Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Data differ depending on OSX version
by Kasper Jessen 05 Jan '16

05 Jan '16

Dear freesurfer, As i understand from a previous forum thread, it is recommended that all the data is run on the same computer with the same operating system. However, what is the reason for the differing results when I am running the same 10 subjects on a MacPro and iMac respectively (please see below): *MacPro:* build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 13.4.0 Darwin Kernel Version 13.4.0 *iMac: * build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 11.4.2 Darwin Kernel Version 11.4.2 All the values are different. For example, the lh_caudalmiddlefrontal_thickness is on the iMac 2.472 and on the MacPro 2.537. Is it because of a randomization generator in FreeSurfer? Best regards, Kasper Jessen

2 3

recon-all get stucked
by salvatoreandrea.92＠libero.it 05 Jan '16

05 Jan '16

Hi Freesurfer experts! I am running recon-all with a Toshiba Satellite (16 Gb RAM and 4 CPU). My OS is Ubuntu 14.04 LTS (Trusty). Unfortunately recon-all gets stucked at the following: CORRECTING DEFECT 0 (vertices=30357, convex hull=5730) XL defect detected... I am using the Freesurfer development version, because I need to use Recon Edit. Attached you find the recon-all log. Best regards, Salvatore

2 1

control point edit
by maryam koochaki 04 Jan '16

04 Jan '16

Hi,I have some subjects which need some point seeding. For the first round they accept control points perfectly, but or more improvement they seem that they will not improve any more!!Should I leave it as it is? I attached one image as an example. Thanks,Maryam

1 0

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

1 0

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…>

1 0

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

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Freesurfer January 2016