Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

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inflated surface - dots
by Fire Tech 06 Sep '16

06 Sep '16

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sulcus measurement from aparcstat2table
by tulu 06 Sep '16

06 Sep '16

Dear FS expert I use the aparcstat2table and generate the cortical volume/thickness. I have a question regarding sulcus volume and thickness meaning. For example, it generate lh_S_front_inf volume and thickness, which represents as left inferior frontal sulcus. Did the volume represent as CSF volume in this sulcus ? and what is the thickness of sulcus meaning ? Thanks JLH

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Recon-all GNU parallel Error. : Segmentation fault
by Dev vasu 06 Sep '16

06 Sep '16

Dear Sir / madam, I have tried running recon-all with GNU parallel and i am incurring following error kindly review the recon-all.log ( see below ). Could you please let me know why such problem persists for me. Is it the issue with memory space ? Thanks Vasudev Calling the GNU parallel in terminal " ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s {} -i {}.nii.gz -all -qcache " ------------------------recon-all-log................ Fr 2. Sep 17:59:48 CEST 2016 /media/vasudev/Daten/VBCT_results/PAT30 /usr/local/bin/freesurfer/bin/recon-all -s PAT30 -i PAT30.nii.gz -all -qcache subjid PAT30 setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results FREESURFER_HOME /usr/local/bin/freesurfer Actual FREESURFER_HOME /usr/local/bin/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15208 maxlocks unlimited maxsignal 15208 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3915432 3730516 184916 17476 21512 505448 -/+ buffers/cache: 3203556 711876 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ####################################### GCADIR /usr/local/bin/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/bin/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /media/vasudev/Daten/VBCT_results/PAT30 mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz /media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting

2 1

how to change threshold value in qdec window
by wanghaibao 06 Sep '16

06 Sep '16

hello,everyone I used the freesurfer 5.3 in fedora 20,there is a question in my reseach,may be not a question! When i view the results of analysis in the qdec window,why did i cannot change the value of the Threshold,such as min(which had been seted with the value of 2) ,in the same way,the max is 5?If i want to change the value of them,how can i do it? what wrong with it and how to solve it? thank you in advance haibao wang sep-6, 2016

1 0

white matter errors due to inhomogeneities (bright spots) in cortex
by Benjamin Baird 05 Sep '16

05 Sep '16

Dear Freesurfer experts, We are currently working with some scans that were collected on a GE 3T scanner. The goal is to analyze cortical thickness. The scans seem to be relatively high quality with the exception that there are what appear to be inhomogeneities in the intensity of the gray matter (appears too bright in places), which is causing the WM to extend/jump into cortex (see attached image). We're wondering if there are any parameter adjustments to recon that might help with this as the errors occur frequently enough that fixing them all manually will be fairly cumbersome. This type of error doesn’t seem to be discussed very much in the available information on freesurfer quality control as far as we’ve seen. Thanks in advance for any advice you might be able to offer. Best regards, Ben [image: Inline image 1]

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switching between different linux versions
by freesurfer＠web.de 04 Sep '16

04 Sep '16

1 0

White matter surface don't change after editing
by Cong 04 Sep '16

04 Sep '16

Dear freesurfer team： I have some MRI images from a GE scanner, it seems that images’ quality is poor because grey matter is bright in so much area and these grey matter is included in wm.mgz. So I deleted wrong voxels in wm.mgz by freeview and rerun through command “ recon-all -autorecon2-wm -autorecon3 -subjid subjname”. But ?h.white (yellow line) don’t change after rerunning as you can see in the attached picture. Is this problem caused by deleting too many voxels and how to fix it? Thanks very much. Regards Cong Chen I

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Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
by Chung, Yoonho 03 Sep '16

03 Sep '16

I found out why it didn't work. One of the script that bedpostx_postproc.sh calls is written in python2. I set my default to python3 and therefore caused the error in the last step. After I loaded python2 environment, i got the merged files and finished properly. Thanks for your help as always! Yoon

2 1

Recon-all GNU parallel Error. : Segmentation fault
by Dev vasu 02 Sep '16

02 Sep '16

1 0

trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
by Chung, Yoonho 02 Sep '16

02 Sep '16

Hi Anastasia, trac-all -prep completed without error. I thought trac-all -bedp starts and ends without any error but trac-all path failed with these messages. Loading BEDPOST parameter samples from */dmri.bedpostX niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read */dmri.bedpostX/merged_ph1samples.nii.gz I looked at the dmri.bedpostX directory and all slices exist in the dmri.bedpostX/diff_slices directory but realized the trac-all -bedp phase did not create the merged samples in this directory. I am currently runnning with FSL/5.0.6 Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ and freesurfer version 5.3 I looked through the mailing list to see if someone ran into a similar problem but could not find a good solution. Do you have what may have caused this? Any other files I would like to look into? Thank you Yoon

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Freesurfer September 2016