Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] sulcus measurement from aparcstat2table
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Recon-all GNU parallel Error. : Segmentation fault
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 stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15208 maxlocks unlimited maxsignal15208 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 39154323730516 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Recon-all GNU parallel Error. : Segmentation fault
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 stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15208 maxlocks unlimited maxsignal15208 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 39154323730516 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex
Hi Bruce and Clara, Thanks for your comments. Indeed the bright points are segmented as WM in wm.mgz, however these errors do not occur only in a few places but in many slices throughout the brain so manual edits will be quite extensive, which is why we wanted to double check that there is no parameter tweak to recon that might at least help some of these errors. But sounds like there's no way to adjust the parameters of recon to mitigate this type of error? If not we will move forward with manual edits to wm.mgz as you suggest. Thanks! Best regards, Ben On Fri, Sep 2, 2016 at 8:36 AM, Clara Kühnwrote: > Hello Ben, > > I am no expert, I can only talk from my experience. > I've had similar images in my data. Those might be blood vessels or dura > that were included in the surface. If they are included in the surface on > more than 5 slices and pretty well visible you could delete those voxels > from the brainmask. From the looks of the attached screenshots however I > wouldn't worry about the brainmask but rather remove a few voxels from the > wm.mgz. Then you rerun the subject with the -wm flag and check again. If it > is only on one or two slices, though, I wouldn't edit it at all. The > surfaces are just not going to be perfect. > > Hope I could help. > Clara > > > - Ursprüngliche Mail - > Von: "Benjamin Baird" > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Donnerstag, 1. September 2016 21:56:58 > Betreff: [Freesurfer] white matter errors due to inhomogeneities (bright > spots) in cortex > > 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 > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex
Hello Ben, I am no expert, I can only talk from my experience. I've had similar images in my data. Those might be blood vessels or dura that were included in the surface. If they are included in the surface on more than 5 slices and pretty well visible you could delete those voxels from the brainmask. From the looks of the attached screenshots however I wouldn't worry about the brainmask but rather remove a few voxels from the wm.mgz. Then you rerun the subject with the -wm flag and check again. If it is only on one or two slices, though, I wouldn't edit it at all. The surfaces are just not going to be perfect. Hope I could help. Clara - Ursprüngliche Mail - Von: "Benjamin Baird"An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 1. September 2016 21:56:58 Betreff: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
Hi Yoon - It sounds like FSL's bedpostx postprocessing script failed. You can run it like this: bedpostx_postproc.sh /path/to/your/subject/dmri This script merges the results from all the slices. It's possible that something went wrong with the slices (you ran out disk space for example). If the slice results are ok, this'll do it. Best, a.y On Fri, 2 Sep 2016, Chung, Yoonho wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.