Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

pial surface vs. aparc segmentation inconsistency
by Gabor Perlaki 12 Jan '17

12 Jan '17

Somehow, my earlier post is unvisible on the maillist, therefore I send it again without the attached image. Dear all, In some of our subjects the border of ctx_lh_parahippocampal (green color) is inconsistent with the border of pial surface (red color) in the sense that some small region within the pial surface is segmented as cerebellum (orange) coming from the subcortical segmentation stream. This problem is present in all three planes. It is hard to decide whether the colored border of ctx_lh_parahippocampal or the pial surface is more realistic, but it would be nice to know which one is used for the parahippocampal statistics in lh.aparc.stats file. Do I need to correct for this inaccuracy? How should I correct this type of missegmentation? Best Regards, Gabor <petzinger.gabor(a)gmail.com>

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CONFERENCE: ICON2017, 5-8 AUGUST, AMSTERDAM
by Mike X Cohen 12 Jan '17

12 Jan '17

[image: Inline image 1] We are happy to send a reminder for the ICON XIII conference, which will take place on 5-8 August 2017 in Amsterdam (the Netherlands). Amsterdam is an easily-accessible and progressive city. The venue is the Beurs van Berlage, located in downtown Amsterdam and one of the most beautiful conference venues in Europe! Visit the website: http://www.icon2017.org NOTE THE DEADLINES!! 2 January : Registration opened 1 February : Symposia/ask-the-experts/hackathons submissions close! 31 March : Poster submissions close 1 May : Notification of submission acceptance 15 May : Early-bird discount registration ends PRE-CONFERENCE WORKSHOPS/SATELLITES We welcome pre-conference satellites, and will be happy to advertise them on the ICON website. Note that satellites are independent from ICON in terms of organization, registration, and costs. FOLLOW US ON TWITTER For up-to-date announcements before and during the ICON meeting, follow @icon2017 (see also "Media" tab on the website). QUESTIONS ABOUT THE MEETING OR SPONSORSHIP? email icon2017(a)icon2017.org http://www.icon2017.org We look forward to seeing you in beautiful Amsterdam! Mike X Cohen and Birte Forstmann

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Re: [Freesurfer] autorecon1 crash (with nu_correct).
by Jamie Hanson 11 Jan '17

11 Jan '17

I'm seeing it for multiple subjects, same issue. I can't get passed the autorecon1 steps. Any thoughts?

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Re: [Freesurfer] mris_expand command and flags
by Antonin Skoch 11 Jan '17

11 Jan '17

Dear Paul, mris_expand can be used only in the hypothetical cases, where in all brain systematically the surface is shifted to equal amount from the position which is anatomically relevant. Therefore it cannot be used to correct for local errors. To ilustrate the use of this tool, see the screenshot where I tried to use this tool to "move" white surface to the half of the thickness towards the pial surface. Red is original white surface, yellow is original pial surface, blue is the surface produced by mris_expand. The error you showed in the screenshot (part of the gyrus not encircled by pial and white surface) is usually corrected by placing control points to the white matter, see the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview By correcting the white surface this way usually also pial surface is moved to correct position. Regards, Antonin Hello Antonin, GM/WM boundary = thickness. correct me if i am wrong. Shouldn't expanding/shrinking the ?h.white or ?h.pial surface to the correct size and shape help with that? I have moved the position of the ?h.white to capture most of the WM using mris_expand but i haven't been successfully with ?h.pial using mris_expand because the input and output were identical. Hence, I am looking for a way to do it with ?lh.pial and how to tell recon-all to incorporate my changes. Please correct me since I am still new to this (i.e., using individual recon-all scripts). Thank you. Best, PaulOn Wed, Jan 11, 2017 at 12:32 PM, Antonin Skoch <a...(a)ikem.cz> wrote: > Dear Paul, > > I am quite surprised that you were successful to estimate correct GM/WM > boundary using this tool. As far as I know and looking at the source code, > this tool GLOBALLY moves the position of the specified surface to some > amount, so it cannot be used to correct local errors. It is used e.g. for > estimating the surface ad the midthickness of the gray matter. > > See e.g. > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-July/011152.html > > Antonin > > > Thanks bruce for your response. I am trying to expand the pial surface (see > attached image) in order to estimate the GM/WM boundary properly. I have > successfully expanded the white matter but when i tried the mris_expand > scripts for pial surface (mris_expand -thickness lh.pial 0.5 lh.newpial), > the output looked identical to the input. Please can you direct me on how > to successfully achieve this for the pial surface and how to incorporate my > changes (expanded surfaces) into recon-all. Thanks. > Best, > Paul > > On Wed, Jan 11, 2017 at 11:37 AM, Bruce Fischl <fis...(a)nmr.mgh.harvard.edu> > wrote: > > > Hi Paul > > > > it's hard to answer your questions without knowing what you are trying to > > achieve > > > > cheers > > Bruce > > > > On Wed, 11 Jan 2017, miracle ozzoude wrote: > > > > Hello freesurfer, > >> I have several questions about mris_expand command. I know it can be used > >> to expand or shrink a point on a surface by a fixed amount or distance. My > >> questions are: > >> 1) Can it be used to expand the pial surface? if yes, please can you > >> confirm if this is the right script= mris_expand -thickness rh.pial 0.5 > >> rh.newpial. If the script is > >> wrong, please can you give me a directions on how to change it and what > >> new flags to add. > >> 2) When I looked up mris_expand description, -thickness was the only flag > >> displayed. Are there other hidden flags? If yes, where can I find them? > >> 3) After expanding ?lh.white and ?h.pial, what steps of recon-all should > >> i run in other to incorporate my changes? Thank you. > >> > >> Best, > >> Paul

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Re: [Freesurfer] mris_expand command and flags
by Antonin Skoch 11 Jan '17

11 Jan '17

Dear Paul, I am quite surprised that you were successful to estimate correct GM/WM boundary using this tool. As far as I know and looking at the source code, this tool GLOBALLY moves the position of the specified surface to some amount, so it cannot be used to correct local errors. It is used e.g. for estimating the surface ad the midthickness of the gray matter. See e.g. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-July/011152.html Antonin Thanks bruce for your response. I am trying to expand the pial surface (see attached image) in order to estimate the GM/WM boundary properly. I have successfully expanded the white matter but when i tried the mris_expand scripts for pial surface (mris_expand -thickness lh.pial 0.5 lh.newpial), the output looked identical to the input. Please can you direct me on how to successfully achieve this for the pial surface and how to incorporate my changes (expanded surfaces) into recon-all. Thanks. Best, PaulOn Wed, Jan 11, 2017 at 11:37 AM, Bruce Fischl <fis...(a)nmr.mgh.harvard.edu> wrote: > Hi Paul > > it's hard to answer your questions without knowing what you are trying to > achieve > > cheers > Bruce > > On Wed, 11 Jan 2017, miracle ozzoude wrote: > > Hello freesurfer, >> I have several questions about mris_expand command. I know it can be used >> to expand or shrink a point on a surface by a fixed amount or distance. My >> questions are: >> 1) Can it be used to expand the pial surface? if yes, please can you >> confirm if this is the right script= mris_expand -thickness rh.pial 0.5 >> rh.newpial. If the script is >> wrong, please can you give me a directions on how to change it and what >> new flags to add. >> 2) When I looked up mris_expand description, -thickness was the only flag >> displayed. Are there other hidden flags? If yes, where can I find them? >> 3) After expanding ?lh.white and ?h.pial, what steps of recon-all should >> i run in other to incorporate my changes? Thank you. >> >> Best, >> Paul

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mris_expand command and flags
by miracle ozzoude 11 Jan '17

11 Jan '17

Hello freesurfer, I have several questions about mris_expand command. I know it can be used to expand or shrink a point on a surface by a fixed amount or distance. My questions are: 1) Can it be used to expand the pial surface? if yes, please can you confirm if this is the right script= mris_expand -thickness rh.pial 0.5 rh.newpial. If the script is wrong, please can you give me a directions on how to change it and what new flags to add. 2) When I looked up mris_expand description, -thickness was the only flag displayed. Are there other hidden flags? If yes, where can I find them? 3) After expanding ?lh.white and ?h.pial, what steps of recon-all should i run in other to incorporate my changes? Thank you. Best, Paul

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Question regarding missing pial surface
by Piyush Walia 11 Jan '17

11 Jan '17

Hi, I have been working on segmentation of brain scans using Freesurfer and I came across a few scans in which the pial surface does not extend all the way. I have attached two screen shots of the problem I have been encountering. Any suggestion to resolve this kind of error is appreciated. Thanks, Piyush Walia, D.Eng Confidentiality Note: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may include ImageIQ legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately by reply e-mail and destroy copies of the original transmission.

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failed recon
by Marianna Riello 11 Jan '17

11 Jan '17

Hello Freesurfer users, The reconstruction is giving this error (check attached file) with the nifti file, do you know why? Thanks Marianna

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Error message
by shi yao wang 11 Jan '17

11 Jan '17

Dear FS teams: when I running FS, there is a message like this: Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf Is it a real Error message? Cause, it seems that the recon -all process successfully finished. thanks Lawrence

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hippocampal subfields
by Ferdi van de Kamp 11 Jan '17

11 Jan '17

Hi all, I'm trying to perform the longitudinal hippocampal subfields processing on a cluster. When I simply access a core on the cluster directly and use it to run the hippocampal subfields it will run, but if I try to submit the process to the cluster, it will either throw errors as I have pasted below or stop after some registration steps. The recon-all steps have run on the cluster (submitted) without problems. Some notes: As I'm testing things, the data is not in the original folder, so the path names in recon-all log are not correct, but if that is the problem I'd imagine it would be a problem for both submitting and direct processing. Matlab runtime is installed, though in a separate folder, linking it in the way described on the Freesurfer website. The problem persists no matter how much memory I allocate to the process (20GB RAM was the highest I tried). Kind regards, Ferdi van de Kamp #-------------------------------------------- #@# Longitudinal Hippocampal Subfields processing (T1) left Wed Jan 4 03:06:40 CET 2017 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/ Warning: Unable to open display 'localhost:10.0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG of Base Point /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop: line 3: 65931 Segmentation fault (core dumped) kvlAutoCrop.bin "$@" /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop /exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask.mgz 6 >/dev/null: Segmentation fault gzip: /exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in SegmentSubfieldsT1Longitudinal (line 228) MATLAB:badSwitchExpression @#@FSTIME 2017:01:04:03:06:40 /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh N 8 e 12.17 S 0.80 U 3.63 P 36% M 680932 F 530 R 118193 W 0 c 10055 w 5994 I 439360 O 194448 L 4.58 4.59 4.59 @#@FSLOADPOST 2017:01:04:03:06:52 /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh N 8 4.72 4.62 4.60 #-------------------------------------------- #@# Longitudinal Hippocampal Subfields processing (T1) right Wed Jan 4 03:06:52 CET 2017 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/ Warning: Unable to open display 'localhost:10.0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG of Base Point /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop: line 3: 66086 Segmentation fault (core dumped) kvlAutoCrop.bin "$@" /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop /exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_right//hippoAmygBinaryMask.mgz 6 >/dev/null: Segmentation fault gzip: /exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_right//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in SegmentSubfieldsT1Longitudinal (line 228) MATLAB:badSwitchExpression @#@FSTIME 2017:01:04:03:06:52 /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh N 8 e 6.50 S 0.64 U 3.59 P 65% M 678904 F 1 R 119401 W 0 c 3877 w 3509 I 65600 O 194416 L 4.72 4.62 4.60 @#@FSLOADPOST 2017:01:04:03:06:58 /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh N 8 4.84 4.65 4.61 If you have used results from this software for a publication, please cite: Iglesias J.E., Van Leemput K., Augustinack J., Insausti R., Fischl B., Reuter M., Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases, Neuroimage, in press. http://dx.doi.org/10.1016/j.neuroimage.2016.07.020

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