Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

recon-all crashing
by Biekman, Brian Darnell 02 Nov '15

02 Nov '15

To Whom It May Concern: I am conducting FreeSurfer analysis for a multi-site project and I'm unable to run recon-all on the T1 data for all but one of the sites. The problem I'm dealing with is identical for all of the subjects for which recon-all crashes. I do not want to speculate as to why recon-all works for one of the sites but it's worth mentioning that that site has a slightly different T1 protocol and that these images were uploaded via a physical backup disk while for the other sites, I downloaded the T1 data for the other sites from a database shared by all of the project investigators. I would like to upload the images for one the T1-weighted sequences that crashes recon-all. If somebody could let me know how to go about that, I would really appreciate it. Thank you. Here is the requested information for anyone reporting a bug: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 15.0.0 x86_64 Subject Name: 14-140-0052 Command Line Executed: recon-all -all -i /users/brianbiekman/Desktop/Brain_Scope/14-140-0052/00001.dcm -s 14-140-0052 Error message generated: Screenshot of error message attached recon-all log: Attached

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wrong segmentation
by Thục Trinh 02 Nov '15

02 Nov '15

Hi Freesurfer experts, I ran recon-all for our subjects and there is a problem with the wrong segmentation between the white/gray matter. this error appears in couples continued slices. Picture are attached. Do you have any suggestion to fix this error. Thank you, Trinh

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Questions about beta.nii.gz
by Reza Rajimehr 31 Oct '15

31 Oct '15

Hi, I have two questions: 1) In an fMRI experiment, we have 64 stimulus conditions and a baseline condition. All conditions are presented in each run. After running the analysis: mkanalysis-sess -a category.rh -surface self rh -fsd bold -fwhm 3 -event-related -paradigm paradigm_category.par -nconditions 64 -refeventdur 1 -TR 2 -polyfit 2 -spmhrf 0 -mcextreg -per-run -force selxavg3-sess -s subj1sess1 -a category.rh We load beta.nii.gz in Matlab. It has 131546 rows corresponding to the vertices in rh, and 118 columns. The first 64 columns correspond to the stimulus conditions that we have. I guess the next 6 columns correspond to the motion regressors. What are the remaining 48 columns? 2) When we run selxavg3-sess with -run-wise: selxavg3-sess -s subj1sess1 -a category.rh -run-wise We have a beta.nii.gz file for each run. But this time, each beta.nii.gz file has 70 columns. Why the number of columns here is different from that in the beta file generated without -run-wise? Thanks for shedding light on this issue! Reza

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OHBM white paper on best practices in Data Analytics and Sharing
by Thomas Yeo 31 Oct '15

31 Oct '15

Dear FreeSurfer List, In 2014 OHBM Council created the Committee on Best Practices in Data Analysis and Sharing (COBIDAS) to identify best practices of data analysis and data sharing in the brain mapping community. The COBIDAS committee has prepared a white paper organizing these practices and seek input from the OHBM community before ultimately publishing these recommendations. You can find the whitepaper here: http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3668. Feedback can be provided here: http://cobidas.wordpress.com/ Regards, Thomas

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Fwd: 2015 Call for Communications Committee Members
by Douglas N Greve 30 Oct '15

30 Oct '15

-------- Forwarded Message -------- Subject: 2015 Call for Communications Committee Members Date: Fri, 30 Oct 2015 11:34:52 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Dear OHBM Members: The Organization for Human Brain Mapping is pleased to announce the formation of a Communications Committee. The Council elected Randy Gollub as Chair and Nikolaus Kriegeskorte as Chair Elect of the Communications Committee. The formation of this Committee was approved by the OHBM Council at it's recent strategic planning meeting. The primary goal of this Committee is to increase the visibility and impact of members' work within the OHBM community and to extend it to a broader audience. The Communications Committee is now seeking volunteers from a variety of interest areas, geographic locations and experience levels, to serve on this Committee for a three year term. The Communication Committee will be comprised of twelve to fifteen current OHBM members with interest and experience in writing, editing, social media, media relations or communications. We are seeking candidates with skills in these areas to support communication efforts for different audiences, content areas and functions. We welcome you to participate in this very important new OHBM initiative. If interested, please complete the Call for Volunteers online form <https://www.surveymonkey.com/r/9Y3RBQR> no later than Monday, November 16. To apply you must be current member of OHBM (Renew membership now at www.humanbrainmapping.org <http://www.humanbrainmapping.org/>). Submitted applications will be presented to the Communications Committee Chair, Randy Gollub, and Co-Chair Niko Kriegeskorte for consideration and selection. If you have any questions, please contact OHBM at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org>. Sincerely, Karl Zilles, Chair Organization for Human Brain Mapping Randy Gollub, Chair OHBM Communications Committee Niko Kriegeskorte, Chair-Elect OHBM Communications Committee *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org <http://www.humanbrainmapping.org> info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>. <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3662> *Save the Date! June 26-30, 2016* <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3662>

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Free surfer dev env doesn't extract bvals/bvecs
by Emad Ahmadi 30 Oct '15

30 Oct '15

Hi Freesurfers, I’m using the dev env on Launchpad to analyze DTI dicoms using TRACULA. It cannot extract the bvecs from the dicom header since it gives me the following error: ERROR: Must specify input table of gradient vectors I’ve attached the TRACULA configuration file (dmrirc3.txt) and the log file. I would appreciate your help! Best, Emad Emad Ahmadi, MD ----------------------------------------------- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation
by Peled, Noam 30 Oct '15

30 Oct '15

Hey Bruce, I meant for the Lausanne250 parcellation (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048121) The problem is with the #index column. To create a custom lookup table, I need to know what is the #index each label gets in the output file of mri_aparc2aseg. I want to users to be able to load this new mgz file into freeview with the right lookup table. Thanks, Noam On Fri, 30 Oct 2015, Bruce wrote: > what is the laus250 parcellation? The lookup tables are in text so you > should be able to open one in an editor and see what the format is. It's > pretty straightforward. # lines are comments, then it is > <index #> <text name> <red> <green> <blue> <alpha (not used> > cheers > Bruce On Fri, 30 Oct 2015, Peled, Noam wrote: > Hey all, > I used mri_aparc2aseg to map the cortical labels from the laus250 > parcellation. > Now I need to create a new lookup table, mainly for displaying the labels' > names in freeview. > How can I know what id each label gets in my new laus+aseg.mgz file? > > Thanks, > Noam > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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unit in 'search area' in the glmfit log
by Jeni Chen 30 Oct '15

30 Oct '15

Hello, When running the Clusterwise Correction for Multiple Comparisons, I used a label as a mask to restrict search area. I want to find out the size of that label, so I guess I can pull that information out from the "mri_glmfit.log", specifically under 'searchspace'? Also I only see a numerical value there, I assume it is in mm2? Thanks. Jeni

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average z-score of each subject from a common cluster
by stdp82＠virgilio.it 30 Oct '15

30 Oct '15

Hi list,I have two queries, please. I'd like to have the z-score from my rsfMRI data (seed-analyis). 1) I have extract the z-score from the Vtx Max In details, after groups comparison analysis, I have opened the cache.th13.pos.sig.cluster.summary contained in group.diff folder and I have read the Vtx Max coordinates.Next, I have open the z.nii.gz of each subject and I have expected the z-score from the vertex which have the Vtx Max coordinates. Is this procedure corrected? 2) z-score of each subject from a common cluster I would like to use the cluster which shows the group difference (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would extract from it the average of the z-score which is contained in each subject.How should I do? Thanks. Stefano

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lables id in a new aparc+aseg file, created from laus250 parcellation
by Peled, Noam 30 Oct '15

30 Oct '15

Hey all, I used mri_aparc2aseg to map the cortical labels from the laus250 parcellation. Now I need to create a new lookup table, mainly for displaying the labels' names in freeview. How can I know what id each label gets in my new laus+aseg.mgz file? Thanks, Noam

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Freesurfer October 2015