Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

Re: [Freesurfer] wm.mgz manual editing
by Antonin Skoch 02 Mar '17

02 Mar '17

Dear Eli, I have looked at your data. Due to the fact that the white matter does have intensity well below 110 in the large portion of white matter area under your problematic spot, I think that instead of editing wm.mgz the better way in your case would be to add some control points to the white matter surrounding region 112,49,128. Btw, it seems that the white matter has generally very inhomogeneus signal intensity. Does not the image originate from the subjects with some kind of severe pathology of white matter? What is the large hypointense spot centered at 102,64,126? This causes large hole in wm.mgz But there are other hypointensities, for example at 96,77,151. Does not your problematic spot correspond to some pathology? Regards, Antonin Bruce, Main problem area that I can see is at coordinates [104,42,124].My first attempt, I don't think I had the recon editing box checked when I was editing the white matter, but I used a brush value of 255. My second attempt I painted over the same voxels but with the recon editing box checked. Both times, after saving wm.mgz I ran the following command: "recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`" Only thing different from the guide is I specify a different subject directory. Below are download links for the important files, let me know if you would like to look at anything else. If you look at wm.mgz along with the rh.white, you can see the surface doesn't appear to acknowledge my edit. 001.mgz: https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc recon-all.logs.tar.gz: https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji brainmask+surf+wm.tar.gz https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3 Thanks tremendously for your time, Eli > ------------------------------ > > Message: 4 > Date: Wed, 1 Mar 2017 16:39:33 -0500 (EST) > From: Bruce Fischl <fis...(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] wm.mgz manual editing > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.1703011… > > > Content-Type: text/plain; charset="utf-8" > > Hi Eli > > hmm, maybe you should just upload the subject and email us the voxel > coords you are talking about? > > Also, in general it is hard for us to help you unless you include more > information. What exact command did you run? What was the screen output? > What was in the recon-all.log? > > cheers > Bruce > > > On Wed, 1 > Mar 2017, Rockers, Elijah D. wrote: > > > Couple of questions: > > > > 1) > > > > I edited wm.mgz following the instructions in the wiki guide, but it did > > not change anything after reconstruction. I am still using 5.3 right > > now, so maybe the guide is wrong for me. What is the brush value > > supposed to be? I used 255 but it did not extend the white matter > > surface to include my edits. I checked to make sure they saved > > correctly, they did, but the surface didn't change. Any ideas? > > > > 2) > > > > The reason I am editing wm.mgz is to try to include some cortex that was > > left out of the pial surface. I don't suppose there's any way to fix > > this without editing wm.mgz? Because the white matter surface actually > > looks fine the way it is. > > > > Thanks, > > Eli > > > > Houston Methodist. Leading Medicine. > >

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Re: [Freesurfer] recon-all exited with error.
by Antonin Skoch 02 Mar '17

02 Mar '17

Dear Paul, the slash problem prevents to properly create symbolic link to fsaverage in your SUBJECTS_DIR. Then, the mri_label2label could not find the fsaverage label file since symbolic link for fsaverage does not exist, hence produces the error.log you are attaching. Regards, Antonin Thanks Antonin. Also, I got this error.log file in my label folder. Do you think it is due to the slash problem? Best, PaulOn Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch <a...(a)ikem.cz> wrote: > Dear Paul, > > I suppose the clue is following messages from your recon-all.log file: > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/ > > and > > cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - > > ln: failed to create symbolic link './fsaverage': File exists > > The problem is that your FREESURFER_HOME contains slash in the end. Remove it > and rerun relevant part of recon-all. It should work then. > > Antonin > > > > > Hello Freesurfer, > I was running recon-all in steps (recon-all -autorecon1, recon-all > -autorecon2, and recon-all - -T2 /T2 volume -T2pial autorecon3). However, > it exited with error during the BA_exvivo labels part of autorecon3 (please > see attached recon-all.log file). Please, how can I fix it? Thanks > Best, > Paul

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Re: [Freesurfer] wm.mgz manual editing
by Rockers, Elijah D. 02 Mar '17

02 Mar '17

Bruce, Main problem area that I can see is at coordinates [104,42,124]. My first attempt, I don't think I had the recon editing box checked when I was editing the white matter, but I used a brush value of 255. My second attempt I painted over the same voxels but with the recon editing box checked. Both times, after saving wm.mgz I ran the following command: "recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`" Only thing different from the guide is I specify a different subject directory. Below are download links for the important files, let me know if you would like to look at anything else. If you look at wm.mgz along with the rh.white, you can see the surface doesn't appear to acknowledge my edit. 001.mgz: https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc recon-all.logs.tar.gz: https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji brainmask+surf+wm.tar.gz https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3 Thanks tremendously for your time, Eli > ------------------------------ > > Message: 4 > Date: Wed, 1 Mar 2017 16:39:33 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] wm.mgz manual editing > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.1703011… > > Content-Type: text/plain; charset="utf-8" > > Hi Eli > > hmm, maybe you should just upload the subject and email us the voxel > coords you are talking about? > > Also, in general it is hard for us to help you unless you include more > information. What exact command did you run? What was the screen output? > What was in the recon-all.log? > > cheers > Bruce > > > On Wed, 1 > Mar 2017, Rockers, Elijah D. wrote: > > > Couple of questions: > > > > 1) > > > > I edited wm.mgz following the instructions in the wiki guide, but it did > > not change anything after reconstruction. I am still using 5.3 right > > now, so maybe the guide is wrong for me. What is the brush value > > supposed to be? I used 255 but it did not extend the white matter > > surface to include my edits. I checked to make sure they saved > > correctly, they did, but the surface didn't change. Any ideas? > > > > 2) > > > > The reason I am editing wm.mgz is to try to include some cortex that was > > left out of the pial surface. I don't suppose there's any way to fix > > this without editing wm.mgz? Because the white matter surface actually > > looks fine the way it is. > > > > Thanks, > > Eli > > > > Houston Methodist. Leading Medicine. > > Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital 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] recon-all exited with error.
by Antonin Skoch 02 Mar '17

02 Mar '17

Dear Paul, I suppose the clue is following messages from your recon-all.log file: FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/ and cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - ln: failed to create symbolic link './fsaverage': File exists The problem is that your FREESURFER_HOME contains slash in the end. Remove it and rerun relevant part of recon-all. It should work then. Antonin Hello Freesurfer, I was running recon-all in steps (recon-all -autorecon1, recon-all -autorecon2, and recon-all - -T2 /T2 volume -T2pial autorecon3). However, it exited with error during the BA_exvivo labels part of autorecon3 (please see attached recon-all.log file). Please, how can I fix it? Thanks Best, Paul

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Re: [Freesurfer] apply CVS morph to a list of coordinates
by Donos, Cristian 02 Mar '17

02 Mar '17

Hi Lilla, It’ s a Mac Pro with 64Gb Ram. Best, Cristian

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recon-all exited with error.
by miracle ozzoude 02 Mar '17

02 Mar '17

Hello Freesurfer, I was running recon-all in steps (recon-all -autorecon1, recon-all -autorecon2, and recon-all - -T2 /T2 volume -T2pial autorecon3). However, it exited with error during the BA_exvivo labels part of autorecon3 (please see attached recon-all.log file). Please, how can I fix it? Thanks Best, Paul

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Re: [Freesurfer] Strange wm error
by Antonin Skoch 02 Mar '17

02 Mar '17

Dear Mel, if your recon in 5.3 version finished without error, there must be files lh.orig.nofix and rh.orig.nofix present in the subj_id/surf directory. This type of error is most frequently due to incorrectly fixed topological defect. The original wm.mgz and orig.nofix errors can be quite a large distance from the area of your white surface error. The fix you are referring to (editing the wm.mgz) makes perfect sense in this context. Antonin That does not make sense. Can you run this subject in v6? If the problem goes away, then there is not much we can do about it in 5.3 On 02/28/2017 05:27 AM, Melanie Ganz wrote: > Hi Doug, > > the orig looks fine and we cannot see a file orig.nofix in the subject > dirs. We still use v5.3. > > But what we tried now for another similar subject was to remove > falsely labelled white matter in dura which was far away, but that > fixed the white matter errors so far inside the brain. Does that make > any sense to you why that helps? > > Cheers, > Mel > > > > On 27-02-2017 5:23, Douglas Greve wrote: >> >> Hi Mel, how does the orig or orig.nofix look? >> >> >> On 2/24/17 9:21 AM, Melanie Ganz wrote: >>> Dear list, >>> >>> we are experiencing a strange wm surface error that we are not quite >>> sure about how to fix. The errors is at a location where the wm.mgz >>> look absolutely fine as well as the brainmask.mgz. Also the >>> intensities in the norm.mgz look fine. >>> >>> Please find 6 pics showing the error highlighted by the cursor on >>> the brainmask.mgz and the wm.mgz in all three views. >>> >>> Cheers, >>> Mel

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Re: [Freesurfer] FreeSurfer v6.0 in an AWS cloud configuration (hipposubfield/brainstem failures)
by Antonin Skoch 02 Mar '17

02 Mar '17

Dear Randy, from the log file you provided it seems that both of your jobs exited on the insufficient RAM. You should check your available RAM resources. brainstem-structures: std::bad_alloc hippocampal subfiels: Out of memory. Regards, Antonin Hello FreeSurfer Experts/Community, I am currently working with NITRC (as a novice user) to build and investigate the operability of FreeSurfer v6.0 in their Computational Environment (NITRC-CE). We have been able to get a "recon-all" run to work, but we are failing to get the sub-calls -hippocampal-subfields-T1 https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields -brainstem-structures https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures ... to run correctly / run to completion. We are aware that Matlab Runtime needed to be installed, and a partial completion is a testament to that. However, they seem to choke near the end, and it would be good to get some insight as to why. To wit, I am pasting the last dozen or so lines from each (see below) in the hopes we might get a tip or a comment from this forum. For this exercise, we used an ADNI subject (N3-corrected, downloaded from ADNI/LONI as *.nii) The syntax/command I used was: recon-all -s ADNI_003_S_2374_m00 \ -i $SUBJECTS_DIR/ADNI_003_S_2374__MRI_m00__EMCI-EMCI__20110506__S108554_I235638.nii \ -all -hippocampal-subfields-T1 -brainstem-structures I'm simply not sure if there's something wrong with my syntax or if there is something else we're missing. Any help would be greatly appreciated, and I can pass on what is shared to my developer (and so that eventually everyone might begin to have a vetted version of v6.0 using NITRC-CE if they wish in the future) -Randy From: /scripts/brainstem-structures _______________________________________________________________ <<<start excerpt>>> Resolution level 3 iteration 3 deformation iterations 8 Did one deformation step of max. 1.6685e-05 voxels in 8.485 seconds minLogLikelihoodTimesPrior = 7.5772e+06 Resolution level 3 iteration 3 deformation iterations 9 Did one deformation step of max. 5.3959e-05 voxels in 3.4185 seconds minLogLikelihoodTimesPrior = 7.5772e+06 Resolution level 3 iteration 3 deformation iterations 10 Did one deformation step of max. 0 voxels in 6.782 seconds minLogLikelihoodTimesPrior = 7.5772e+06 maximalDeformation is too small; stopping Fitting mesh to image data mask took 919.7675 seconds numberOfLabels: 21 Rasterizing mesh...here: 21 here2: 21 done Error using kvlGEMSMatlab std::bad_alloc Error in kvlRasterizeAtlasMesh (line 11) Error in segmentSubject (line 1151) ______________________________________________________ <<<end of logfile>>>______________________________________________________ ______________________________________________________ From: /scripts/hippocampal-subfields-T1 _______________________________________________________________ <<<start excerpt>>> Making alveus map to reduced label 3 -------------- Making Left-Lateral-Ventricle map to reduced label 4 -------------- Making hippocampal-fissure map to reduced label 5 -------------- Making Left-Pallidum map to reduced label 6 -------------- Making Left-Putamen map to reduced label 7 -------------- Making Left-Caudate map to reduced label 8 -------------- Making Left-Thalamus-Proper map to reduced label 9 -------------- Making Left-choroid-plexus map to reduced label 10 -------------- Making Left-VentralDC map to reduced label 11 -------------- Making Left-Accumbens-area map to reduced label 12 -------------- Making Unknown map to reduced label 13 Computing hyperparameters for estimation of Gaussian parameters Estimating typical intensities of alveus numberOfLabels: 13 Rasterizing mesh...here: 13 here2: 13 done Error using double Out of memory. Type HELP MEMORY for your options. Error in segmentSubjectT1_autoEstimateAlveusML (line 834) MATLAB:nomem ______________________________________________________ <<<end of logfile>>>

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Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data
by Xiuyi Wang 02 Mar '17

02 Mar '17

Hi, I am learning Group Analysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis These are the commands that I typed: freeview -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot :annot_outline=1: overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_thres hold=4,5 -viewport 3d But I got an error message "Unrecognized sub-option flag ‘annot_outline’ " when running this command to visualize uncorrected significance map with freeview. Douglas Greve told me it's because the outline only works on 6.0. I am wondering what commands should I use to visualize the uncorrected significance map with freeview 5.3. Thank you for your help. > On 10 February 2017 at 17:47, Douglas Greve <greve(a)nmr.mgh.harvard.edu> > wrote: > >> The outline only works on 6.0 >> >> On 2/10/17 11:57 AM, Xiuyi Wang wrote: >> >> Hi, >> >> >> I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. >> >> >> I followed the detailed instruction on the tutorial website. >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >> >> >> But I got an error message when running this command to visualize >> uncorrected significance map with freeview. >> >> >> This is the command I typed: >> >> freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:a >> nnot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness >> -age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d >> >> >> >> I received this error message: >> >> Unrecognized sub-option flag ‘annot_outline’ >> >> >> I browsed the internet and found that “That option is only available in >> the development version of freeview. You can try removing :annot_ouline=1 >> from the command-line and turn it on manually from the GUI.” >> >> >> So I deleted “:annot_outline=1” and the command line is : >> >> freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o >> verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 >> -viewport 3d >> >> >> >> But I received another error message: >> >> Did not find any volume geometry information in the surface. >> >> >> I found some researchers also have encountered this problem, but it has >> not been solved. >> >> >> Could you please tell me the solution of the problem? >> >> Thank you for your suggestion. >> >> >> Best. >> >> Xiuyi Wang >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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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White matter segmentation
by yusif Al-kheder 02 Mar '17

02 Mar '17

Hello, Is it possible to segment the brain into these parts if possible using freesurfer; Cerebellum Midbrain Pons Medulla Oblongata Hippocampus Thalamus Hypothalamus Anterior and Posterior Commissura Corpus Callosum Hypophysis Dura Mater Youssif

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Freesurfer March 2017