Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Volume output from Stable 5 isxconcat-sess
by Adam Nitenson 28 Jan '11

28 Jan '11

Hi Freesurfers, I am running isxconcat-sess for the first time in Stable 5 using the following command: isxconcat-sess -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH -d /cluster/roffman/users/Stable5_PerRun -analysis SIRP_Stable5 -c Cond1v3 -c Cond1vFix -c Cond3vFix -c Cond1v5 -c Cond1v7 -c Cond5vFix -c Cond7vFix -o /cluster/roffman/users/Stable5_PerRun/16_PreScan_Genotyped_Stable5 However, the output does not seems to contain the tal.ces.nii files that I expect from Stable 4. Instead are mni305.ces.nii, which do not seem to be the same thing as the tal data. Is there a way to get a tal output? I noticed a -talres argument, but I wasn't sure if that was necessary. Running the above command with the -hemis argurment seems to produce lh.ces.nii, etc as in Stable 4. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Repost: fixing cortical parcellations
by Kerstin Pannek 27 Jan '11

27 Jan '11

Dear freesurfer experts I am having some trouble with inaccurate cortical parcellation after autorecon3. Cortical regions seem to be "spilling over" into neighbouring regions (for example supramarginal in inferior parietal as seen in the attachment). How can I manually adjust these errors? Thanks! Cheers Kerstin

2 1

Network License for Freesurfer?
by Shahaan Ayyub 27 Jan '11

27 Jan '11

Hi and thanks in advance, I was wondering if it's possible to obtain a network license for freesurfer which multiple users (students) can use. Thanks and regards, Shahaan -- Shahaan Ayyub eResearch Software Specialist (High Performance Computing) Research Support Services Information Technology Services Division Telephone +61 3 9902 0714 Facsimile +61 3 9902 0193 Mobile +61 448 502 491 www.monash.edu.au/eresearch

2 1

ROI mask
by Palzes, Vanessa 27 Jan '11

27 Jan '11

Hi all, I am currently exploring anatomical ROI analysis in FreeSurfer. I would like to create ROIs based on a Brodmann Area atlas, since unfortunately FreeSurfer currently only segments a few of these regions automatically. I know I could define the ROI manually in FreeSurfer, but I would prefer to use an atlas instead. From a tutorial I found on the Wiki, it seems as though I could import an ROI mask in the form of a volume file. Since FreeSurfer registers volumes with the Talairach atlas, I would presumably need an ROI mask in this same coordinate space. I have tried using the Wake Forest University PickAtlas to create an ROI mask, but it uses MNI and the ROI label is not where I expect it to be when I view it in tkmedit. Has anyone attempted doing this, and if so what software have you used to create the ROI mask? Thanks, Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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DTI bvecs/bvals question
by swoodman＠nmr.mgh.harvard.edu 27 Jan '11

27 Jan '11

Hello all, We have a question regarding DTI data we aquired a few years ago (2005-2006). For those of you who use DTI sequences, 1.) Do you use normalized bvals/bvecs files or do you use the files that come direct from the scanner for each individual subject? 2.) When scanning on either bay 3 or 4, are the same bval/bvecs files used? ie is there a difference between magnets when using the same sequence? Thanks for your help! Sandra

2 1

Brain Volume
by Justin Eisenberg 27 Jan '11

27 Jan '11

Hi all, What is the best way to calculate total brain volume? It seems that there are multiple ways to do it--mris_volume and mris_wm_volume, add up the structures in the aseg.stats and ?h.aparc.stats files, or using the BrainSegVol or BrainSegVolNotVent from aseg.stats. What do you recommend? Thanks! Justin -- Justin Eisenberg Washington University in St. Louis Arts & Sciences | 2013 JEisenberg(a)wustl.edu JEisenberg323(a)gmail.com 262.914.4648

4 4

mri_glmfit error
by Rafa x 27 Jan '11

27 Jan '11

Dear Freesurfers, In Freesurfer v5.0 when I try to run the command: mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast.mat --fsgd fsgd.txt dods --mask lh.fsgd_subj/mask.mgh --y CNTRL_MCI_RAFA_stats/lh.fsgd_subj.mgh --sim perm 625 2.301 csd1 --sim-sign pos --seed 6555731749 I always get the following error: ERROR: you must supply --fwhm with --sim, even if it is 0 Is there a bug in the mri_glmfit function? Thank you all in advance, Rafael.

2 3

mkblockpar
by Kathryn Devaney 27 Jan '11

27 Jan '11

Hi all, I may be the only one still using mkblockpar, but I'm wondering if there's an update for the new version of freesurfer? Currently it still outputs 2-column par files. Thanks! Katie

2 1

New v5.0.0 release
by Nick Schmansky 26 Jan '11

26 Jan '11

Announcement! There is a new release of FreeSurfer, v5.0.0! Features and fixes are described in the ReleaseNotes page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes It is available for download at: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Please pose questions about the release to the freesurfer mailing list. The FreeSurfer Team

6 8

CUDA installation and configuration...
by Gonzalo Rojas Costa 26 Jan '11

26 Jan '11

Hi: I am currently configuring Freesurfer 5 in a new workstation that we received... That workstation has Ubuntu 10.10, and a NVIDIA Quadro FX 1800 graphics card... Could you please send me the steps necessary to install and configure CUDA support ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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