Freesurfer

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30096 discussions

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

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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

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

02 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

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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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Tracula Error -preproc Segmentation fault (core dumped)
by Kristina Jelinkova 01 Sep '16

01 Sep '16

Hello everyone, I've been using Tracula for a while now with much success (and help from the archive) but I've run into an error I haven't been able to solve. I have several subjects for which trac-all -preproc ends with Segmentation fault (core dumped) I don't think it's a mistake with my directories, they appear correct and I've ran numerous subjects successfully like this already. The dti data and aparc+aseg also appear normal. I'm attaching the trac-all log and error log from one of these problematic subjects. Any insight would be greatly appreciate! Thank you, Kristina Jelinkova

2 1

white matter errors due to inhomogeneities (bright spots) in cortex
by Benjamin Baird 01 Sep '16

01 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 thoughts recommendations or advice you might be able to offer. Best regards, Ben

2 1

bigventricles, inaccurate segmentation
by Carol Nguyen 01 Sep '16

01 Sep '16

Hello FreeSurfer Developers, I am attempting to segment a brain with large ventricles. I was able to create a decent brainmask.mgz but the aseg segmentation after running autorecon2 and autorecon3 is neglecting a part of one hemisphere (see a picture attached). I tried to readjust the talairach parameters with tkregister without success. Running autorecon2 with "-bigventricles" flag did yield a similar result as running without it. Lastly, for your information, I use FS v5.3. I am also attaching the recon-all.log from the most recent attempt. Can you please advise me how to get the correct segmentation of such a brain? Thank you! Best regards, Carol *Carol Nguyen* University of Minnesota, Twin Cities Researcher | Department of Pediatrics Division of Neuropsychology nguy1903(a)umn.edu

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white matter errors due to inhomogeneities (bright spots) in cortex
by Benjamin Baird 01 Sep '16

01 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. (ps I tried to post this yesterday but I think I made a mistake and it didn't go through so I am resending) Thanks in advance for any advice you might be able to offer. Best regards, Ben

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