Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Error after manual edits in freesurfer 6
by Chethana 23 Aug '17

23 Aug '17

To, The Freesurfer experts I am analysing a set of MRI images in freesurfer 6. In the step 1 of freesurfer data processing the dura and skull are stripped and during the process of inspection with manual edits of the aux volume if I save the progress and reopen the same image for review they appear very brightly intense and unable to differentiate grey from white matter. Attaching two pictures for the same the first picture is without saving The second brightly intense picture attached is when the edit is opened for review after saving the volume where the grey white matter differentiation is difficult to see Can you kindly suggest how do I rectify this error or any other solution for the same? Thanks and regards Chethana

1 0

Re: [Freesurfer] FW: CNDA update: Processing failed for SD10013_1
by Iglesias Gonzalez, Eugenio 22 Aug '17

22 Aug '17

Dear Allison, The error happened in the old hippocampal subfield module. I would recommend that you used the new hippocampal subfield code in FreeSurfer 6.0. Having said that, if you really want to run the 5.3 subfield version, Koen Van Leemput maybe knows what the problem might have been. Kind regards, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Chen, Allison" <allisonchen(a)wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 22 August 2017 at 21:06 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] FW: CNDA update: Processing failed for SD10013_1 Hello Team, I have run ”recon-all args -qcache -all -hippo-subfields” command, but there are some errors. I used freesurfer 5.3 on CNDA: https://cnda.wustl.edu Attached and below are the error information. There is no any problem with our image. Could you give me any suggestions? Thanks a lot! Allison From: cnda-ops(a)nrg.wustl.edu [mailto:cnda-ops@nrg.wustl.edu] Sent: Thursday, August 17, 2017 9:21 PM To: Chen, Allison; cnda-ops(a)nrg.wustl.edu Subject: CNDA update: Processing failed for SD10013_1 The pipeline Freesurfer 5.3 encountered an error. * User: achen<mailto:allisonchen@wustl.edu> * Project: MEDEX * Experiment: SD10013_1 * Pipeline Step: RUN_FS The CNDA technical team is aware of the issue and will notify you when it has been resolved. We appreciate your patience. Please contact cnda-ops(a)nrg.wustl.edu with questions or concerns. The stdout and stderr log files are attached. PIPELINE PARAMETERS qc_rating 1 workdir builddir/SD10013_1 logdir workdir/LOGS XNAT_CSRF 7790fecf-8edf-41cc-8b26-caadb8150e06 email_csv_in cnda-ops(a)nrg.wustl.edu<mailto:cnda-ops@nrg.wustl.edu> freesurfer_subjectdir workdir/PROCESSED/SD10013_1 rawdir workdir/RAW id CNDA_E162884 paramsFile workdir/LOGS/SD10013_1.bashparams tempdir workdir/temp qc_rating_scale ' scan_ids [3] recon_all_args -qcache -all -hippo-subfields freesurferdir workdir/PROCESSED adminemail cnda-ops(a)nrg.wustl.edu<mailto:cnda-ops@nrg.wustl.edu> host https://cnda.wustl.edu/ relaunch false use_manual_qc 0 assessorId CNDA_E162884_freesurfer_20170817112729 label SD10013_1 format DICOM workflowid 6438524 freesurfer_tempdir workdir/PROCESSED/temp project MEDEX builddir /data/CNDA/build/MEDEX/20170817_112717/restlaunch u 2be260df-0fcb-4dda-9cdc-1ae13d9f02bd pwd ******** environment LOCAL useremail allisonchen(a)wustl.edu<mailto:allisonchen@wustl.edu> xnatserver CNDA datestamp 20170817112729 user 2be260df-0fcb-4dda-9cdc-1ae13d9f02bd mailhost mail.nrg.wustl.edu userfullname g.chen TAIL stdout Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Time taken to solve the Levenberg-Marquardt system of equations: 0.09901 ...done! maximalDeformation: 67.1108 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt... numberOfEntries: 24131 /nrgpackages/tools/freesurfer53-patch/bin/kvlSegmentHippocampalSubfields.sh: line 18: 400668 Segmentation fault (core dumped) kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt failed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt Linux nrglab08.nrg.mir 2.6.32-642.13.1.el6.x86_64 #1 SMP Wed Jan 11 20:56:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SD10013_1 exited with ERRORS at Thu Aug 17 21:20:53 CDT 2017 For more details, see the log file /data/CNDA/build/MEDEX/20170817_112717/restlaunch/SD10013_1/PROCESSED/SD10013_1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting TAIL stderr rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. + die 'recon-all failed' + echo 'recon-all failed' recon-all failed + exit 1 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

FW: CNDA update: Processing failed for SD10013_1
by Chen, Allison 22 Aug '17

22 Aug '17

Hello Team, I have run ”recon-all args -qcache -all -hippo-subfields” command, but there are some errors. I used freesurfer 5.3 on CNDA: https://cnda.wustl.edu Attached and below are the error information. There is no any problem with our image. Could you give me any suggestions? Thanks a lot! Allison From: cnda-ops(a)nrg.wustl.edu [mailto:cnda-ops@nrg.wustl.edu] Sent: Thursday, August 17, 2017 9:21 PM To: Chen, Allison; cnda-ops(a)nrg.wustl.edu Subject: CNDA update: Processing failed for SD10013_1 The pipeline Freesurfer 5.3 encountered an error. * User: achen<mailto:allisonchen@wustl.edu> * Project: MEDEX * Experiment: SD10013_1 * Pipeline Step: RUN_FS The CNDA technical team is aware of the issue and will notify you when it has been resolved. We appreciate your patience. Please contact cnda-ops(a)nrg.wustl.edu with questions or concerns. The stdout and stderr log files are attached. PIPELINE PARAMETERS qc_rating 1 workdir builddir/SD10013_1 logdir workdir/LOGS XNAT_CSRF 7790fecf-8edf-41cc-8b26-caadb8150e06 email_csv_in cnda-ops(a)nrg.wustl.edu<mailto:cnda-ops@nrg.wustl.edu> freesurfer_subjectdir workdir/PROCESSED/SD10013_1 rawdir workdir/RAW id CNDA_E162884 paramsFile workdir/LOGS/SD10013_1.bashparams tempdir workdir/temp qc_rating_scale ' scan_ids [3] recon_all_args -qcache -all -hippo-subfields freesurferdir workdir/PROCESSED adminemail cnda-ops(a)nrg.wustl.edu<mailto:cnda-ops@nrg.wustl.edu> host https://cnda.wustl.edu/ relaunch false use_manual_qc 0 assessorId CNDA_E162884_freesurfer_20170817112729 label SD10013_1 format DICOM workflowid 6438524 freesurfer_tempdir workdir/PROCESSED/temp project MEDEX builddir /data/CNDA/build/MEDEX/20170817_112717/restlaunch u 2be260df-0fcb-4dda-9cdc-1ae13d9f02bd pwd ******** environment LOCAL useremail allisonchen(a)wustl.edu<mailto:allisonchen@wustl.edu> xnatserver CNDA datestamp 20170817112729 user 2be260df-0fcb-4dda-9cdc-1ae13d9f02bd mailhost mail.nrg.wustl.edu userfullname g.chen TAIL stdout Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal Time taken to solve the Levenberg-Marquardt system of equations: 0.09901 ...done! maximalDeformation: 67.1108 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt... numberOfEntries: 24131 /nrgpackages/tools/freesurfer53-patch/bin/kvlSegmentHippocampalSubfields.sh: line 18: 400668 Segmentation fault (core dumped) kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt failed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt Linux nrglab08.nrg.mir 2.6.32-642.13.1.el6.x86_64 #1 SMP Wed Jan 11 20:56:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SD10013_1 exited with ERRORS at Thu Aug 17 21:20:53 CDT 2017 For more details, see the log file /data/CNDA/build/MEDEX/20170817_112717/restlaunch/SD10013_1/PROCESSED/SD10013_1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting TAIL stderr rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. + die 'recon-all failed' + echo 'recon-all failed' recon-all failed + exit 1 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

Appropriate number of control points
by Huang, Caleb (NIH/NINDS) [F] 22 Aug '17

22 Aug '17

Hi Freesurfer experts, A co-worker and I are having some issues figuring out a consistent Freesurfer editing protocol. How many control points are generally needed for a T1 scan of fair quality? Would there be a problem with consistency if one set of subjects has 10-80 control points and another set of subjects has 500-700 control points? If relevant, our subjects are patients with localized brain atrophy. What is the suggested time/number of edits to reach an acceptable surface quality? Thanks, -Caleb

1 0

Re: [Freesurfer] mri_vol2surf
by John Anderson 22 Aug '17

22 Aug '17

> Thank you for the response > > It is FDG SUV map > > need more info, eg, what kind of map is that? what modality? > >> -------- Original Message -------- >> Subject: mri_vol2surf >> Local Time: August 22, 2017 11:04 AM >> UTC Time: August 22, 2017 3:04 PM >> From: John.anderso(a)protonmail.com >> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> >> Dear FS experts, >> I ran voxel-wise analysis between two groups using randomise in FSL and the final statistical maps is as attached. >> I aim to to repeat the analysis using surface based analysis. I followed the steps as in wiki. I am not sure what is the correct value for projfrac int he command "mri_vol2surf" that is more appropriate to show the findings that I have in the voxel-wise (more int eh white matter) on surface. >> >> Thank you for any suggestion >> John

2 1

Freesurfer Contrast Issues
by Leavitt, Mackenzie 22 Aug '17

22 Aug '17

Hello, Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though. Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have. I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor. These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images. We greatly appreciate the assistance and support. Best, Mackenzie Leavitt =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

3 8

mri_vol2surf
by John Anderson 22 Aug '17

22 Aug '17

Dear FS experts, I ran voxel-wise analysis between two groups using randomise in FSL and the final statistical maps is as attached. I aim to to repeat the analysis using surface based analysis. I followed the steps as in wiki. I am not sure what is the correct value for projfrac int he command "mri_vol2surf" that is more appropriate to show the findings that I have in the voxel-wise (more int eh white matter) on surface. Thank you for any suggestion John

2 1

how to get aseg.mgz without transform
by Ritesh Mahajan 22 Aug '17

22 Aug '17

Hello Team, I have run "recon-all -i subject.nii -s subject -all -notalairach" command, i wanted to run it with notalairach. I am getting the following error: "No such file or directory mris_anatomical_stats: could not open atlas transform file /subject/mri/transforms/talairach.xfm" How can i get the aseg.mgz image without transform? Thanks, Ritesh Mahajan

2 1

mri_gtmpvc
by Joudy.carter 22 Aug '17

22 Aug '17

Dear experts, I have suv data and I want to do pve using pet surfer. I have the following questions and would appreciate your help: 1. The output of mgx is three maps mgx.{ctxgm,subctxgm,gm} these maps are pvc corrected. I am wondering where can I find pvc corrected maps for whole brain (white matter and gray matter)? 2. can I register these mgx files to standard space and run voxel-wise comparison using FSL randomise? 3. The output of RBV method is rbv.nii.gz. I want to concatenate all the rbv files for two groups and run voxel-wise analysis comparison. Is this possible? The size of these files is pretty large! Do you recommend better way to study the difference between two groups using these RBV files? 4. Are these RBV files for white matter and gray matter? 5. The suv data is an output of single frame PET data with no arterial blood sampling. Do I still need to re-scale over the pons? Thanks in advance Joudi

2 1

info on samseg routines
by Antonin Skoch 21 Aug '17

21 Aug '17

Dear experts, I would like to ask, whether I could obtain a basic general info on samseg routines - what specifically are they doing (publication reference) and how to use them? Regards, Antonin Skoch

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer