Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

Some notes on getting Tracula to work for newbies
by Kirstie Whitaker 25 Aug '14

25 Aug '14

Hi Anastasia and the freesurfer list, I've been working on getting the latest version of tracula to run and I thought I would post here the errors that I've worked around. It's all been based on looking through the mailing list archives but I thought it would be useful to add them here all in one place! The goal of this email is simply to save time for others in the future (including myself when I forget all these things!) [Note that if I've written something between < > then it will be specific to your files/directories etc] When running trac-all on an input nii file with corresponding bval and bvec files: 1) If you're getting an error that says: nifti1Read(): unsupported slice timing pattern 5 in <NAME OF YOUR DTI NIFTI FILE> Try running the command: fslmaths <NAME OF YOUR DTI NIFTI FILE> <NAME OF YOUR DTI NIFTI FILE> eg: fslmaths dti.nii.gz dti.nii.gz I'm really not clear on what exactly is wrong with my files (created using an in house dicom converter) but taking in the file and writing it straight back out again gets rid of this problem for me. 2) If you're getting an error that says ERROR: Could not open <SUBJECTS_DIR>/<SUBID>/dmri/bvals for reading Then you're probably using the centos4 update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if the centos6 update works then switch to that, otherwise all other steps in trac-all -prep work *except* for the quality control. So you can run trac-all -prep -noqa and all should be well. To install the update just download it (I used wget <TRACULA_UPDATE_LINK>) and the untar it (tar -zxvf <TRACULA_UPDATE_TAR.GZ_FILE>). Copy the files inside the folder you've created into the $FREESURFER_HOME/bin/ directory. 3) If you're getting an error that says (something along the lines of) mri_convert --frame 0 14 27 41 54 68 <SUBJECTS_DIR>/<SUBID>/dmri/dwi.nii.gz <SUBJECTS_DIR>/<SUBID>/dmri/lowb.nii.gz mri_convert: extra arguments ("41" and following) type mri_convert -u for usage Then you're probably using an old version of trac-all. Double check that you've replaced the appropriate files in your $FREESURFER_HOME/bin directory with those contained in the appropriate update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. (See my instructions at point 2). Some fun facts from my experience: You can have decimal points (not commas though) in your bvals files. You can run trac-all in either a bash or tcsh shell. (These were not the droids I was looking for) Thanks again for the really excellent software. And please correct anything that I've written here if it's wrong! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com

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Extracting Group Means for Cortical Thickness
by Bronwyn Overs 24 Aug '14

24 Aug '14

Dear Mailing List, I have just completed a QDEC (v5.1.0) analysis of the following design: Measure: thickness Smoothing (FWHM): 10 Hemisphere: lh 2 Discrete (Fixed Factors): group (2 levels, AtRisk & Control) and gene (2 levels, CC & TTorTC) 1 Nuisance Factos: age On completion of the analysis, I have selected the following results in the display tab: "Does the average thickness, acounting for group, differ between CC and TTorTC?". I have then completed an FDR correction by clicking the "Set Using FDR" (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit "Find Clusters and Goto Max" and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2. I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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Transforming functional image while retaining voxel size
by Jackie Lam 22 Aug '14

22 Aug '14

Hello all, I’m trying to register and transform a functional image to my high resolution anatomical image. As I understand, it can be done with mri_vol2vol, but the resulting functional image is resampled into 1x1x1 voxels (the resolution of my high res anatomical). Is there a way to transform the functional image so that it is in the same space as the anatomical image while retaining its original voxel size? Many thanks, Jack

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installing mris_decimate
by Nicholas Heugel 22 Aug '14

22 Aug '14

So I just redownloaded the recent version of Freesurfer for Mac, Lion operating system, making sure to grab the most recent version. I need to use the tool mris_decimate but it is not in any of the files I downloaded, nor was it in any of the files I had previously. Where can I get mris_decimate, and what are the steps for installing it? Nicholas

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problem with format of CT dicoms
by Borzello, Mia 22 Aug '14

22 Aug '14

Hi Freesurfers, I'm in the process of creating the ct.mgz file, but it is erroring and saying there is a "segmentation fault (core dumped)." What can I do to remedy this? Thanks, m

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head surface
by Meryem Ayse Yucel 22 Aug '14

22 Aug '14

Hi Doug, I used mkheadsurf function. Meryem

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Best Way To Edit?
by Lindsay Gubernick 22 Aug '14

22 Aug '14

Hello, I was just looking for some suggestions for the best way to manually edit an image such as the one attached. As you can see, there is both white and gray matter excluded from the pial surface on the medial aspect of the right hemisphere. Is this best corrected by adding voxels to the brainmask.mgz, adding a new control set, both, or something else entirely? Thank you very much for the help. Lindsay Gubernick [image: Inline image 1].

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Left and Right Vessels
by Mohammed Goryawala 22 Aug '14

22 Aug '14

Hello Freesurfer experts, In a study I found significant differences in the volume of the left and right vessels of the freesurfer atlas. I wanted to know what regions are included in that ROI and if there are any known functions of these regions. Thank you Mohammed Goryawala, PhD Miller School of Medicine, University of Miami

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mean cortical thickness on N ROIs
by elisa veronese 21 Aug '14

21 Aug '14

Dear FreeSurfers, suppose I should estimate the mean cortical thickness on a number N of ROIs (for instance, the left inferior temporal, the left middletemporal, and the left superior temporal). How would you suggest me to proceed? - Just performing a simple average of the 3 cortical thickness values obtained with the aparcstats2table? - Computing a weighted average of the 3 cortical thickness values obtained with the aparcstats2table? In this case, what would you use as weight? The area of the 3 regions? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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Fwd: Re: Custom aseg Color Lookup Table
by C.P. Frost 21 Aug '14

21 Aug '14

Thanks for the reply, Doug. The main problem is that areas not included in my custom table appear colored in freeview. These areas' numbers correctly correspond to their indices on the default FreeSurferColorLUT, although they don't appear labeled in the info panel, nor are they listed to the left of the main display. For instance, the left cerebral cortex (not on my list) is colored, and clicking on it yields an index of 3 in the info panel, but no label. The good news is so far as I can tell, every area I specified does show up colored appropriately and has a label associated, but I have no idea where the ones I DIDN'T specify are coming from. -------- Original Message -------- Subject: Re: [Freesurfer] Custom aseg Color Lookup Table Date: Wed, 20 Aug 2014 11:12:56 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Try loading aseg.mgz as the aux volume so you can see the number at a particular voxel. If the color is not correct, see what the number is and what it corresponds to in the LUT doug On 08/19/2014 05:57 PM, C.P. Frost wrote: > Hi all, > > I'm trying to use Freeview to display subcortical regions in aseg.mgz > with a custom color lookup table. RGB colors will indicate on a jet > scheme how well that region's volume correlates to performance on a > behavioral measure. In other words, an R^2 coefficient of -1 is dark > blue, 0 is green, and 1 is dark red. I adapted the approach for aseg > structures from this method: > http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours/ > > When I try right now, by e.g. loading > subjects_dir/average/mri/aseg.mgz, and choosing Color map > Lookup > Table, Lookup Table > Load lookup table... and selecting my custom > table file, it *almost* works. The file is copied below (it has no > headers). > > 4 Left-Lateral-Ventricle 92 255 163 0 > 5 Left-Inf-Lat-Vent 224 255 31 0 > 7 Left-Cerebellum-White-Matter 112 255 143 0 > 8 Left-Cerebellum-Cortex 133 255 122 0 > 10 Left-Thalamus-Proper 153 255 102 0 > 11 Left-Caudate 102 255 153 0 > 12 Left-Putamen 61 255 194 0 > 13 Left-Pallidum 102 255 153 0 > 14 3rd-Ventricle 0 224 255 0 > 15 4th-Ventricle 61 255 194 0 > 16 Brain-Stem 71 255 184 0 > 17 Left-Hippocampus 102 255 153 0 > 18 Left-Amygdala 41 255 214 0 > 26 Left-Accumbens-area 92 255 163 0 > 28 Left-VentralDC 122 255 133 0 > 30 Left-vessel 102 255 153 0 > 31 Left-choroid-plexus 102 255 153 0 > 43 Right-Lateral-Ventricle 173 255 82 0 > 44 Right-Inf-Lat-Vent 122 255 133 0 > 41 Right-Cerebellum-White-Matter 82 255 173 0 > 42 Right-Cerebellum-Cortex 122 255 133 0 > 49 Right-Thalamus-Proper 173 255 82 0 > 50 Right-Caudate 143 255 112 0 > 51 Right-Putamen 92 255 163 0 > 52 Right-Pallidum 41 255 214 0 > 53 Right-Hippocampus 133 255 122 0 > 54 Right-Amygdala 20 255 235 0 > 58 Right-Accumbens-area 82 255 173 0 > 60 Right-VentralDC 122 255 133 0 > 62 Right-vessel 122 255 133 0 > 63 Right-choroid-plexus 143 255 112 0 > 72 5th-Ventricle 92 255 163 0 > 85 Optic-Chiasm 112 255 143 0 > 251 CC_Posterior 71 255 184 0 > 252 CC_Mid_Posterior 31 255 224 0 > 253 CC_Central 10 255 245 0 > > The index numbers were chosen to match those found in the default aseg > LUT, as listed on the FS wiki: FSTutorial > AnatomicalROI > > FreeSurferColorLUT. Some regions appear correctly, but others either > a) display with incorrect labels, particularly > Right-Cerebellum-White-Matter or Right-Cerebellum-Cortex on *cortical* > white matter and ribbon, or b) display with no label in the info > panel, which makes it unclear whether it's working. > > > Notes: > - Originally indices were simply 1 to n, but that caused a wider array > of problems, and I inferred (perhaps incorrectly) freeview was > matching regions with indices rather than label names. > -This particular map is mostly green since most correlations are > small, which is fine; others will have a broader range of values. > -I'm not sure what the effect is of pressing the "Show existing labels > only" toggle, which eliminates a couple areas from the label list, but > it's unclear how it chooses them. > > > Can anyone offer advice on how to ensure the correct colors are > displayed in the correct regions? (Or an easier way to do this?) > > Cheers, > C.P. Frost > UW-Madison > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer August 2014