Freesurfer January 2011

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

Segmentation problems
by Tetiana Dadakova 02 Feb '11

02 Feb '11

Dear FreeSurfer users, I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction? Thank you, Tetiana.

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Phantom data
by Alan Francis 31 Jan '11

31 Jan '11

Hi Bruce, Nick, Doug and others: I have Phantom data from around 900 scans collected across 5 sites in the US. Does FS have a way of processing Phantom data. Thanks much, Alan Alan Francis Beth Israel Deaconess Medical Center

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white matter volume and qdec
by tulu＠ms36.hinet.net 31 Jan '11

31 Jan '11

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postmortem analysis
by Sarah Whittle 30 Jan '11

30 Jan '11

Hi, I have some post-mortem MR images that I'd like to run through FreeSurfer to obtain thickness estimates. I've had a look at the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo. The images were obtained with a T1-weighted fast gradient echo sequence (1.5-mm slice thickness, FOV = 25 cm; NEX = 1; matrix = 256 x 192; TR = 35 ms; FA = 60). Although the images are T1-weighted, they appear to look like T2-weighted images (ie, dark WM, white GM). I haven't worked with post-mortem MRI before, and my knowledge of MR physics isn't great, so I'm not sure why that is. So, my questions are, 1) can I use these images in the processing stream described on the wiki? 2) Is it possible to do the automated atlas-based cortical and subcortical parcellations? Thanks, Sarah

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[Fwd: dice_labels help]
by jentis＠nmr.mgh.harvard.edu 29 Jan '11

29 Jan '11

---------------------------- Original Message ---------------------------- Subject: dice_labels help From: jentis(a)nmr.mgh.harvard.edu Date: Fri, January 28, 2011 1:14 pm To: nicks(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- Hi Nick, Last year you helped me with the dice_labels script. I have not used it since then, and I am having trouble running it remotely. I have recently installed matlab on my laptop, and copied the dice_labels.m script you sent me last year into my matlab folder. As of now, that is the only thing in that folder. When I try to run it, I get the following error: >> dice_labels ('/Users/j_entis/Desktop/Amygdala_paper/jon_round_1/120/jon_left_amyg.label', '/Users/j_entis/Desktop/Amygdala_paper/priya/120/amyg_left_pd.label') ??? Undefined function or method 'read_label' for input arguments of type 'char'. Error in ==> dice_labels at 29 label1 = read_label('',lname1); Any ideas? Thanks, Jon

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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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Freesurfer January 2011