Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

how to register my surface label to the epi volume
by limeilingcheng 29 Apr '13

29 Apr '13

Hi all, Now I got some results by freesurfer, finally I selected two vertexs which the coordinate values were(Talx=-40.5, Taly= -14.5,Talz=-12.7 and Tal x=55.1, Tal y=-23.9, Tal z=-1.8 ), the corresponding regions reported by freesurfer were left superiortemporal and right superiortemporal. In the following step, I want to make the left and right superiortemporal as ROIs and observe the functional connectivity between the ROIs and the voxels in the whol brain. However, it is difficult for me to understand how to register this surface label to the epi volume. and how to created the masks in FSL using the labels and Harvard-Oxford atlas to ensure the correct anatomical location. 2013-04-29 limeilingcheng

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Re: [Freesurfer] adding grey matter
by Claudia Dacquino 29 Apr '13

29 Apr '13

The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Claudia > > can you describe the problems? And cc the list so that others can help? > thanks > > Bruce > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? >> >> I'm trying to upload data, but I've problems with your server. >> Cheers, >> Claudia >> >> >> 2013/4/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Claudia >> >> it really depends on the individual case and what's causing the >> exclusion. Does the wm.mgz look accurate? If so, you may have a >> topological defect that is being fixed incorrectly. Usually we >> focus on fixing the white boundary and that will also correct >> the pial. You can set the expected gray matter intensities in >> the xopts file, but that is rarely necessary and only if your >> gray matter looks very different than the sequences we are used >> to. >> >> If you can't sort it out feel free to upload you data. >> >> cheers >> Bruce >> >> >> On Mon, 29 Apr 2013, Claudia Dacquino wrote: >> >> Hi Freesurfers,I have a question about pial editing. >> I have some reconructions in which there's a lot of >> grey matter excluded, >> and consequently white metter too. I did correct >> these images manually by >> control points editing, and then autorecon2-cp >> autorecon3, but some cortical >> grey matter continues to not be included in the pial >> surface, and I have >> white matter areas that are still not included in >> either the pial or white >> matter boundaries. >> Is there anyother ethods for adding grey matter in >> the pial surfeces other >> than editing control points (such as by editing >> voxels to add grey matter), >> or something like that? >> Thanks for your help. >> Claudia >> >> >> >> >> 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<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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Trouble with flip angle map when computing T1 maps
by Johannes Klein 29 Apr '13

29 Apr '13

Dear all, I've had some trouble feeding a flip angle map into mri_ms_fitparms. If I don't provide it, the estimates look fine; with the FA map however, all brain voxels in the resultant T1.mgz are set to 50000. I've checked that all images are registered, and the nominal values in the FA map look good to me. I'm running Freesurfer 5.1.0 Here's the output: johannes$ mri_ms_fitparms -afi B1Map_in_degrees.mgz DESPOT_FA_18.mgz DESPOT_FA_4.mgz t1_fs using flip angle map DESPOT1HIFI_B1Map_in_degrees.mgz with nominal value 60.0 degrees reading DESPOT_FA_18.mgz...TE = 3.70, TR = 8.00, flip angle = 18.00 reading DESPOT_FA_4.mgz...TE = 3.70, TR = 8.00, flip angle = 4.00 using 2 FLASH volumes to estimate tissue parameters. parameter rms = 77.083 non-equal flip_angle found for the volume 1. Flip_angle is set to zero. TR = 8.00, TE = 3.70, Flip_angle = 0.00 are used writing PD estimates to t1_fs/PD.mgz... writing T1 estimates to t1_fs/T1.mgz... writing residual sse to t1_fs/sse.mgz... writing faf map to t1_fs/faf.mgz... writing synthetic images to t1_fs/flash18.mgz... writing registration matrix to t1_fs/flash18.lta... writing synthetic images to t1_fs/flash4.mgz... writing registration matrix to t1_fs/flash4.lta... parameter estimation took 1 minutes and 18 seconds. Any thoughts on what I'm doing wrong? Thanks for your help, Johannes

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Re: [Freesurfer] adding grey matter
by Claudia Dacquino 29 Apr '13

29 Apr '13

Hi Bruce, I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Claudia Dacquino <claudia.dacquino(a)gmail.com> > Hi Bruce, > I think wm.mgz it's accurate enough, but what you mean? > I'm trying to upload data, but I've problems with your server. > Cheers, > Claudia > > > 2013/4/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Hi Claudia >> >> it really depends on the individual case and what's causing the >> exclusion. Does the wm.mgz look accurate? If so, you may have a topological >> defect that is being fixed incorrectly. Usually we focus on fixing the >> white boundary and that will also correct the pial. You can set the >> expected gray matter intensities in the xopts file, but that is rarely >> necessary and only if your gray matter looks very different than the >> sequences we are used to. >> >> If you can't sort it out feel free to upload you data. >> >> cheers >> Bruce >> >> >> On Mon, 29 Apr 2013, Claudia Dacquino wrote: >> >> Hi Freesurfers,I have a question about pial editing. >>> >>> I have some reconructions in which there's a lot of grey matter excluded, >>> and consequently white metter too. I did correct these images manually by >>> control points editing, and then autorecon2-cp autorecon3, but some >>> cortical >>> grey matter continues to not be included in the pial surface, and I have >>> white matter areas that are still not included in either the pial or >>> white >>> matter boundaries. >>> Is there anyother ethods for adding grey matter in the pial surfeces >>> other >>> than editing control points (such as by editing voxels to add grey >>> matter), >>> or something like that? >>> Thanks for your help. >>> Claudia >>> >>> >>> >> >> 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<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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adding grey matter
by Claudia Dacquino 29 Apr '13

29 Apr '13

Hi Freesurfers, I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia

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question on mri_segstats
by Fang CAO 29 Apr '13

29 Apr '13

Hi, I have some question on mri_segstats 1) --seg-erode Nerodes Is it the size of the window for erosion? 2) --robust percent Is it the percentage of tissue in each voxel? 3) If I want to combine Left and Right together and calculate the statistics, for example the mean and std of the "Left/Right Caudate", how to do that? Thank you, Fang

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Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all
by Lukas.Scheef＠ukb.uni-bonn.de 28 Apr '13

28 Apr '13

Dear Matt! Many thanks for your help! I will try it... All the best, Luke Matt Glasser <matt(a)ma-tea.com> An 28.04.2013 17:26 <Lukas.Scheef(a)ukb.uni-bonn.de> Kopie <freesurfer(a)nmr.mgh.harvard.edu> Thema Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all Those pipelines will hopefully be available publicly this summer. The relevant code is this though: recon-all -i <input image> -subjid $SubjectID -sd $SubjectDIR -motioncor -talairach -nuintensitycor -normalization mri_convert <input brain extracted image> "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz --conform mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz "$SubjectDIR"/"$SubjectID"/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca "$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca "$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta "$SubjectDIR"/"$SubjectID"/mri/T1.mgz "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 –autorecon3 Basically, you make mri_em_register give a more accurate registration (this is typically what fails when you get a bad brain extraction from FreeSurfer in my experience), and then use FreeSurfer's own very nice brain extraction algorithm with the better registration to get the final brain mask. Peace, Matt. From: <Lukas.Scheef(a)ukb.uni-bonn.de> Date: Sunday, April 28, 2013 4:21 AM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all Hi Matt! Refering to an older mail from 06 Mar 2013 I would be also interested to integrate BET-results for the initial registration step. Using the -B option in BET I get very robust results. You recommend: "... using the BET extracted image instead of the image with skull for the initial registration step, and then you can use mri_watershed on the original image..." How can this be implemented practically? Are the HCP protocols / pipelines you mentioned later available for the research community? Many thanks in advance, Luke Matt Glasser Wed, 06 Mar 2013 16:09:44 -0800 I would check the mri_em_register registrations of the step that immediately precedes mri_watershed (and produces talairach_with_skull.lta). We found that most of the variability and failures occurred in this step, and mri_watershed itself is a very robust brain extraction algorithm when it is given an accurate registration (my experience with BET is that it is probably not the best tool for getting very accurate brainmasks and sometimes takes away too much). I would recommend using the BET extracted image instead of the image with skull for the initial registration step, and then you can use mri_watershed on the original image and get good results every time. This is the type of strategy we use in the HCP Pipelines (except we use something more robust than BET for the initial mask). Note that the "talairach" registration (done by the -talairach step with the talairach_avi tool) has nothing to do with the registration that precedes brain extraction. Perhaps it should is more robust and should be used, but the affine would have to be converted to the correct format. Peace, Matt. On 3/6/13 3:53 PM, "Bruce Fischl" <fis...(a)nmr.mgh.harvard.edu> wrote: >you can use > >mri_convert -rl ... > >to reslice the output of bet so that it has the same geometry as the rest >of our stream > >cheers >Bruce > >On Wed, 6 Mar 2013, Winter, Warren wrote: > >> Hi again, >> We have had some suboptimal results from FreeSurfer's skullstripping >>algorithm, even after iteratively trying different >> watershed thresholds and after checking the quality of Talairach >>registration. The results are pretty good, but often leave >> some dura matter and bits of neck behind whose higher intensity values, >>I believe, may end up skewing recon-all's later >> estimation of the range of intensity values within grey matter, and >>consequently compromising the accuracy of pial surface >> estimation. >> >> FSL's BET, however, seems to do a better job of extracting the brain, >>at least for our dataset. So, I was wondering if I >> might be able to skip over mri_watershed and feed autorecon2 and >>autorecon3 a brainmask.mgz file created using BET. I tried >> this procedure: >> >> >> 1) mri_convert <path/to/T1dcm> T1.nii.gz >> 2) bet T1.nii.gz BET_brainmask.nii.gz -A >> 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz >> 4) recon-all -s <subjid> -autorecon1 -noskullstrip >> 5) mv BET_brainmask.nii.gz ./<subjid>/mri/brainmask.mgz >> 6) recon-all -s <subjid> -autorecon2 -autorecon3 >> >> And I got this error message, right after normalization2: >> >> " >> #@# Mask BFS Tue Mar 5 22:52:05 EST 2013 >> >>/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/20 >>12_bet/mri >> >> mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz >> >> threshold mask volume at 5 >> ERROR: dimension mismatch between source and mask >> Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 >>x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s 2012_bet exited with ERRORS at Tue Mar 5 22:52:06 EST 2013 >> " >> >> I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match >>those of brainmask.mgz, resulting during normalization2 >> in a mismatch between brain.mgz and brainmask.mgz. Does that seem >>right, and is there a possible workaround? >> >> Thank you! >> >> Warren >> >> -- >> Warren Winter >> Research Coordinator >> Boston Children's Hospital >> Sheridan Laboratory of Cognitive Neuroscience >> Division of Developmental Medicine >> 1 Autumn Street, AU 650 >> Boston, MA 02215 >> 857-218-5224 >> >> >>_______________________________________________ >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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://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.

1 0

Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all
by Lukas.Scheef＠ukb.uni-bonn.de 28 Apr '13

28 Apr '13

Hi Matt! Refering to an older mail from 06 Mar 2013 I would be also interested to integrate BET-results for the initial registration step. Using the -B option in BET I get very robust results. You recommend: "... using the BET extracted image instead of the image with skull for the initial registration step, and then you can use mri_watershed on the original image..." How can this be implemented practically? Are the HCP protocols / pipelines you mentioned later available for the research community? Many thanks in advance, Luke Matt Glasser Wed, 06 Mar 2013 16:09:44 -0800 I would check the mri_em_register registrations of the step that immediately precedes mri_watershed (and produces talairach_with_skull.lta). We found that most of the variability and failures occurred in this step, and mri_watershed itself is a very robust brain extraction algorithm when it is given an accurate registration (my experience with BET is that it is probably not the best tool for getting very accurate brainmasks and sometimes takes away too much). I would recommend using the BET extracted image instead of the image with skull for the initial registration step, and then you can use mri_watershed on the original image and get good results every time. This is the type of strategy we use in the HCP Pipelines (except we use something more robust than BET for the initial mask). Note that the "talairach" registration (done by the -talairach step with the talairach_avi tool) has nothing to do with the registration that precedes brain extraction. Perhaps it should is more robust and should be used, but the affine would have to be converted to the correct format. Peace, Matt. On 3/6/13 3:53 PM, "Bruce Fischl" <fis...(a)nmr.mgh.harvard.edu> wrote: >you can use > >mri_convert -rl ... > >to reslice the output of bet so that it has the same geometry as the rest >of our stream > >cheers >Bruce > >On Wed, 6 Mar 2013, Winter, Warren wrote: > >> Hi again, >> We have had some suboptimal results from FreeSurfer's skullstripping >>algorithm, even after iteratively trying different >> watershed thresholds and after checking the quality of Talairach >>registration. The results are pretty good, but often leave >> some dura matter and bits of neck behind whose higher intensity values, >>I believe, may end up skewing recon-all's later >> estimation of the range of intensity values within grey matter, and >>consequently compromising the accuracy of pial surface >> estimation. >> >> FSL's BET, however, seems to do a better job of extracting the brain, >>at least for our dataset. So, I was wondering if I >> might be able to skip over mri_watershed and feed autorecon2 and >>autorecon3 a brainmask.mgz file created using BET. I tried >> this procedure: >> >> >> 1) mri_convert <path/to/T1dcm> T1.nii.gz >> 2) bet T1.nii.gz BET_brainmask.nii.gz -A >> 3) mri_convert BET_brainmask.nii.gz BET_brainmask.mgz >> 4) recon-all -s <subjid> -autorecon1 -noskullstrip >> 5) mv BET_brainmask.nii.gz ./<subjid>/mri/brainmask.mgz >> 6) recon-all -s <subjid> -autorecon2 -autorecon3 >> >> And I got this error message, right after normalization2: >> >> " >> #@# Mask BFS Tue Mar 5 22:52:05 EST 2013 >> >>/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/20 >>12_bet/mri >> >> mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz >> >> threshold mask volume at 5 >> ERROR: dimension mismatch between source and mask >> Linux rc-thunderball 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 >>x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s 2012_bet exited with ERRORS at Tue Mar 5 22:52:06 EST 2013 >> " >> >> I'm guessing that the dimensions of norm.mgz and aseg.mgz didn't match >>those of brainmask.mgz, resulting during normalization2 >> in a mismatch between brain.mgz and brainmask.mgz. Does that seem >>right, and is there a possible workaround? >> >> Thank you! >> >> Warren >> >> -- >> Warren Winter >> Research Coordinator >> Boston Children's Hospital >> Sheridan Laboratory of Cognitive Neuroscience >> Division of Developmental Medicine >> 1 Autumn Street, AU 650 >> Boston, MA 02215 >> 857-218-5224 >> >> >>_______________________________________________ >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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer on Ubuntu/Mint/Debian?
by Graham Wideman 27 Apr '13

27 Apr '13

Hi all, My "System Recommendations?" post of a few days ago got some useful and interesting input on hardware and software. For Linux flavor, Nick S. commented that Centos was the OS of choice at home base. My question for today -- is Ubuntu, Mint or Debian equally satisfactory for Freesurfer and related software, both in terms of installation, and of use? Or are awkward obstacles encountered? Thanks, Graham

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tracall longitudinal default options
by vbrunsch＠nmr.mgh.harvard.edu 26 Apr '13

26 Apr '13

Hi all! I am almost ready to do my first longitudinal run with Tracula. I guess that for the remaining insecurities it is probably best to stick with the default options but I'd like to be more confident with it and just wanted to ask which option to choose and why or why not: My config file contains information about two time points of 39 subjects. - Perform "Registration-based B0-inhomogeneity compensation" If I understand correctly, although I would have the fieldmap information this step (as well as BET) is not necessary as I can use the respective T1 weighted image (usemaskanat=1) for registration? - Number of sticks in the ball-stick model Since last month it is possible to change the default value of 2. Would you recommend a higher value? That would give me more information also about crossing fibers, right? But if so, which value would be reasonable and why? - MCMC burn-in iterations (default:200), iterations (default:7500) and frequency (default:5) (Why are we allowed to change these options at all?) Thank you! Best, Vincent

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