Freesurfer

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30099 discussions

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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downloads of freesurfer from website doesn't work
by Lau Møller Andersen 19 Aug '14

19 Aug '14

Dear List I get the following error: „550 Failed to change directory.” I tried on two operating systems. The wget also doesn’t work. Says the file doesn’t exist. Do you get the same errors, or is it specific to my system? Best Lau

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download link broken?
by Wynn Legon 18 Aug '14

18 Aug '14

Hi, Trying to download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux…>. Link gives 550 error and terminal error is: No such directory 'pub/dist/freesurfer/5.3.0' Please advise -- -------------------------------------------------------------------------------------------------------------------------------------------- Wynn Legon PhD Assistant Professor Department of Physical Medicine and Rehabilitation School of Medicine University of Minnesota R398 - 426 Church St. E Minneapolis, MN 55455 USA Ph. (612) 626-1183

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mismatch between FWHM data in fwhm.dat & specified smoothing kernel
by Vy Dinh 18 Aug '14

18 Aug '14

Dear Surfers, While running a mri_glmfit-sim (monte carlo simulation) for roi analyses generated using mri_glmfit, I encountered the following error code: ERROR: cannot find /Applications/MRI/freesurfer_5.30_x86_64/average/mult-comp-cor/fsaverage/lh/cortex/fwhm31/abs/th13/mc-z.csd I checked the fwh.dat file within my glm/ directories and realize that there is a discrepancy between the fwhm I set for the analyses and the fwhm in this file (which explains why I encountered the error above.) Can someone explain why there is a large discrepancy for these roi analyses (which is specified using the --label option)? What kinds of things can I do to run the monte carlo simulation appropriately? Thank you, Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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None region label number (color) not in FreeSurferColorLUT.txt
by Axelson, Eric D 18 Aug '14

18 Aug '14

I am trying to make a custom label color scheme and wanted to change the None. Region but the FreeSurferColorLUT.txt only lists the unknown region (0) rather than None. I replaced the unknown region label name with None. to no avail like this. Is the None. region a different label number and color code? 0 None. 120 120 120 0 1 bankssts 120 120 120 0 2 caudalanteriorcingulate 120 120 120 0 3 caudalmiddlefrontal 120 120 120 0 4 corpuscallosum 120 120 120 0 5 cuneus 120 120 120 0 6 entorhinal 120 120 120 0 7 fusiform 120 120 120 0 8 inferiorparietal 120 120 120 0 9 inferiortemporal 120 120 120 0 10 isthmuscingulate 120 120 120 0 11 lateraloccipital 120 120 120 0 12 lateralorbitofrontal 120 120 120 0 13 lingual 120 120 120 0 14 medialorbitofrontal 120 120 120 0 15 middletemporal 120 120 120 0 16 parahippocampal 120 120 120 0 17 paracentral 120 120 120 0 18 parsopercularis 120 120 120 0 19 parsorbitalis 120 120 120 0 20 parstriangularis 120 120 120 0 21 pericalcarine 255 0 0 0 22 postcentral 120 120 120 0 23 posteriorcingulate 120 120 120 0 24 precentral 255 192 203 0 25 precuneus 120 120 120 0 26 rostralanteriorcingulate 120 120 120 0 27 rostralmiddlefrontal 255 99 71 0 28 superiorfrontal 120 120 120 0 29 superiorparietal 240 128 128 0 30 superiortemporal 120 120 120 0 31 supramarginal 120 120 120 0 32 frontalpole 120 120 120 0 33 temporalpole 120 120 120 0 34 transversetemporal 255 69 0 0 35 insula 120 120 120 0 Eric Axelson Research Specialist Department of Psychiatry Iowa Neuroimaging Consortium<http://www.medicine.uiowa.edu/iowaneuroimagingconsortium/> University of Iowa 319-384-9206 eric-axelson(a)uiowa.edu<mailto:eric-axelson@uiowa.edu> ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Cortical thickness via freesurfer
by Laura Golz 18 Aug '14

18 Aug '14

Dear all. I have a question concerning the estimation of cortical thickness in freesurfer. My overall goal is the comparison of a patient and matched control group with VBM and cortical thickness. My first try was the recon-all with masked MP2RAGE UNI-Images. Unfortunately it executed with error due to a not successfull skull-stripping.... Secondly I was going to skull-strip in AFNI and feed the skull-stripped image to the recon-all, but unfortunately the skull-stripping in AFNI was better but not as good as hoped. Next idea now is using the output of the VBM8 of SPM. Is it possible to use the segmented grey matter image from SPM in the recon-all to calculate overall cortical thickness and which steps of the recon-all are needed to be excluded for that? I am basically not interested in white matter...is it needed in the algorithm in general? The step 15 starts with the wm edits. So in case I am able to use only the segmented grey matter image from the VBM toolbox to avoid needing to skull-strip, I need to start with the step 21 (autorecon2-pial) of the recon-all? Or is there a possibility to improve the skull-stripping somehow? I tried lowering the threshold by adding the watershed trying to be more liberal, but it did not work as I was hoping... Thank you all so much in advance! Best Regards, Laura

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Steps for Longitudinal trac-all
by Chung, Yoonho 18 Aug '14

18 Aug '14

Dear FS experts. I am trying run trac-all - the longitudinal version - on the cluster and not by using the dmrirc file. I am looking at the 'trac-all -help' and also the wiki, but I couldn't find a flag or option where I could specify the use of unbiased-template (e.g. [subjectID-base]) and other steps that may be necessary for the longitudinal analysis. Could someone please provide the steps that is required for running the longitudinal stream using 'trac-all' ? Thank you very much. Best, Yoon

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