Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

tkmedit
by Ali Radaideh 20 Aug '14

20 Aug '14

Dear FreeSurfer experts, I have installed FreeSurfer on multiple machines in our image processing lab (15 PC, Linux Ubuntu) and made sure that the setting are fine. However, I have tried to test if freesurfer works or not by typing the following: tkmedit bert orig.mgz Unfortunately, I have got the following error message on all PCs A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. So what would be the error? Many thanks in advance, Ali, -- *Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

4 10

problem downloading freesurfer
by gamaliel huerta urrea 20 Aug '14

20 Aug '14

Hi I tried for three days download freesurfer even today but pressing the download link in http://surfer.nmr.mgh.harvard.edu/fswiki/Download These are fallen and message "This web page is not available" I have understood that the site was in maintenance, however the links do not even respond. any help? I need to download for Mac OS XV FreeSurfer 10.9.4 64bit regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso*

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Custom aseg Color Lookup Table
by C.P. Frost 20 Aug '14

20 Aug '14

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

2 1

Creating the FSDG file for more than one discrete variable
by Isotalus, Hanna 20 Aug '14

20 Aug '14

Dear Freesurfer gurus, I am trying to create an FSDG file for my data set and I have a question regarding discrete variables. So say this is my data: Two discrete variables (two with two levels, one with eight), one continuous variable. I'm interested in one discrete variable (Patient/Control) with two levels and want to account for the effect of the others in the analysis. How should I construct my FSDG file? Can I have three columns for discrete variables (1) or should I have one column (2)? Or is there another way? (1) So should I do: GroupDescriptorFile 1 Title GroupAnalysis Class Male Class Female Class Patient Class Control Class ImagingsiteOne Class ImagingsiteTwo [and so on...] Class OccupationEight Variables Age Subject1 Male Patient ImagingsiteThree 16 Subject2 Male Control ImagingsiteSeven 18 Subject3 Female Patient ImagingsiteThree 23 And so on OR (2) Should I do GroupDescriptorFile 1 Title GroupAnalysis Class MalePatientImagingsiteOne Class MalePatient?ImagingsiteTwo [and so on..] Class MalePatient?ImagingsiteEight Class MaleControlImagingsiteOne [and so on...] Class FemalePatient?ImagingsiteOne [and so on until...] Class FemaleControl?ImagingsiteEight Variables Age Subject1 MalePatientImagingsiteThree 16 Subject2 MaleControlImagingsiteSeven 18 Subject3 FemalePatientImagingsiteThree ?23 And so on Thank you! Best wishes, Hanna

2 1

tracula update link not working
by Kirstie Whitaker 20 Aug '14

20 Aug '14

Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks 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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Error with the brainmask
by Mads Jensen 20 Aug '14

20 Aug '14

Dear list, I have problem with the brainmask from a subject where there is removed to much of the gray matter. So, I would like to hear if someone has a good idea where I should start to fix this issue? I have attached a jpgs of the brainmask and orig, and a link to the recon-all.log best regards, mads https://dl.dropboxusercontent.com/u/915037/recon-all.log

1 0

Flipped Hemisphere longitudinal analysis
by Bastian Cheng 19 Aug '14

19 Aug '14

Dear Freesurfers, Has anyone accomplished analysis of longitudinal cortex changes in a dataset with "flipped" hemispheres? I am currently struggling with data from stroke patients, half of them with lesions on the right, half of them on the left side of the brain. What I am planning: flip all healthy hemispheres to left and perform longitud. analysis of cortical thickness change on that (helthy) hemisphere. I have read the notes on Surface-based Interhemispheric Registration (xhemi) and most of the comments here. It seems to me that this would allow me to compare both hemisph. sides at ONE timepoint. (but not actually analyzing ONE (flipped) hemisphere over time). Any help to point me in the right direction is greatly appreciated! Bastian

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mri_glmfit group analyses in FDR in Freeview
by Vy Dinh 19 Aug '14

19 Aug '14

Dear Surfers, In qdec, one can obtain a list of the significant clusters for a contrast by clicking the "find clusters..." button. Is there a file equivalent or button in Freeview that can give us that kind of information? Additionally, is there an option in Freeview to calculate and view clusters with FDR-corrected value? Thanks in advance, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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Checking in about FLAIR Registration Problem
by Zamroziewicz, Marta Karolina 19 Aug '14

19 Aug '14

Good morning, I wrote several weeks ago about a bbregister problem that we’ve encountered (I’ve attached the original email below). I’d like to check back in about the status of the patch that was being developed. Thank you for your time and assistance! Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzamro2(a)illinois.edu<mailto:mzamro2@illinois.edu> 815-980-3882 This email is related to the archived “bbregister and FLAIR” email chain posted by Kayle Sawyer on 5/23/2014 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html) We have also been registering with FLAIR scans, and have run into a problem with approximately half of our subjects. Recon-all completes successfully but a bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve attached two screenshots, the first of which shows a bad registration and the second of which shows a good registration. Per your previous suggestion, we ran bbregister using the following flag: bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat --t2 --lta reg.test.lta This did result in a good registration, and we are hoping to incorporate this into our processing pipeline to ensure that we can use the FLAIR for refining the pill surface. The problem that we’ve run into is that we aren’t sure at which point this bbregister step occurs within the recon-all process flow. We were thinking there are a couple of possibilities: 1. manually create the transformation matrix for the FLAIR using the command mentioned above, and then re-run whichever steps necessary in recon-all to include this manually created xform; 2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with whatever steps/flags we need to include this FLAIR image to refine the pial surface. Unfortunately we're not exactly sure which flags to include in recon-all in order to most efficiently re-process our data with the manually created FLAIR transformation, and we were hoping you might offer some advice on this point. Please let me know if I can provide any additional information. [cid:795E512B-0727-4B3D-8B43-17BE1640FBD8@beckman.uiuc.edu][cid:9003C1C6-AA59-46E3-BF4A-0CEE22C57030@beckman.uiuc.edu]

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load_nifti.m - empty header
by Nadine Schlichting 19 Aug '14

19 Aug '14

Dear Freesurfers, I am struggling with a very basic step at the very beginning of my processing pipeline. This is what I've done: registered BOLD to anatomical data using bbregister, results checked with tkregister2 - all seems fine. Then I want to project BOLD data to the surfaces using mri_vol2surf - no error so far. BUT when trying to load the mri_vol2surf output into matlab (load_nifti.m) I get this error: *??? Attempted to access hdr.dim(2); index out of bounds because numel(hdr.dim)=0.* *Error in ==> load_nifti_hdr at 121* *if(hdr.dim(2) < 0)* *Error in ==> load_nifti at 80* *hdr = load_nifti_hdr(niftifile);* It seems that the hdr struct is completely empty. Thanks in advance for any kind of help, have a nice week, Nadine

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Freesurfer August 2014