Freesurfer December 2008

freesurfer@nmr.mgh.harvard.edu

65 participants
107 discussions

QDEC and FDR note of caution
by Michael Harms 09 Dec '08

09 Dec '08

Hello, When changing the FDR rate in QDEC it appears to be necessary to either hit 'enter' or alternatively move the cursor focus to another field prior to clicking the 'Set Using FDR' button. Otherwise the Rate used for the calculation of the thresholds is the PREVIOUSLY entered FDR rate. This can easily lead to a situation where the map for a given FDR rate may not reflect the displayed Rate (e.g., if a user does not hit Enter after changing the Rate). It would thus be desirable to remove the need to hit Enter after changing the FDR rate. Is that possible? This was observed using QDEC from v4.1.0, although I believe that I've experienced behavior consistent with this in previous versions as well. cheers, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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extracting cortical volume measures from multiple subjects
by d.g.lawyer＠medisin.uio.no 09 Dec '08

09 Dec '08

Dear FreeSurfer, I'd like to generate a spreadsheet with the cortical parcellations measures (grey matter volume, surface area) and including all subjects in my subjects directory. I seem to recall that there was a script which did this, but cannot find it in the mailing list archives. Do you recall the name of the script/program? Or is it easier to call mris_anatomical_stats on each subject and concatenate the results? +glenn ------------------------------------ Here miracles become marvels, and marvels recurring wonders. -- William Beebe Dr. Glenn Lawyer +352 661 967 244 Instituttgruppe for psykiatri Seksjon Vinderen PB 85 Vinderen 0319 Oslo http://folk.uio.no/davidgl

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starting freesurfer with skull stripped, bias corrected images
by Mira Michelle Raman 08 Dec '08

08 Dec '08

Hi Freesurfers, I am a little stuck. I have some 3T data that has had the skull stripping manually corrected. In addition we have some unusual bias artifacts that FAST seems to handle better than n3, so I have done my own bias correction. Since I had to run FAST anyway, I created brainmask.mgz from the partial volumes I have. So I did an mri_convert --conform on both to get nu.mgz(which is skull stripped) and brainmask.mgz. So now I need to deal with the transformation issues. I was thinking I could just run recon-all -gcareg to get talairach.lta and then copy that to talairach_with_skull.lta and clip out the transform matrix and substitute it into a copy of talairach.xfm. But none of this seems to work. So if anyone has any suggestions I would greatly appreciate them, also I may be missing something, so if there is another step or file I am missing before I can run autorecon2 and autorecon3 please enlighten me. Thanks in advance, -Mira Mira Michelle Raman Center for Interdisciplinary Brain Sciences Research Stanford University

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questions about installing on Linux
by Bai Xue 08 Dec '08

08 Dec '08

Hi there, After I install the latest version of freesurfer on my Linux machine, I got the following errors: tar: freesurfer/diffusion/mgh-dti-seqpack: Cannot utime: Operation not permitted tar: freesurfer/diffusion: Cannot utime: Operation not permitted tar: freesurfer: Cannot utime: Operation not permitted tar: Error exit delayed from previous errors What's the problem here? How can I solve that? I have tried "testing your FreeSurfer installation" and it seems OK. Thanks. Bai Xue

2 4

mri_volcluster
by Gregory Dierksen 08 Dec '08

08 Dec '08

Hi, I'm trying to use the mri_volcluster command to make label files from a single volume of binary voxel clusters. Once I have split the volume into individual label files I want to convter the label files back into individual cluster volumes (I am trying to use mri_label2vol to do this). The commands I've been using are: mri_volcluster --in microbleeds-reslice.mgz --allowdiag --thmin .5 --labelbase ../scripts/clusters/testing/cluster mri_label2vol --label ../scripts/clusters/testing/cluster-0001.label --temp orig-flip-reslice.mgz --o cluster-0001.mgz (NOTE: the -reslice is because these volumes have been resliced from 0.4492, 0.4492, 6.0000 sized voxels to conform to 1 mm^3 sized voxels; the dimensions of the image were altered as well, from 384 x 512 x 23 voxels to 173 x 230 x 138 voxels) When I view cluster-0001.mgz with tkmedit the result is a 3D checkerboard like pattern with no two voxels having common edges (despite the original cluster in microbleeds-reslice.mgz being a solid cluster of 90 mm^3). What I wanted to see was that each cluster could be reconstructed in a single volume (i.e. cluster-0001.mgz, cluster-0002.mgz, etc with each volume containing only one cluster). Also, when I use mri_cor2label and then mri_label2vol to switch between label files and volumes files, the clusters (despite not being split up like I want) are solid and do not display this checkerboard effect...leading me to think that its an issue with mri_volcluster. Any help you can offer would be great. Thanks. Greg --

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qdec message
by Julia Altenburg 08 Dec '08

08 Dec '08

Hey all, I'm getting the following message while using qdec Error in Analyze: command failed: mri_glmfit --y /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh --fsgd /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec.fsgd dods --glmdir /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled --surf fsaverage lh --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contrasts/lh-Avg-thickness-alter-Cor.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contrasts/lh-Diff-BPD-KG-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contrasts/lh-Diff-BPD-KG-Cor-thickness-alter.mat I've a qdec.table and a fsgd.file included in my subject folder. Do I have to type a command to get the fsgd. file connected? I'm not really sure what causes the error. While using an older freesurfer version on a different mac this (but some other) error doesn't show up. FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0 Kernel info: Darwin 8.11.1 i386 Thank you in advance Cheers Julia

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freesurfer 4.02 for red-hat
by Lúcia Garrido 08 Dec '08

08 Dec '08

Hello, I've been running Freesurfer v4.0.2 in Debian and now wanted to use a computer that has Red Hat 9 to also run some subjects. Could you let me know if it's possible to download version 4.0.2 for Red Hat? Many thanks, Lucia

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Question about qdec smoothing
by Richard Frye 08 Dec '08

08 Dec '08

>From my understanding qdec fits a glm to each vertex. It also smooths the data. >From the documentation I do not have a clear understanding of whether qdec uses smoothed data for input (It appears that is does) or smooths the coefficients or t-tests after analysis, or both. Additionally, the resulting contrast results appear to have patches of significance. What is the processes that makes patches out of individual vertex results? Do a certain number of contiguous vertexes need to be significant for their values to be connected into a patch? -- Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assistant Professor of Pediatrics and Neurology University of Texas Medical School at Houston 7000 Fannin -- UCT 2478 Houston, TX 77030 Office: 713-500-3245 e-mail: richard.frye(a)gmail.com

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matlab dependencies
by Siddharth Srivastava 07 Dec '08

07 Dec '08

Hi all, 1) which steps of the freesurfer processing pipeline depend on/ use matlab for execution? I am trying to find out if we have to have matlab installed on all the computing nodes on our cluster here, or, if there is just one step, we can process it locally, and submit the downstream steps back to the cluster. 2) if anyone would like to share their experiences with running freesurfer on a cluster/grid computing environment, I would be happy to know, and maybe optimize my computing environment based on your recommendations 3) If there a canonical list of dependencies for the output generated by the -localGI flag. I was wondering if, if LGI is the only thing i need at the end, do i have to let freesurfer run through the entire processing steps? I mean, i do need other outputs as well, but can i chose a subset of processing steps based on what i would ultimately be using? :-) best regards, sid.

2 1

overlay
by luketseng＠gmail.com 07 Dec '08

07 Dec '08

hi, how do i overlay a .mgz image over an image in qdec so i can compare the two?

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Freesurfer December 2008