you the info you're looking for? >> >> Thanks, >> >> Sandra >> >> >> >> >> >> >>> which version are you using? >>> >>> swoodman(a)nmr.mgh.harvard.edu wrote: >>> >>> >>>> Hello everyone, >>>> >>>> I keep encountering the same error when running some preprocessing steps >>>> (spatial smooting part). >>>> >>>> I run the command line: >>>> >>>> preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 >>>> -smin >>>> fmc5 -smout fmcsm5 >>>> >>>> And I encounter this error: >>>> >>>> ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip >>>> ERROR: ipfsl failed >>>> ERROR: spatialsmooth-sess failed >>>> >>>> Any help/advice would be much appreciated! >>>> >>>> Thanks, >>>> >>>> Sandra >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >>> >>> >> >> > > -- 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

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preproc-sess error
by swoodman＠nmr.mgh.harvard.edu 02 Aug '10

02 Aug '10

Hello everyone, I keep encountering the same error when running some preprocessing steps (spatial smooting part). I run the command line: preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 And I encounter this error: ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed Any help/advice would be much appreciated! Thanks, Sandra

2 3

Question re: "Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction"
by Andrea L. Gold 02 Aug '10

02 Aug '10

Hi, My question is in reference to the recommended high res structural scans (T1) for optimal FS reconstruction. Within the "Documentation" section of the FS wiki, the page titled "Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction <http://martinos.org/~andre/>" lists two MPRAGE scans, which I understand has been recommended for 1.5T scanners. Is it still the recommendation to collect two high res structurals on 3T scanners (in our case, Siemens TIM Trio) or is one sufficient? Thanks, Andrea -- Andrea Gold Graduate Student Dept. of Psychology Yale University P.O. Box 208205 New Haven, CT 06520-8205 andrea.gold(a)yale.edu

2 1

Errors with the "Cut Plane" feature in tksurfer
by Salzwedel, Andy 02 Aug '10

02 Aug '10

I've been trying to implement the cut plane feature to get an occipital patch but every time my tksurfer crashes and I get this message: % tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort I can't figure out if I am doing something drastically wrong with selecting my cutting points or whether my system is having the problem. Any advice would be most appreciated, Andy

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