Freesurfer

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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.

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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

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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Re: [Freesurfer] Problems visualizing hippocampal subfields
by Erin Walsh 26 Apr '13

26 Apr '13

Thanks all! Very helpful. Happy Friday, Erin -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh(a)gmail.com On Fri, Apr 26, 2013 at 4:43 PM, Marcos Martins da Silva < marcosmds(a)terra.com.br> wrote: > ** > I guess during the copy/paste something not clearly visible was included > and resulted in error. If you pay attention to freeview's info panel you > will see each file loading along the time. Depending on the slices you are > seeing at axial, sagital and coronal views you will see just a few colored > points but after some time all the subfields will appear. I did not check > the time but the process also takes about 5-10 minutes in my environment.. > > > Em Sex, 2013-04-26 às 15:58 -0500, Erin Walsh escreveu: > > Hi Eugenio and Zeke, > > > I attempted to enter the command line in again (re-copying/pasting) from > the website. Perhaps I had entered in an error somewhere before because > after 10+min, both volumes were able to load with the color maps. I will > try replicating this to ensure it works. > > > Apologies for my previous premature email-- I had tried the command a > few times with the same errors, clearly I made an error somewhere. > > > > Just a few other questions: > > > The "invalid drawable" message: Is that standard or is something truly > awry with the command? It continues to appear. > > > Does it normally take 10+min for the segmentation maps to appear? > > > > Many thanks, > > Erin > > > -- > Erin Walsh, Ph.D. > Postdoctoral Research Associate > University of Wisconsin-Madison > Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> > 6001 Research Park Blvd. > Madison, WI 53719 > edubwalsh(a)gmail.com > > > > On Fri, Apr 26, 2013 at 3:08 PM, Erin Walsh <edubwalsh(a)gmail.com> wrote: > > Thank you both! Much appreciated. > > > Best, > > Erin > > > > -- > Erin Walsh, Ph.D. > Postdoctoral Research Associate > University of Wisconsin-Madison > Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> > 6001 Research Park Blvd. > Madison, WI 53719 > edubwalsh(a)gmail.com > > > > > On Fri, Apr 26, 2013 at 3:07 PM, Juan Eugenio Iglesias < > iglesias(a)nmr.mgh.harvard.edu> wrote: > > The visualization Erin is shooting for actually weights the colors of > each subfield by their probabilities, generating a nice, smooth, soft > segmentation. > Erin, Zeke is looking into the problem and will get back to you > (hopefully) soon. > Cheers, > /Eugenio > > > > > On Fri, 2013-04-26 at 16:03 -0400, Louis Nicholas Vinke wrote: > > Hi Erin, > > Try this command after cd into the subject's mri dir, treating the hippo > > subfields as volumes. > > > > freeview nu.mgz posterior_Left-Hippocampus.mgz:colormap=heat > > posterior_Right-Hippocampus.mgz:colormap=heat > > > > The labels are probability maps (Eugenio correct me if wrong) so > > displaying with the FS look-up table makes them look like confetti. As a > > heatmap makes more sense. > > -Louis > > > > On Fri, 26 Apr 2013, Erin Walsh wrote: > > > > > Hi Freesurfers, > > > > > > I have been experiencing issues with visualizing the hippocampal > subfields. > > > I have attempted to try fixes I found in previous threads with no > success. > > > Hopefully someone here may have a solution. > > > > > > Thanks for any help! > > > > > > Erin > > > > > > > > > > > > Freesurfer Info: > > > > > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > > > Kernel info: Darwin 12.2.0 x86_64 > > > > > > > > > Error Message: > > > > > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% freeview nu.mgz \ > > > > > > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ > > > > > > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ > > > > > > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt > > > > > > 2013-04-26 14:19:16.237 freeview.bin[42704:f07] invalid drawable > > > > > > 2013-04-26 14:19:16.238 freeview.bin[42704:f07] invalid drawable > > > > > > 2013-04-26 14:19:16.250 freeview.bin[42704:f07] invalid drawable > > > > > > 2013-04-26 14:19:16.251 freeview.bin[42704:f07] invalid drawable > > > > > > 2013-04-26 14:19:16.262 freeview.bin[42704:f07] invalid drawable > > > > > > 2013-04-26 14:19:16.263 freeview.bin[42704:f07] invalid drawable > > > > > > 2013-04-26 14:19:16.274 freeview.bin[42704:f07] invalid drawable > > > > > > 2013-04-26 14:19:16.275 freeview.bin[42704:f07] invalid drawable > > > > > > QObject::connect: Connecting from QAbstractButton::toggled(bool) to > COMPAT > > > slot (QGroupBox::setShown(bool)) > > > > > > QObject::connect: Connecting from QAbstractButton::toggled(bool) to > COMPAT > > > slot (QGroupBox::setShown(bool)) > > > > > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels > > > posterior_left_* posterior_Left-Hippocampus.mgz \ > > > > > > -p-labels: Command not found. > > > > > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels > > > posterior_right_* posterior_Right-Hippocampus.mgz \ > > > > > > -p-labels: Command not found. > > > > > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-prefix > posterior_ > > > -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt > > > > > > -p-prefix: Command not found. > > > > > > > > > > > > -- > > > Erin Walsh, Ph.D. > > > Postdoctoral Research Associate > > > University of Wisconsin-Madison > > > Department of Psychiatry: Abercrombie Lab > > > 6001 Research Park Blvd. > > > Madison, WI 53719 > > > edubwalsh(a)gmail.com > > > > > > > > > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhD > http://www.jeiglesias.com > iglesias(a)nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > Department of Radiology, MGH, Harvard Medical School > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > > > > > > 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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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Re: [Freesurfer] Problems visualizing hippocampal subfields
by Erin Walsh 26 Apr '13

26 Apr '13

Hi Eugenio and Zeke, I attempted to enter the command line in again (re-copying/pasting) from the website. Perhaps I had entered in an error somewhere before because after 10+min, both volumes were able to load with the color maps. I will try replicating this to ensure it works. Apologies for my previous premature email-- I had tried the command a few times with the same errors, clearly I made an error somewhere. Just a few other questions: The "invalid drawable" message: Is that standard or is something truly awry with the command? It continues to appear. Does it normally take 10+min for the segmentation maps to appear? Many thanks, Erin -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh(a)gmail.com On Fri, Apr 26, 2013 at 3:08 PM, Erin Walsh <edubwalsh(a)gmail.com> wrote: > Thank you both! Much appreciated. > > Best, > > Erin > > > -- > Erin Walsh, Ph.D. > Postdoctoral Research Associate > University of Wisconsin-Madison > Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> > 6001 Research Park Blvd. > Madison, WI 53719 > edubwalsh(a)gmail.com > > > On Fri, Apr 26, 2013 at 3:07 PM, Juan Eugenio Iglesias < > iglesias(a)nmr.mgh.harvard.edu> wrote: > >> The visualization Erin is shooting for actually weights the colors of >> each subfield by their probabilities, generating a nice, smooth, soft >> segmentation. >> Erin, Zeke is looking into the problem and will get back to you >> (hopefully) soon. >> Cheers, >> /Eugenio >> >> >> >> On Fri, 2013-04-26 at 16:03 -0400, Louis Nicholas Vinke wrote: >> > Hi Erin, >> > Try this command after cd into the subject's mri dir, treating the hippo >> > subfields as volumes. >> > >> > freeview nu.mgz posterior_Left-Hippocampus.mgz:colormap=heat >> > posterior_Right-Hippocampus.mgz:colormap=heat >> > >> > The labels are probability maps (Eugenio correct me if wrong) so >> > displaying with the FS look-up table makes them look like confetti. As >> a >> > heatmap makes more sense. >> > -Louis >> > >> > On Fri, 26 Apr 2013, Erin Walsh wrote: >> > >> > > Hi Freesurfers, >> > > >> > > I have been experiencing issues with visualizing the hippocampal >> subfields. >> > > I have attempted to try fixes I found in previous threads with no >> success. >> > > Hopefully someone here may have a solution. >> > > >> > > Thanks for any help! >> > > >> > > Erin >> > > >> > > >> > > >> > > Freesurfer Info: >> > > >> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 >> > > Kernel info: Darwin 12.2.0 x86_64 >> > > >> > > >> > > Error Message: >> > > >> > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% freeview nu.mgz >> \ >> > > >> > > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ >> > > >> > > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ >> > > >> > > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt >> > > >> > > 2013-04-26 14:19:16.237 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.238 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.250 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.251 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.262 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.263 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.274 freeview.bin[42704:f07] invalid drawable >> > > >> > > 2013-04-26 14:19:16.275 freeview.bin[42704:f07] invalid drawable >> > > >> > > QObject::connect: Connecting from QAbstractButton::toggled(bool) to >> COMPAT >> > > slot (QGroupBox::setShown(bool)) >> > > >> > > QObject::connect: Connecting from QAbstractButton::toggled(bool) to >> COMPAT >> > > slot (QGroupBox::setShown(bool)) >> > > >> > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels >> > > posterior_left_* posterior_Left-Hippocampus.mgz \ >> > > >> > > -p-labels: Command not found. >> > > >> > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels >> > > posterior_right_* posterior_Right-Hippocampus.mgz \ >> > > >> > > -p-labels: Command not found. >> > > >> > > [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-prefix >> posterior_ >> > > -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt >> > > >> > > -p-prefix: Command not found. >> > > >> > > >> > > >> > > -- >> > > Erin Walsh, Ph.D. >> > > Postdoctoral Research Associate >> > > University of Wisconsin-Madison >> > > Department of Psychiatry: Abercrombie Lab >> > > 6001 Research Park Blvd. >> > > Madison, WI 53719 >> > > edubwalsh(a)gmail.com >> > > >> > > >> > _______________________________________________ Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> >> ------------------------------------------------------------------------------------- >> Juan Eugenio Iglesias, PhD >> http://www.jeiglesias.com >> iglesias(a)nmr.mgh.harvard.edu >> Athinoula A. Martinos Center for Biomedical Imaging >> Department of Radiology, MGH, Harvard Medical School >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> >> >> >> >> 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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Problems visualizing hippocampal subfields
by Erin Walsh 26 Apr '13

26 Apr '13

Hi Freesurfers, I have been experiencing issues with visualizing the hippocampal subfields. I have attempted to try fixes I found in previous threads with no success. Hopefully someone here may have a solution. Thanks for any help! Erin Freesurfer Info: Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.2.0 x86_64 Error Message: [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt 2013-04-26 14:19:16.237 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.238 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.250 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.251 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.262 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.263 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.274 freeview.bin[42704:f07] invalid drawable 2013-04-26 14:19:16.275 freeview.bin[42704:f07] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels: Command not found. [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-labels: Command not found. [HeatherLab8s-iMac:subjects/EW2Long/mri] heatherlab8% -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt -p-prefix: Command not found. -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh(a)gmail.com

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Alternate seed points in Tracula
by Sean Hatton 26 Apr '13

26 Apr '13

Hi all, Is it possible to use the Tracula bedpostx data to run Probtrackx with different seed points? For example: 1. Run all of Tracula on subject. 2. Extract seed masks from FS (eg seed superior temporal gurus to target anterior insula). 3. Run Probtrackx with the dbedpost data and masks in diffusion space. Is this feasible? I would get connection strength but how would I get FA, AD, RD etc? Should I correct for ICV? Or am I barking up the wrong tree? Sean Hatton Brain and Mind Research Institute University of Sydney

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R: Re: R: Re: incomplete tracts
by stdp82＠virgilio.it 26 Apr '13

26 Apr '13

Hi Anastasia, I apologize but I do not find CVS template? Where it should be located? Thank you very much, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 9-apr-2013 17.50 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: incomplete tracts Hi Stefano - Did you try CVS for the inter-subject registration? It doesn't look like it from the configuration file. a.y On Tue, 9 Apr 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > yes, I tried.I'm attacking the last configuration file that I used. > > Thanks, > > > Stefano > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 9-apr-2013 1.42 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] incomplete tracts > > > What registration methods are you using for the intra-subject and > inter-subject registration? Have you tried the different options? > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-apr-2013 18.57 > > A: <stdp82(a)virgilio.it> > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > > > > What you say "again" you mean with 5.2? > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > Hi Anastasia, > > > yes, for some subject the low-b volume is in the end. > > > Some subjects have again incomplete tracts. > > > I'm attacking an example of configuration file that I'm using. > > > I hope that you can check it please. > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 5-apr-2013 18.45 > > > A: <stdp82(a)virgilio.it> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts > > > > > > > > > Hi Stefano - In your case we determined that the ones that had the low-b > > > volume in the end didn't run correctly, right? In that case, I didn't > need > > > to see anything, you were going to try running 5.2. > > > > > > a.y > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi Anastasia, > > > > could I send you the data of a subject that I don't run correctly? > > > > > > > > I still have some subjects with tracts incomplete and I do not know if > > it depends > > > from > > > > my analysis or whether the images are not good. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 5-apr-2013 17.37 > > > > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > Hi Gerit - If it's not an issue with the gradient table but instead a > > > > tractography initialization issue, I strongly recommend running 5.2 > with > > > > bbregister for the registration (which is the default in 5.2 anyway). > > > > > > > > You can also upload an example data set with issues (include: dmri, > > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > > > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > > > > > > > Hope this helps, > > > > a.y > > > > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > > > > > > > Dear Anastasia, > > > > > > > > > > thanks for the help. There is also a line option in freeview. > However > > we still > > > have > > > > > brains with missing tracks, I rerun them with increasing the ncpts > and > > registering > > > > to > > > > > bbr (since that is default in Tracula 5.2.). We are reasonable > > confident that our > > > > bvel > > > > > and bvac are correct, since we have roughly 20 cases out of 90 > > processed brains > > > > where > > > > > there are no missing tracts. Further sometimes only one tract is > > missing, > > > sometimes > > > > it > > > > > is more severe. We could not find any correlation with recon-all > > problems or DTI > > > raw > > > > > data issues (all but one were without moving artefacts). Since we > are > > running > > > > bedpostx > > > > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) > > might it be an > > > > issue > > > > > that is solved with installing the 5.2. version? Would that run in > > freesurfer > > > 5.1.0? > > > > > I guess we need to change the dcmrirc files only a bit. > > > > > > > > > > Kind regards > > > > > Gerit Pfuhl > > > > > > > > > > > > > > > On 3 April 2013 16:59, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > > > Hi Benjamin - I'd look in a coronal view to see if the lines > in > > the corpus > > > > > callosum follow the curvature of the corpus callosum, and in a > > sagittal > > > > > view to see if the lines in the cingulum follow the curvature > of > > the > > > > > cingulum. Does this make sense? > > > > > > > > > > a.y > > > > > > > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > > > > > > > Dear Anastasia, > > > > > > > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because > > our > > > > > gradient table is wrong but I am not really sure how to > analyse > > > > > these informations. You wrote to Stefano the lines have to > point > > in > > > > > the right direction and that the eigenvectors are not pointing > > along > > > > > his corpus callosum. Can you give me a more detailed > description > > > > > what I have to do when I dislpay dtifit_V1 as lines, overlaid > on > > > > > dtifit_FA. > > > > > > > > > > Thanks and kind regards > > > > > Benjamin > > > > > > > > > > _______________________________________________ > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > http://gerit-orientation.blogspot.com > > > > > http://team-arzgebirg.blogspot.com > > > > > > > > > > > > > > _______________________________________________ > > > > 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. > > > > > > > >_______________________________________________ > 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 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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Use our own training subjects?
by Susan Kuo 26 Apr '13

26 Apr '13

Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*

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