Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

cortical thickness problem
by burak ozkalayci 11 Apr '07

11 Apr '07

Dear surfers, I ran the recon-all -s bert -autorecon1 recon-all -s bert -autorecon2 recon-all -s bert -autorecon3 commands and all of them finished without any error. The log files of the commands and the file list of the resultant bert folder are attached to the mail. I can see the surface of the pial and the white with the tksurfer and try to load the ?h.thickness files as curvature files to the surfaces. But I only get fully red colored surface. What may be wrong? Also how can I read the ?h.thickness files manually to check is there any meaningful information there. The curvature maps are working but the thickness is not working. The snapshots of the the thickness and curvature are also attached. For the next step I want to ask one more question. In a previous mail in the list it is said that "we compute the closest vertex on the pial from each vertex on the white, and visa-versa, then set the thickness to the average of the two." for the thickness calculation. I understand from this statement that the thickness is just measured for the surface vertices but not for the voxels in the original volume. For voxel based morphometry do you have any advice to get thickness values for the voxels of the grey matter? Thanks in advance for any advice and reply. Burak

4 3

mri_surfcluster error
by Kirk, Gregory 11 Apr '07

11 Apr '07

running freesurfer-v3.0 SUBJECTS_DIR=/home/gkirk/freesurfer-v3.0/freesurfer/subjects/sickle_cell glm is at /home/gkirk/freesurfer-v3.0/freesurfer/subjects/sickle_cell and contains age.mat lh.sickle.glmdir mris_preproc.surface.lh.log rh.sickle.thickness.10.mgh FSGDstudy.txt lh.sickle.thickness.10.mgh mris_preproc.surface.rh.log rh.sickle.thickness.mgh FSGDstudy.txt~ lh.sickle.thickness.mgh rh.sickle.glmdir surfer.log lh.sickle.glmdir contains age ar1.mgh beta.mgh eres.mgh fsgd.X.mat mri_glmfit.log rstd.mgh rvar.mgh Xg.dat y.fsgd age/ contains C.dat F.mgh gamma.mgh maxvox.dat sig.mgh SUBJECTS_DIR has average directory with the group av surf & vol stuff I run mri_surfcluster --src lh.sickle.glmdir/age/sig.mgh --sum lh.sickle.glmdir/age/sig.cluster.sum --ocp lh.sickle.glmdir/age/ sig.cluster.mgh ( on same line of course ) and get ERROR: hemi must be supplied I add --hemi lh and get ERROR: srcsubjid must be supplied etc. can't seem to make it happy. thanks Greg.

2 1

System requirements.
by Goradia, Dhruman D 11 Apr '07

11 Apr '07

Hello All, I have a P4 1.5 GHZ, 1GB ram, 65GB hard disk running redhat fedora core release 5. I am planning to install the latest version of freesurfer on it. It will be a dedicated system for a small study with the only task of processing the data on freesurfer. Will this work? I understand that it will be slow, but are there any chances of installation not working just because of hardware qualifications? Thank you, Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213

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func2tal
by Alessandro Gagliardi 11 Apr '07

11 Apr '07

I'm trying to regester my BOLD images to a common space. I tried func2tal but I got ERROR: only selxavg, selavg, and sfa functypes are currently supported. When I try to run mri_vol2vol --fstal, it expects talmni305 in my subjects directory which I don't have. Did I miss a step in the installation? Should I have talmni305 and if so, where can I get it? Otherwise, is there a new version of func2tal that accepts bshort (or other) volumes as input? Or perhaps there is another way to get my 4D data into talairach space altogether? Thanks, -- Alessandro Gagliardi Integrative Neuroscience Program Rutgers University Mind Brain Analysis alessandro(a)gagliardi.name

2 1

aseg label
by nayoung＠cis.jhu.edu 11 Apr '07

11 Apr '07

Hello, I am trying to identify structures around a hippocampus using the labsl in aparc+aseg.img and FreeSurferColorLUT.txt. I see some structures labeled with 238, 232, 248 and I can't find these numbers on FreeSurferColorLUT.txt. Is there different table for aparc+aseg.mgz than one for aseg.mgz? Thank you. Nayoung

2 1

ANOVA on cortical thickness
by Mike Chee 10 Apr '07

10 Apr '07

Dear Bruce and Co., I was wondering if there is a way to perform ANOVA on the cortical thickness data; for example evaluating the interaction between age, gender and three (categorical variables) levels of blood pressure? Its not obvious how this might be done using the current interface. Mike Chee

5 8

cortical mask for group analysis
by Morgan Hough 06 Apr '07

06 Apr '07

I would like to make a mask for group analysis that excludes the unknown parcellation area. Since I would like to apply the same mask to all subjects (I have already brought them into alignment with mri_preproc), I was wondering how I can convert the average template label/?h.aparc.annot to a .mgz files that I could then convert into a mask. Is there an alternative way to produce such a mask? As a follow-up question, I was wondering if parcellation areas such as the corpus callosum should also be excluded from analysis? Are the thickness estimates made in the corpus callosum parcellation area interpretable? Thanks in advance for your time. Cheers, -Morgan

4 12

credits for talk
by Kirk, Gregory 06 Apr '07

06 Apr '07

Hi Folks, I remember somewhere there was a page describing how we should put the credits for a publication. How do you want the credit to read for a clinical conference talk reporting freesurfer cortical thickness group study results G.

2 1

patches from labels
by Don.Rojas＠UCHSC.edu 06 Apr '07

06 Apr '07

To all, I'm interested in creating some flattened patches from a region of auditory cortex. I have done the full recon-all processing on the datasets with version 3.0.4. Is there some way to create patch files without manually tracing the region you want to flatten in tksurfer? Is there a way to create patch files by combining several contiguous anatomical labels from the annotation file into one patch for flattening using mris_flatten? Thanks, Don Rojas University of Colorado

1 0

Re: [Freesurfer] Recommended Linux flavour
by Istvan Akos Morocz 06 Apr '07

06 Apr '07

freesurfer works fine on Slackware too, v11.0 and v10.1, using Xeon chips. bye, pisti > Date: Thu, 05 Apr 2007 13:08:46 -0400 > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Recommended Linux flavour > To: wade(a)ski.org > Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1175792926.23596.9.camel(a)minerva.nmr.mgh.harvard.edu> > Content-Type: text/plain > > Alex, > > We use Centos 4 (both 32 and 64 bit) at the NMR Center, so freesurfer > works best with it (in that most problems are easy to fix since we can > recreate them easily). Others on the list has been successful with > Debian, SuSE, Ubuntu, Fedora Core and others. But there have been some > display issues with tksurfer with some of the very newest Linux > releases, like Fedora Core 6. > > Nick > > On Thu, 2007-04-05 at 09:39 -0700, Alex Wade wrote: >> We are about to install a few Linux workstations, primarily to run >> Freesurfer and MNISuite. Can I check on what the best Linux flavour >> is? Do you still recommend CentOS 4? >> thanks >> >> Alex >> >> >> >> -- >> A.R. Wade Ph.D. >> Associate Scientist >> The Smith-Kettlewell Eye Research Institute >> 2318 Fillmore Street >> San Francisco, CA 94115 >> >> tel. 415 345 2083 >> fax. 309 416 6533 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ----- pisti(a)bwh.harvard.edu

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