Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Seg fault
by Cooke, Gillian 06 Jun '14

06 Jun '14

Hi, I've been working with Freesurfer for years and have suddenly been getting this fault: tkmedit started: Fri May 30 10:08:23 2014 /Applications/freesurfer/tktools/tkmedit.bin ACCE633_1 brainmask.mgz -aux T1.mgz -surfs $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/gilliancooke Set subject home dir to /Volumes/HealthAging/ACCE/Freesurfer/ACCE633_1 Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: Any suggestions? Many thanks, Gill _____________________ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain & Cognition Lab Beckman Institute University of Illinois, Urbana

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How to deal with a skewed T1 image
by Vy Dinh 06 Jun '14

06 Jun '14

Dear Freeesurfer community, I've attached a coronal view of a T1 image in tkmedit that is slightly oriented away from the center. The subject has been processed through the initial recon-all -all process without any error, but I am afraid that this orientation may cause a problem later on in my processing. Do I need to do any correction or should the normalization process correct the skewed orientation? Thank you, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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?need to edit pial surf in med temp lobe
by Kev 05 Jun '14

05 Jun '14

Dear freesurfers, Basic question that arose when reviewing the attached screenshots (salmon rectangles: axial and coronal view of same location). How much editing would require this subject in terms on pial surface? Is the highlighted area computed in lobar cortical thickness? Thanks and regards, Kev

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error when make_average_subject
by Qijing Yu 05 Jun '14

05 Jun '14

Hi Freesurfer, I ran into the following error when running make_average_subject. The following output is shown after make_average_surface is done. /Volumes/fMRI/Scanner_Data setenv SUBJECTS_DIR /Volumes/fMRI/Scanner_Data/ sdout /Volumes/fMRI/Scanner_Data/ mri_convert /Volumes/fMRI/Scanner_Data//P022/output/mri/orig.mgz /Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh --apply_transform /Volumes/fMRI/Scanner_Data//P022/output/mri/transforms/talairach.xfm -oc 0 0 0 mri_convert /Volumes/fMRI/Scanner_Data//P022/output/mri/orig.mgz /Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh --apply_transform /Volumes/fMRI/Scanner_Data//P022/output/mri/transforms/talairach.xfm -oc 0 0 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Volumes/fMRI/Scanner_Data//P022/output/mri/orig.mgz... TR=2200.00, TE=4.26, TI=1200.00, flip angle=9.00 i_ras = (-1, -1.16415e-10, 1.27329e-11) j_ras = (1.0732e-10, -7.26432e-08, -1) k_ras = (3.49246e-10, 1, -7.07805e-08) INFO: Reading transformation from file /Volumes/fMRI/Scanner_Data//P022/output/mri/transforms/talairach.xfm... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/fMRI/Scanner_Data//P022/output/mri/transforms/talairach.xfm... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.182 0.047 -0.032 -0.505; -0.064 1.202 0.238 18.683; 0.093 -0.236 1.271 -31.892; 0.000 0.000 0.000 1.000; INFO: Transform dst volume info is not used (valid flag = 0). INFO: LTA dst geometry information missing! We assume that the dst volume passed is the same as the dst for the transform. INFO: LTA src geometry information missing! We assume that the src volume passed is the same as the src for the transform. mghWrite(/Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh, -1): could not open file --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh... ERROR: failure writing /Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh /Volumes/fMRI/Scanner_Data ERROR: mri_convert failed. ERROR: make_average_volume Thank you very much in advance for helping out! Best, Qijing

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Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing
by Douglas Merkitch 05 Jun '14

05 Jun '14

Dear Martin and FreeSurfer experts, Thanks for your response. I have just finished re-running some subjects from scratch in 5.3 and it appears that the edits from brain.finalsurfs.manedit.mgz are not being applied to the longitudinal subject directories. Just to clarify, I have been doing ALL of the pial surface edits in the brain.finalsurfs.manedit.mgz, not just the pial surface edits that have extended into the cerebellum. The rationale for doing this is mainly continuity, as the previous research assistant made all pial surface edits in this way because of a response she had received from the FS forum saying that there shouldn't be any problem with performing all the pial surface edits in the brain.finalsurfs.manedit.mgz file. Is there something in the FreeSurfer longitudinal processing code that would treat edits near the cerebellum of the brain.finalsurfs.manedit.mgz file differently from those made in other parts of the brain (e.g. lateralorbitofrontal, dura, etc.,)? Can you think of anything else that would be causing this or anything that I could try to get the longitudinal processing stream to incorporate the edits from the brain.finalsurfs.manedit.mgz file? Thanks for your help! Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu> Begin forwarded message: From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing Date: May 2, 2014 4:20:17 PM CDT To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Hi Doug, so you 1. edited the cross sectionals and surfaces look fine (make sure you edit the brain.finalsurfs.manedit.mgz file, which you create as a copy of the brain.finalsurfs.mgz) 2. checked/edited the base and surfaces look fine too 3. ran the longitudinal from scratch (w/o any edits) and then in the long, the surface looks not good? Edits should automatically be copied from cross->long (if the manedit file exist). Surfaces are taken from the base to initialize longitudinal processing. That is why both step1 and step2 above are important. Step3 is a good idea to make sure that the longs are not polluted by some earlier edits. For example edits from cross are only copied over if the long has no manedit file, else only the edits in the long will be used. (I think this also answers some of the questions in the archive mail 1 you cite below, the archive mail 2 is a question about cross sectional processing, but I think there the problem is that brainmask.finalsurfs.mgz was edited directly, not the manedit file, so edits probably get overwritten). I also have the feeling that we fixed something about the editing in longitudinal processing after 5.1, but cannot find it documented on the wiki (so not sure). You may want to try to run this with 5.3 if it does not work with 5.1 Best, Martin On 05/02/2014 10:45 AM, Douglas Merkitch wrote: Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525). The problem that I am having is that the edits saved in the brain.finalsurfs.manedit.mgz file do not carry over when processing longitudinally. Previous posts have addressed this topic, but have not (to my knowledge) solved the issue. Please see the threads from the Freesurfer archive below for a brief context: 1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html 2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html Please let me know if more information is needed to understand the issue. Any insight/ideas regarding this issue would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu> reuter(a)mit.edu<mailto:reuter@mit.edu> Web : http://reuter.mit.edu<http://reuter.mit.edu/> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto: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.

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How to use qdec to compare actual to expected thickness changes?
by Rummel, Christian 05 Jun '14

05 Jun '14

Dear FreeSurfers, we have MR scans from a group of healthy subjects (about 40, equal number of males and females, age range 25 to 65 years), who were scanned at two time points (about four months separation). In between they experienced exposure to a condition that might or might not influence cortical thickness or other morphometric measures. From other studies we have a large number of healthy controls in the same age range. The difference is that they were scanned only once and were not exposed to any special condition. We want to find out where cortical thickness changes significantly stronger in our subjects than expected from the controls for normal aging. We know how to do that for the averages over cortical parcellations and sub-cortical segmentations as reported in the aseg.stats and aparc.stats. Is it possible to use qdec to do the same thing vertex-wise? The symmetrized percent changes have been calculated already from FreeSurfer's longitudinal stream (long_mris_slopes). How can we feed the information about the locally expected change rate (and maybe even its variability) into qdec? Thanks, Christian Rummel _____________________________________________________________________ Christian Rummel (PhD) Support Center for Advanced Neuroimaging (SCAN) University Institute for Diagnostic and Interventional Neuroradiology Inselspital, 3010 Bern, Switzerland Tel. 0041 31 6328038 Fax 0041 31 6324872 crummel(a)web.de gpg encryption preferred Key-ID 5BEB9DB8 Fingerprint 8A73 6894 5668 49EA 816C DEFA 78D0 BF87 5BEB 9DB8 Mit TouchDown von meinem Android-Telefon gesendet (www.nitrodesk.com)

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Partly missing slice causes problems in surface formation
by Sami Karadeniz 05 Jun '14

05 Jun '14

Hello Freesurfers, I have a subject who's missing part of one slice in the MR images (on the right hemisphere). This causes problems in the surface formation, as shown in the attached pictures. First I tried to fix the problem by giving the central CC as seed point for the hemisphere cutting plane (-cc-crs), but this didn't help. The pictures were taken after I tried to fix the problem by filling in voxels manually into the wm.mgz. I managed to fix most of white surface problems, but the pial surface is still strongly drawn to the black line caused by the partly missing slice. This causes visible, canyon-like deformation as seen in the 3D view of pial surface. The partly missing slice is probably due to an error in the scanning process - I looked at the DICOM images with a DICOM viewer, and the problem is also present there. Do you have any suggestions on how to force the pial surface to follow a certain path, much like control points for wm? Or any other suggestions for fixing the problem? Getting the subject to do another MRI scan is unlikely at the moment. Thank you in advance, Sami

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subcortical atlases
by Joshua Lee 05 Jun '14

05 Jun '14

Hello Freesurfer Gurus, I was wondering whether the original individual subject atlases used to construct the probabilistic atlases for subcortical segmentation have been made available for download? Thanks! josh -

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FW: Queries about semi-inflated surface for overlay
by Zixuan Yang 04 Jun '14

04 Jun '14

Dear FreeSurfer experts, Really sorry for send my queries again (please see below). Could you please kindly offer us some advices in dealing with semi-inflated surface? Many thanks in advance and kind regards, Zixuan From: Zixuan Yang Sent: Monday, 2 June 2014 6:10 PM To: 'freesurfer(a)nmr.mgh.harvard.edu' Cc: Jiyang Jiang Subject: Queries about semi-inflated surface for overlay Dear Freesurfer experts, I would like to overlay the significance map and gamma.mgh map from cortical thickness GLM on a semi-inflated surface according to one previous post in the mailing list (shown as below) by using the command (shown) under the directory of fsaverage. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-November/012445…<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-November/012445.…> mris_inflate -n <steps> lh.white lh.partially_inflated My questions are: 1) Is it right to generate semi-inflated surface under fsaverage file? Or, I need to generate a semi-inflated surface for each subject (n>500) and make an average surface? How? 2) I tried different 'n', the new generated surface while n=5, 10 or 55 didn't look different at all! Is this normal? It did look very different from lh.white though. 3) Why the generated surface can only be open using tksurfer toolbox, but not a similar command like below? tksurfer fsaverage lh inflated -overlay ./directory_path/gamma.mgh Many thanks for your attention and looking forward to your answers. Best regards, Zixuan -- Zixuan YANG Ph.D candidate Centre for Healthy Brain Ageing (CHeBA) School of Psychiatry, UNSW Medicine NPI, Euroa Centre, Barker Street, Randwick NSW 2031 AUSTRALIA T: +61 (2) 9385 0427 W: www.cheba.unsw.edu.au<http://www.cheba.unsw.edu.au/> E: z.yang(a)student.unsw.edu.au<mailto:s.reppermund@unsw.edu.au> ______________ Mailing address: University of New South Wales Randwick Campus, Building R1f 22-32 King Street, Randwick NSW 2031 Australia

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MCSRCH error and failure at mri_ca_register
by Stacey M Schaefer 04 Jun '14

04 Jun '14

Hello, I'm running recon-all on a file and and running into an unfamiliar error. This error has been mentioned previously in the archives with no clear answer (see below for previous emails), and just as in that case, the brainmask.mgz looks reasonable. The recon-all.log is attached. Any idea what is going on? Its failing finally here: mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Thank you for any and all assistance! Stacey Schaefer ---------------- Hi - Was there ever a solution found for this? I am currently having the same problem. Thanks, Jeff Thompson Can you send us e recon-all.log file? On Aug 8, 2011, at 4:30 AM, "Irwin, William" <WIrwin at memory.ucsf.edu> wrote: > Hi- > > > > I’m at a bit of a loss as to how to address and/or fix these errors. > > > > The native input images are very good quality; the conversion to T1.mgz is fine; the brainmask.mgz is good, a bit of dura remained at the parietal/occipital region (very common); otherwise, the skull stripping is very clean. > > > > The recon-all “finished” but with errors as expected. Processing “continued” to the end, but there is no output except in /mri and /touch. > > > > Doing: #@# Skull Stripping > > > > First under “Computing MAP estimate using 3481 samples...” > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10327.2 tol 0.000010 > > > > Then several of the same under “EM alignment process ...” > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = 1145822.4 tol 0.000000 > > > > Then again at “Computing MAP estimate using 2772 samples...” > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7006.0 tol 0.000010 > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... > > > > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 838978.4 tol 0.000000 > > > > Thanks, > > Wil > > > > ____________________________________ > William Irwin | Brain Imaging Coordinator > UCSF | Memory and Aging Center > 350 Parnassus Avenue, Suite 905 > San Francisco CA 94143-1207 > wirwin at memory.ucsf.edu | memory.ucsf.edu > p: 415.476.1680 | f: 415.476.1816 > > -- --------------------------------------------------- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321

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