Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

error with mri_ca_register in long
by miracle ozzoude 27 Aug '18

27 Aug '18

External Email - Use Caution Hello All, When running the longitudinal pipeline for version 6, i encountered this error " TransformSample: gcam has not been inverted!; Numerical result out of range". I found a thread with similar error but the problem wasn't solved. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-April/051240.html . Just like the previous thread, it happens whenever I include the "-bigventricle" flag. Below is a sample of my recon-all scripts from cross-sectional to longitudinal. The error.log and recon.log files are too large to send. Thank you. Best, Paul Cross-sectional recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename} -hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time Longitudinal recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp 20 -bigventricles -3T -time recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles -3T -time recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles -3T -time

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Resample data for longitudinal comparisons
by James Gullickson 27 Aug '18

27 Aug '18

External Email - Use Caution All, I would like to compare cortical thickness between two timepoints. Timepoint 1 has 1mm^3 data. Timepoint 2 has 0.8mm^3 data. I realize that there are limitations with this change in resolution between timepoints and that no analysis is going to be perfect, but I am trying to come up with the best possible solution. Would it work to resample both timepoints' raw data into 0.9mm^3 ( mri_convert --conform_size 0.9 invol outvol ), and then run the 0.9mm data through Freesurfer 6.0 submilimeter recon? If so, are there any special considerations I need to take into account after the initial recon, or would longitudinal processing after this point be per normal? Thanks, James

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Longitudinal Processing question
by Nillo, Ryan Michael R 27 Aug '18

27 Aug '18

External Email - Use Caution Hello FreeSurfer experts, I have a few questions on the longitudinal processing stream. I am interested in studying longitudinal morphometry changes in a pediatric population. The age range of this population is between 4-20 years with age deltas between a few months to < 2 years. I want to know what are appropriate/acceptable age deltas used for longitudinal processing. I looked through the archives and one researcher asked about age deltas. One of the answers was that “if the time delta is relatively small, this has good chances to work”. What does “relatively small” mean? If the time points exit the longitudinal pipeline without errors and the surfaces look correct, does this mean the data is relevant?? When I correct for head size, should I use the eTIV values from the cross-sectional directories or the longitudinal directories? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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Missingness and recent developments in longitudinal pipeline for pediatric samples
by Mohn, Johannes 27 Aug '18

27 Aug '18

External Email - Use Caution Dear FS Experts and Community, we are working on a longitudinal dataset of structural T1w images in a pediatric sample assessed at 2 waves, 2 years apart (aged 6/7 and 8/9). As far as we know, it is yet unresolved whether the Freesurfer longitudinal pipeline is robust in pediatric samples, where the head size is still changing or have there been any recent developments? Also, is there any documentation on how missingness affects this Pipeline? We look forward to your response Thank you, Laurel and Johannes Jacobs Entwicklungsstudie Max-Planck-Institut für Bildungsforschung Max Planck Institute for Human Development Lentzeallee 94 14195 Berlin Tel.: 030-824 06 371 E-Mail: jacobs-studie(a)mpib-berlin.mpg.de<mailto:jacobs-studie@mpib-berlin.mpg.de>

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Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?
by Yash Patel 22 Aug '18

22 Aug '18

Dear all, I am using mri_segstats to obtain intensity values from each of the 34 cortical parcellations in the Desikan-Killiany Atlas; this provides metrics such as mean, min, max, range, and standard deviation. Is there a way to extract information such as the *mode*, or information to create a histogram for each of the particular regions? Thank you, Yash

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vertex MNI305
by Trisanna Sprung-Much 21 Aug '18

21 Aug '18

External Email - Use Caution Hi there This might be a very silly question but I actually cannot find the answer in the email archive: Assuming I have loaded a label onto fsaverage in Freeview and want to get the MNI305 coordinate of that labelled vertex, am I simply using the x,y,z in brackets in the panel? I attach a photo of what I mean. Best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Ex vivo segmentations
by Fotiadis, Panagiotis 02 Aug '18

02 Aug '18

Hi Bruce and Doug, I have processed a few ex vivo brains with the help of the ex vivo freesurfer pipeline (outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) and have extracted their cortical thickness. So far the range of the cortical thicknesses have been approximately between 3.70-3.90 mm. Does that number sound reasonable for ex vivo brains? I am asking because the typical cortical thickness that I would expect to find on an in vivo brain would be between 2.05 - 2.35 mm. Thanks in advance for any advice! Best, Panos Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869

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Re: [Freesurfer] Surface editing: recon-all exited with errors
by Rockers, Elijah D. 01 Aug '18

01 Aug '18

External Email - Use Caution Oh, yep, sorry about that. I copy the list on this e-mail, and attach the log. I think the list blocks attachments, but if anyone wants to see full log I can send it. Thanks to all, -Eli ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Tuesday, July 31, 2018 2:03:05 PM To: Rockers, Elijah D. Subject: Re: Surface editing: recon-all exited with errors can you cc the list on these emails so others can help? On Tue, 31 Jul 2018, Rockers, Elijah D. wrote: > > External Email - Use Caution > > The recon-all -make all command finished relatively quickly, still with errors. It's still showing > the same errors, and I have attached the new recon-all.log. > > ____________________________________________________________________________________________________ > From: Rockers, Elijah D. > Sent: Tuesday, July 31, 2018 12:32:11 PM > To: Bruce Fischl > Subject: Re: Surface editing: recon-all exited with errors > > Odd. I assumed the individual recon-all commands in the log are just what is reported by the general > pipeline, since I definitely did not issue all those commands separately. I just used the recon-all > -make all command after editing. In anycase, I will run it again to see if anything changes, but I > think that would be surprising. > > > Thanks again > > - Eli > > ____________________________________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Sent: Tuesday, July 31, 2018 11:52:59 AM > To: Rockers, Elijah D. > Subject: Re: Surface editing: recon-all exited with errors > Hi Eli > > it's hard for me to tell since you have so many individual recon-all > commands, but it looks like you didn't recreate all the surfaces after > editing. Errors like thiss one: > > mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match > ../surf/lh.white.preaparc > > typically mean something hasn't been recreated properly. Try running > recon-all -make all > > cheers > Bruce > > > On Tue, > 31 Jul 2018, Rockers, Elijah D. wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > > > I have attached the recon-all.log, regarding an exit with ERRORS that occured after manually > editing > > the surface. Thanks for taking a look. > > > > > > Also, I double checked - the original recon-all command finished with no errors. So it seems the > > message occurs after surface editing. But the new reconstructed surfaces appear accurate, at least > > with respect to gray and white matter boundaries. Let me know if there's anything else you need. > > > > > > Thanks again, > > > > - Eli > > > > Houston Methodist. Leading Medicine. > > > > Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient > > care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet > hospital > > for excellence in nursing. Visit us at http://houstonmethodist.org. Follow us athttps://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_Methodist… > jkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWqTZ4zNG > seN-axVe5fM_ZPQ9W9OHoSzLLo&s=5CE2NSVpAt16S_bmsgO_Okvmb5bkLvXMIjkxSTQ2C5g&e= > > andhttps://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_Houston… > FixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWqTZ > 4zNGseN-axVe5fM_ZPQ9W9OHoSzLLo&s=1x_6X2u7_1TSprfJDQX2_pJs3OEQcXqNYjVB7pVhpzE&e=. > > > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant > > affiliates and may contain restricted and privileged material for the sole use of the intended > > recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you > > are not the intended recipient (or authorized to receive for the recipient), please contact the > > sender and delete all copies of the message. Thank you. > > > > > > > > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… > DiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWq > TZ4zNGseN-axVe5fM_ZPQ9W9OHoSzLLo&s=xCXJrzgzXHHAcYBpjDRMUejaZuRv3TRvaTInF4j-rTw&e= . 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. > > Houston Methodist. Leading Medicine. > > Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient > care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital > for excellence in nursing. Visit us at http://houstonmethodist.org. Follow us at https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHo… > and https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMet…. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant > affiliates and may contain restricted and privileged material for the sole use of the intended > recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you > are not the intended recipient (or authorized to receive for the recipient), please contact the > sender and delete all copies of the message. Thank you. > > > 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… . 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. Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Re: [Freesurfer] fcseed-config
by shahin＠nmr.mgh.harvard.edu 31 Jul '18

31 Jul '18

Your problem solved?

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Surface editing: recon-all exited with errors
by Rockers, Elijah D. 31 Jul '18

31 Jul '18

External Email - Use Caution Hello. I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortical areas, in particular the soft-tissue near the brain stem, and some cerebellar areas. Usually this type of editing (just removing voxels from brianmask.mgz) doesn't give me any trouble, and I use the command recon-all -make all -subjid <subject_id> -sd <subject_dir> to then rebuild the surfaces. However, the tail of the log shows that the pipeline exited with errors, with a few commands near the end related to curvstats and jacobian_white failing. The new surfaces seem to look fine in freeview. The edits to brainmask were registered correctly, but I'm still concerned that the errors might affect an mri_glmfit analysis. This is true for all three subjects I edited, which seems odd, and I'm not sure what would be causing this. Below is a pastebin showing the relevant errors. The rest of the pipeline seems to execute without errors. I could send entire log if necessary. <https://pastebin.com/b4JX04AT>https://pastebin.com/raw/b4JX04AT Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Freesurfer July 2018