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freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011
by Parker, Richard 05 Jan '16

05 Jan '16

Hi Professor Yeo, Sorry for the late reply. In the end I ended up giving in and performing my functional connectivity analysis in MNI space, like any rational person would. As a result, I ended up using the MNI152 versions of network masks you provided. Thanks for all your help, and for providing the split region ROI files! Best wishes, Richard Parker Richard Parker Postgraduate Research Student Maurice Wohl Clinical Neuroscience Institute King's College London Telephone: 07943515208 Email: Richard.r.parker(a)kcl.ac.uk

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Freesurfer 6.0 -hires mri_segment potential issue
by Ajay Kurani 05 Jan '16

05 Jan '16

Hello Freesurfer experts, I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu 14.04 with a high resolution image (0.5mm isotropic). I set OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags in my autorecon 2 line command. Autorecon1 and the beginning parts of Autorecon2 ran in a reasonable amount of time. Currently the program is running the mri_segment -keep -mprage brain.mgz wm.seg.mgz line command however it has been at this step for approximately 5 days! I used top line command to verify that the program is still running and it seems to be still running. I wasn't sure if this time for this step is typical for a high-res image (as this is my first time processing data higher than 1mm iso), or if there is a potential bug. I ran this same subject on another computer using the same version of Freesurfer and Ubuntu (8 core machine) and mri_segment (~ step 15) has been running for over a day so far. Any feedback would be appreciated as to if this amount of processing time is typical for this type of resolution, or if it could be a potential bug and that I should wait for a new beta release? Thanks, Ajay

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Is the x-component of the b vectors extracted by mri_convert inverted?
by Emad Ahmadi 05 Jan '16

05 Jan '16

Hi FreeSurfer Experts, Happy New Year! I am using mri_convert to extract b vectors (bvecs) from diffusion images obtained at Bay 4. Then I use TRACULA for reconstructing white-matter pathways. The shape of the reconstructed pathways are odd, so I checked if the extracted bvecs are correct. To check if the extracted bvecs are correct, I used Diffusion Toolkit together with the extracted bvecs to do deterministic tractography. Then I checked the shape of the extracted nerve fibers. I have put a slide deck in the following dropbox folder showing that the shape of the extracted nerve fibers don’t look right: https://www.dropbox.com/s/1bt6on0rwm9url6/x_inversion.pptx?dl=0 <https://www.dropbox.com/s/1bt6on0rwm9url6/x_inversion.pptx?dl=0> Then I inverted the x-components of the extracted bvecs, and did the tractography again. This corrected the shape of the extracted nerve fibers (see the slide deck). I additionally had a look at the extracted dtift_V1 vectors under the two conditions, i.e. before and after x-component inversion. The results showed the same thing: x inversion corrects the images. I just wanted to see if others have had the same problem and confirm that I should invert the x-component of the bvecs extracted via mri_convert (I had the same experience with dcm2nii tool, where I had to invert the z-component of the extracted bvecs). I hope a wonderful new year for everyone! Emad Emad Ahmadi, MD ----------------------------------------------- Research Fellow in 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 <mailto:emad@nmr.mgh.harvard.edu>

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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

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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

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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

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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

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