Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13
by Daniel Haehn 13 May '13

13 May '13

Hi Nick, I installed it on Ubuntu 13.04 and all tools seem to work. I didn't test recon-all yet. Cheers, Daniel On Sun, May 12, 2013 at 10:41 PM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>wrote: > Fedora 18, Ubuntu 13 and Gentoo 64 users, > > another beta of the upcoming v5.3 is available here: > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-… > > this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users > who wished to test that the segfault problem in v5.2 and the prior beta > v5.3 is fixed. Your help in testing this release is appreciated. > > Thanks, > > Nick > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Daniel Haehn FNNDSC / BCH +1.857.218.5140

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Correction for multiple comparisons question
by Fotiadis, Panagiotis 13 May '13

13 May '13

Hi Freesurfer experts, I was wondering about three things concerning the use of the mri_glmfit-sim command: 1) I tried running it with the --2spaces flag in order to Bonferroni correct over the two hemispheres but it tells me that the specific flag is not recognized. Is there another way to correct over the two hemispheres? 2) I set the cluster-based threshold to 0.999 in order to see all of the clusters and varied the voxel-based threshold in order to see the differences that it would make on the results. Specifically, i set it to be 1.3, 2.0, 2.3, and 3.0. Between the four different occurring cluster summaries, there was only one common cluster that appeared in all four summaries. As expected, the number of voxels of the specific cluster was decreasing as its voxel-wise threshold was increasing. a) However, the reported cluster-wise threshold varied between 0.05 to 0.96 in those four cases. Does this sound reasonable? Shouldn't the cluster wise p values of the same cluster-between the four cases-be less dispersed? b) If there is a cluster reported in only one of the four summaries (i.e. when the voxel-based threshold is 1.3) that say has a cluster-wise p value of 0.03, do I consider that significant or not, since it does not appear in any other summary with such a low cluster wise p value and since the only published p value is the cluster wise one? Thank you in advance for your time, Panagiotis Fotiadis

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Different freesurfer version
by Oya, Hiroyuki (UI Health Care) 13 May '13

13 May '13

Hello Is it fine to process the anatomical data in v4.5 and analyze the results in v5.1? Thanks, Hiroyuki ________________________________ 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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Binary volume to surface label
by Jonathan DuBois 13 May '13

13 May '13

Hi Freesurfer Experts, I have a binary volume label in subject space that I converted from MINC to MGZ. I would like to register it to the surface of that subject as a flat label. I thought I would be able to do so with mri_vol2surf but I am not sure how to generate the required registration file. Is that the correct command, and if so, which registration file should I use? Thanks Jonathan

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Restricting ROI Analysis
by Skyler Gabriel Shollenbarger 13 May '13

13 May '13

Hi everyone, We are trying to restrict an analysis using Qdec to a region of interest. We have successfully created the ROI mask, however the analysis continues to be run on the entire brain. Any help is greatly appreciated. Thanks, Skyler and Jon -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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smoothing result with larger size FWHM kernel
by Glen Lee 13 May '13

13 May '13

[image: Inline image 3]Dear freesurfer expert I've tried both relatively small and large size of smoothing kernel (i.e., 4mm vs. 10mm) on the surface EPI data using mri_surf2surf function (e.g., mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ) Attached are displays of raw EPI, 4mm, and 10 mm FWHM. As can be seen, the areas being smoothed by 10mm FWHM is quite off from those in the raw 2D EPI whereas 4mm result looks reasonable. If anyone has some intuition about why this happened, please help me. -Glen ps) the area with colors show vertices with non-zeros values (also it was reconstructed from slap EPI)

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Unable to run trac-all on a subject from whom it previously worked
by celine＠nmr.mgh.harvard.edu 13 May '13

13 May '13

Hi Freesurfer team I am very new with tracula so my problem might be very obvious. I previously run trac-all -prep on a patient and it worked fine, then when I ran trac-all -bedp, after 30 hours, I thought there might be a problem so that I killed the job. Since then, I am not able to run again trac-all -prep on this subject and I can't see in the log file why. Here are the log files. I deleted all the previous preprocessing, but it didn't change my output. Thanks a lot for your help Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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MRI artifacts detection
by Jordi Delgado 13 May '13

13 May '13

Dear FS experts, I'm studying the most common artifacts on MRI scanning. I started with the SNR calculation (which is included in recent FS versions), but I'm afraid that these artifact is filtered/processed with the scanner control program, and I'm wasting time trying to calculate this ratio. My qüestion is, any one of you know if the scanners control programs are correcting SNR, Inhomogeneties, motion, etc? Have any sense to detect these artifacts, as a quality assurance method before to accept/decline the adquired image with an external method of the scanner control program? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

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obtain a V1 mask.nii.gz
by lujiao luo 13 May '13

13 May '13

Hello, experts, I am trying to obtain a V1 mask and use it as a seed of my fiber tracking. But I do not know how to get the BA.nii.gz file, and I've obtained BA.ctab and lh.BA.annot files by using flag recon_all. Would someone give me some suggestions about this? Thanks so much for your help! Yours Lulu

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thickness
by Tudor Popescu 13 May '13

13 May '13

Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness). 1) How should the contrast vector for a group comparison while factoring out age and gender be built? I didn't quite understand the example in the tutorial <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Contrasts>based on intercept/offset. In my case, shouldn't I have 4 elements in the vector (group1, group2, age, gender), with the first two elements receiving perhaps 1 and -1, since they are directly compared, and the last two elements 0 and 0 since I am not directly interested in their effect on the dependent variable? 2) Are the structures described in the .label files produced by mri_annotation2label in common (MNI) or in that subject's individual space? 3) For my thickness analysis, I have in mind an ROI for which I have a set of centre coordinates from a meta-analysis of relevant functional studies. What is the best way of defining the mask for this ROI as a function of those coordinates, rather than taking the eponymous region from the Destrieux or the Desikan atlas? 4) Exactly which of recon-all's outputs has to be inspected, for each subject, in order to tell whether the surface reconstruction has gone well? 5) Is it statistically correct to run the same design both with a DODS FSGD and with a DOSS FSGD? It's not entirely clear to me what assumptions each one (DODS, DOSS) makes of the data, and which one I should select in my case. Thank you very much indeed. Tudor

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Freesurfer May 2013