Freesurfer

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30086 discussions

anatomical ROI
by francesca strappini 28 Jan '11

28 Jan '11

Hi all, I would ask you about anatomical ROIs. I'm going to begin the analysis of some retinotopic data, my question is: when I draw the closed contours, does automatically my ROI contain the entire inner surface or just the outline? Thank you kindly in advance. Francesca

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jacobian calculation
by Larissa Stanberry 28 Jan '11

28 Jan '11

Dear experts, I'm interested in computing the determinant of the average jacobian matrix for a given brain region. If I run mris_anatomical_stats with a flag --t ?h.jacobian_white separately for positive/negative jacobian values, the "thickness" output will be an average of the pos/neg Jacobian dets for each structure, am I right? It's not exactly what I want, so is there a way to get a jacobian matrix for each vertex as an output, rather than its determinant? Many thanks Larissa

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FW: QDEC 1.2 displays different results depending on variable selection in the design tab
by Dominic Dwyer 28 Jan '11

28 Jan '11

Dear developers, I recently found that if you have two discrete variables in QDEC, then the order in which you select them in the design tab drastically effects results. It appears that the selection dictates the definition of the covariate. In particular, regardless of the comparison you choose to view in the display tab (i.e. "Does the average thickness, accounting for X, differ between 1 & 2" OR "Does ..., accounting for Y, differ between 1 & 2") the results depend on what you click in the design tab rather than these definitions. Is this correct? If so, then how do we verify that the contrast that we think we're testing is correct? Should we just not use QDEC 1.2 and set up the models manually? Many thanks for your help. best, Dominic PS. I suspect that this problem has been fixed in the new version, but it wouldn't work with our data which has been processed with FS4.5. On this note, is there a way that around this to use FS4.5 images with the new QDEC?

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tpef question
by Sebastian Moeller 28 Jan '11

28 Jan '11

Hi Doug, I have a number of runs with some bad k-space arcing artifacts that I still would like to analyse. Now spikedet-sess makes childs play to turn the detected spikes into a timepoint exclusion file. But when I try to use this file with fs-fast (from freesurfer v4.5 x86_64) I get errors from fast_selxavg3.m (see below). Do you have any idea how I can use tpefs for fs-fast analysis again (it worked in 3.0.5). Also will this work in V5 (a very compelling reason to upgrade :))? Thanks in advance Sebastian Here is the output when I tried to exclude 87 of 272 timepoints (when trying to exclude 11 timepoints I get the same result) outanadir = /home/helios/data/moeller/cooked/2011/110105Bert/bold/a1 Found 162817/497664 (32.7) voxels in mask Creating Design Matrix Excluding 87 points Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 1.665831e-43. > In fast_selxavg3 at 212 -- Sebastian Moeller telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 mobile: +1-626-325-8598 US CDMA: + 1 - 626 - 807 - 5242 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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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

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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

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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

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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

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