Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

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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tracula longitudinal
by Dabbs (Kevin) 18 Aug '14

18 Aug '14

Getting ready to run longitudinal tracula. Does the sublist entries in the dmrirc.long file refer to the cross-sectional or longitudinal processed subject time points? set subjlist = ( huey-scan1 \ huey-scan2 \ dewey-scan1 \ dewey-scan2 \ louie-scan1 \ louie-scan2 ) Thanks, Kevin Dabbs Department of Neurology University of Wisconsin-Madison

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Interpreting clusters 'holistically' vs in terms of max coordinates
by Francesco Puccettone 18 Aug '14

18 Aug '14

Hello, If a QDEC analysis returns a certain cluster as being significantly different between the groups (after MC correction) in terms of some measure, which part of this cluster's description should my interpretation of this result be based on: its spatial extent (how it looks when projected onto the template brain, and what your knowledge of brain anatomy makes of that) or the coordinates of its maxima (as reported in the terminal window)? For instance, my result cluster is labeled as the postcentral gyrus, I guess because that is the parcel that overlaps most with the cluster (or perhaps because that is where the maximum point of the cluster falls?!), but looking at the cluster, it clearly extends into the parietal lobe: So how does one go about describing this cluster and interpreting the meaning of the effect in a Discussion section? Should I focus on the postcentral gyrus label and link it to other PCG effects in the literature? Or should I instead try to find in the literature maxima coordinates that are similar to what I get here? Any help much appreciated! --Francesco

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Re: [Freesurfer] holes in inflated using mris_label2annot
by Douglas N Greve 18 Aug '14

18 Aug '14

what was your command line? On 07/21/2014 03:43 PM, April Clausen wrote: > Hi Dr. Greve, I tried to upload the images with the Martinos Centre > Dropbox but I could not activate the dropbox … so the images are > attached. The 6 labels and annot file were created on fsaverage and > the image shows no holes in the regions. The 6 labels were mapped to a > subject and an annot file was created … the subject files shows holes > in the regions. > > April Clausen > -- 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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trac-all -prep problem
by Shantanu Ghosh 18 Aug '14

18 Aug '14

Hi Freesurfer experts, I ran the command <trac-all -prep -c dmrirc.txt> on a bunch of subjects and all of them finished in ~90 minutes except one. This subject keeps on going into a seemingly endless loop. It has been running for almost 12 hours now. A section of the console output is reproduced below. What is the issue here, and how can this be solved? I am using the dev version on a Linux box. Thanks in advance for all help. Shantanu ------ SAMPLE CONSOLE OUTPUT ------ INFO: Distances between consecutive points in test subject's space are 11 11 10 10 10 WARN: Could not find satisfactory control point fit - try 1831 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 91 voxels Selecting 6 points on center streamline INFO: Minimum allowable distance between dominant points is 9 INFO: Minimum allowable curvature at a dominant point is 0.0283381 INFO: Points where local peeks in curvature occur are 106 105 67 (curv = 0.0284049) 112 108 77 (curv = 0.0450985) 115 108 98 (curv = 0.0526145) 113 104 116 (curv = 0.0460477) 107 103 128 (curv = 0.0759711) INFO: Intermediate dominant points are 103 98 50 112 108 77 114 108 89 115 108 98 107 103 128 105 106 145 INFO: Final dominant points are 103 98 50 112 108 77 114 108 89 115 108 98 107 103 128 105 106 145 WARN: Defaulting to equidistant dominant points WARN: Defaulting to equidistant control points INFO: Selected control points are 103 98 50 108 106 69 114 108 89 114 105 108 108 103 126 105 106 145 INFO: Distances between consecutive points are 21 21 19 19 19 INFO: Selected control points in test subject's space are 80 62 23 81 66 31 84 68 40 84 66 48 82 64 56 81 65 64 INFO: Distances between consecutive points in test subject's space are 9 10 8 8 8 WARN: Could not find satisfactory control point fit - try 1832 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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Freesurfer August 2014