Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

stuck in 'Fix Topology lh
by maryam koochaki 04 Jan '16

04 Jan '16

Hi,I have a subject that every time I run it, it stuck in 'Fix Topology lh or rh' step.The error which I find it in brainmask volume is, some part of the brain is excluded.So I edited it manually (clone from T1 volume ), then I run it with the following command line;recon-all -subjid test_emc_039 -autorecon2 -autorecon3 -no-wsgcaatlasHave anybody had this kind of problem?ThanksMaryam

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problem with hard coded directory (/scratch)
by Fengji Geng 04 Jan '16

04 Jan '16

Dear all, I am currently using freesurfer 6.0 (development version) to run hippocampal subfields segmentation and encountered a 'mkdir' error, which is attached below. Our troubleshooting found that some scripts in the ...freesurfer/dev/sys/bin directory with things like: if(-e /scratch) set tmpdir = /scratch/tmpdir.bbmask.$$ if(! -e /scratch) set tmpdir = $outdir/tmpdir.bbmask.$$ However, /scratch is a directory that is not writable in our server. So, we made changes to all of the scripts that testing the existence of /scratch. However, there are several places where they incorrectly test for the /scratch directory using -e instead of -dw, the /scratch is hard coded in there so it can't be changed. Looking forward to hearing suggestions and comments. Fengji ----------------------------------------------------------------------------------------------------------- Here begins the error message: hippocampus:/<2>hippocampus/HMN/data/FG_Temp: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Nov 18 21:57:45 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Nov 18 21:57:50 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError End of error message.

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Fwd: OHBM 2016 Call for Abstracts
by Douglas N Greve 04 Jan '16

04 Jan '16

fyi -------- Forwarded Message -------- Subject: OHBM 2016 Call for Abstracts Date: Mon, 04 Jan 2016 09:55:43 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu *Call for 2016 Abstracts Reminder The OHBM 2016 Call for Abstracts will close THIS Thursday, January 7th at 11:59 EST.* This is your last chance to submit an abstract for consideration for OHBM 2016. *Click here to submit your abstract today!* <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33…> ------------------------------------------------------------------------ *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 info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=33…>. Click here to Unsubscribe <http://www.humanbrainmapping.org/i4a/etrack/unsub.cfm?campaignID=3375&conta…>

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cortical thickness longitudinal analysis
by Enrica Cavedo 04 Jan '16

04 Jan '16

Dear Freesurfers, I'm going to perform a longitudinal analysis of cortical thickness using 3D-T1 images with a voxel size of 1mm isotropic. Could you kindly explain the robustness of free surfer longitudinal pipeline to calculate sub-mm changes on the cortex. thank you in advance for your help, best regards, enrica

2 1

Qdec Clusters Graph Extracted
by Katherine Damme 03 Jan '16

03 Jan '16

Hello FreeSurfer Group I would like to make my own box plot out of a cluster that I identified as significant in Qdec. Is there any easy way to extract the information that appears in the graph window so that I can create a box plot? I've tried extracting it by drawing an roi and using mris_anatomical_stats and mri_label2label, but the numbers look different than what appears in the qdec graph. Any advice would be very appreciated!! Thank you! Kate Damme

1 0

Using custom segmentations with recon-all
by james pardon 02 Jan '16

02 Jan '16

Dear All, I was wondering whether there is a simple way to pass T1 segmentations I have from another software to Freesurfer, in order to do the remaining recon-all steps? Thank you in advance, James

2 3

Longitudinal data analysis
by John Anderson 02 Jan '16

02 Jan '16

2 1

Fwd: LME FDR2 corrected results
by Hanbyul Cho 01 Jan '16

01 Jan '16

Dear FreeSurfer Team, My name is Han. I am wondering how I can save the FDR2 corrected results. I processed in MATLAB for Linear mixed effects models analysis, as follow: [lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4) [lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, lhTh01,lhcortex,2,95); lhstats01 = lme_mass_fit_Rgw(X,[1],Y,ni, lhTh01, lhRgs01, lhsphere,[],'euc','exp',4) F_lhstats01=lme_mass_F(lhstats01,CM,4); dvtx = lme_mass_FDR2(F_lhstats01.pval, F_lhstats01.sgn, lhcortex, 0.05, 0); length(dvtx) ans = 8000 In this case, I search the corrected results that were 8000 vertices. I think the dvtx value was for saving the significant each vertex numbering label, is it right? However, I don't know the next step for save the 8000 corrected vertices. fs_write_fstats(F_lhstats01,mri,'%%$.mgh','sig'); I can save the whole results 'F_lhstats01' as the mgh format. However these were uncorrected results, is it right? Could you let me know the method for saving the FDR2 corrected results as a mgh format? Best Regards, Han.

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Question on longitudinal stats directory
by Govindarajan, Koushik Athreya 01 Jan '16

01 Jan '16

Hi there, I have run my subjects from multiple time points through a cross-sectional stream and a longitudinal stream. When I look at the 'stats' directory for the same subject from the cross-sectional pipeline and the longitudinal pipeline, I see that the numbers are different. For example, the cortical thickness values in the lh.aparc file for the same subject are different. Is one estimation more accurate than the other? Where is the difference coming from? Thanks Koushik Govindarajan

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Files needed for qdec
by Tara Miskovich 01 Jan '16

01 Jan '16

Hello Freesurfer experts, I need to upload some data to a public domain and I am trying to best limit the amount of files needed. I am wondering what subjects files are absolutely necessary to run an analysis in qdec. This is for an lgi analysis. I tried only using the surf directory, but qdec would fail. Could someone let me know what other directories/files from freesurfer are needed just to recreate one surface analysis in qdec. -- Thank you, Tara

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