Re: [Freesurfer] dual installation question
Thanks. Best, - Josh On Thu, Feb 21, 2013 at 10:05 AM, Shantanu Ghosh < shant...@nmr.mgh.harvard.edu> wrote: > Or you may have multiple freesurfer versions within the freesurfer > director, something like > /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc. > and then > export FREESURFER_HOME=/freesurfer/5.1 > etc > Hth, S. > > > On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote: > > Hi Josh, > > you can modify the SetUpFreeSurfer.sh to source the correct version. > > Hth, Shantanu > > > > On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote: > >> If I want to install the new Freesurfer version but retain the older > >> Freesurfer install as well, what issues might I face? > >> Is it simply sourcing the usual setup scripts? > >> > >> export FREESURFER_HOME=/freesurfer > >> source $FREESURFER_HOME/SetUpFreeSurfer.sh > >> > >> - > >> Josh > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > Shantanu Ghosh, Ph.D. > > Harvard Medical School & Massachusetts General Hospital > > Martinos Center for Biomedical Imaging > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > > > > 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@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] mri_vol2vol call
Hi I found my old notes ( re my message earlier) I think this is now correct for mapping subject 822 FA onto my template 816, I know the cvs technology is recent, so just asking to make sure there is now a newer/prefered way. mri_vol2vol --targ /study5/aa-scratch/TEENEMO/twins_freesurfer/816/mri/norm.mgz --m3z /study5/aa-scratch/TEENEMO/twins_freesurfer/822/cvs/combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/822/dmri/xfms/anatorig2diff.bbr.dat --mov /study5/aa-scratch/TE ENEMO/twins_tracula/recons/822/dmri/dtifit_FA.nii.gz --o /study5/aa-scratch/TEENEMO/twins_freesurfer/822/cvs/FA.mgz --no-save-reg done thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tkregister2 / Tksurfer / Tkmedit Won't Open
Daniel, What operating system are you on? If your using MacOS, you must have XQuartz installed in order to use the the Tkregister2/Tksurfer/Tkmedit tools. Check the Application->Utilities folder to see if its already installed. If not, you can download it from here: http://xquartz.macosforge.org/landing/ If your are on Linux than I am sorry but someone else will have to chime in with a potential solution. -Zeke > Hello freesurfers, > I just ran registration of my functional images and am trying to visualize > the registration for assessment. However, when I use the commands > "tkregister-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold -funcstem > f" > or > > "tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID --surf --mov > $FUNCTIONAL_MRI --reg $REG_DAT --plane sag --movbright $MYBRIGHTNESS" > > the command gets stuck on "Opening window SUBJECT01". > > > I've also tried just opening tksurfer and tkmedit but the terminal > produces > no output/windows opening and simply freezes. > > Any ideas to why this could be occurring? I've let it sit at this stage > for multiple hours without anything popping up and without any errors. > > > Thanks! > > Daniel > > > -- > Daniel Cole > University of Rochester > Brain and Cognitive Sciences > dcol...@u.rochester.edu > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Help with the error info: mghRead subject/surf/lh.inflated.H, could not open file
The weird problem is solved after I traced a day. The real problem is that my full path contains dot. After I removed the dot, everything works fine. Then I guess this maybe some kind of mri_read bug in mriio.c or FreeSurfer file name convention I don't know. Xiaowei On Thu, Feb 21, 2013 at 2:04 PM, Xiaowei Song wrote: > No one ever encountered this kind of full path problem? > recon-all works fine, but recon-all -qcache stopped because of this kind > of problem. > > Any hint would be appreciated. > > Xiaowei > > > On Wed, Feb 20, 2013 at 5:07 PM, Xiaowei Song wrote: > >> Dear Bruce and freesurfer experts, >> >> I am trying to use mri_average_subjects, but encountered the error: >> mghRead(/fullpath/surf/lh.inflated.H, -1): could not open file. >> . >> >> Then I tried >> mri_info subject/surf/lh.inflated.H >> , and it worked. >> >> But when I tried >> mri_info $(readlink -f subject/surf/lh.inflated.H) >> , the same error information is told. >> >> Besides, I tried the same command to the downloaded buckner_data and no >> error happened. >> >> How to fix this? >> >> >> The following information is from bugr: >> FREESURFER_HOME: /usr/local/freesurfer >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >> RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) >> Kernel info: Linux 2.6.32-279.22.1.el6.x86_64 x86_64 >> >> >> Thanks >> >> -- >> Xiaowei Song >> > > > > -- > Xiaowei Song > -- Xiaowei Song ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tkregister2 window error: Remote login
Hello, I am remotely logged in to my Ubuntu system(from Mac). I have previously run tkregister2 but am now having trouble; Opening window subj Window type not found register: tkoinitwindow(name) failed. Is there a solution to this? Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_vol2vol call problem
Greetings lords of freesurfer! I am having a problem getting a combined cvs warp+bbregister to map an FA volume onto a template. mri_vol2vol --targ 816 --m3z combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat --mov /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz --o test --no-save-reg spits out Using the m3z file as it is; no assumed location. movvol /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz targvol 816 outvol test regfile /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1362252270 corRead(): can't open file /study5/aa-scratch/TEENEMO/twins_freesurfer/816/COR-.info i know i have not seen a file COR-.info in the top level subject directory in the modern age of the universe. i know i saw this before but my notes from the last time i figured this out got lost in a file system cleanup. can one of you tell me where i went astray ? thank you Greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Help with the error info: mghRead subject/surf/lh.inflated.H, could not open file
No one ever encountered this kind of full path problem? recon-all works fine, but recon-all -qcache stopped because of this kind of problem. Any hint would be appreciated. Xiaowei On Wed, Feb 20, 2013 at 5:07 PM, Xiaowei Song wrote: > Dear Bruce and freesurfer experts, > > I am trying to use mri_average_subjects, but encountered the error: > mghRead(/fullpath/surf/lh.inflated.H, -1): could not open file. > . > > Then I tried > mri_info subject/surf/lh.inflated.H > , and it worked. > > But when I tried > mri_info $(readlink -f subject/surf/lh.inflated.H) > , the same error information is told. > > Besides, I tried the same command to the downloaded buckner_data and no > error happened. > > How to fix this? > > > The following information is from bugr: > FREESURFER_HOME: /usr/local/freesurfer > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) > Kernel info: Linux 2.6.32-279.22.1.el6.x86_64 x86_64 > > > Thanks > > -- > Xiaowei Song > -- Xiaowei Song ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tkregister2 / Tksurfer / Tkmedit Won't Open
Hello freesurfers, I just ran registration of my functional images and am trying to visualize the registration for assessment. However, when I use the commands "tkregister-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold -funcstem f" or "tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID --surf --mov $FUNCTIONAL_MRI --reg $REG_DAT --plane sag --movbright $MYBRIGHTNESS" the command gets stuck on "Opening window SUBJECT01". I've also tried just opening tksurfer and tkmedit but the terminal produces no output/windows opening and simply freezes. Any ideas to why this could be occurring? I've let it sit at this stage for multiple hours without anything popping up and without any errors. Thanks! Daniel -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcol...@u.rochester.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] dual installation question
Or you may have multiple freesurfer versions within the freesurfer director, something like /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc. and then export FREESURFER_HOME=/freesurfer/5.1 etc Hth, S. On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote: > Hi Josh, > you can modify the SetUpFreeSurfer.sh to source the correct version. > Hth, Shantanu > > On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote: >> If I want to install the new Freesurfer version but retain the older >> Freesurfer install as well, what issues might I face? >> Is it simply sourcing the usual setup scripts? >> >> export FREESURFER_HOME=/freesurfer >> source $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> - >> Josh >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] dual installation question
Hi Josh, you can modify the SetUpFreeSurfer.sh to source the correct version. Hth, Shantanu On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote: > If I want to install the new Freesurfer version but retain the older > Freesurfer install as well, what issues might I face? > Is it simply sourcing the usual setup scripts? > > export FREESURFER_HOME=/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > - > Josh > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] dual installation question
If I want to install the new Freesurfer version but retain the older Freesurfer install as well, what issues might I face? Is it simply sourcing the usual setup scripts? export FREESURFER_HOME=/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] nb0 question
Of course! But, if I understood correctly, Stefano only has one, either at the beginning of the end of the gradient table, and in both cases nb0=1 Cheers, /Eugenio On Thu, February 21, 2013 12:20 pm, Shantanu Ghosh wrote: > Hi Juan, > The number of b0 images can be more than 1; it is specified when you > acquire the image. > Hth, Shantanu > > On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote: >> Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter >> where in the table it is. From the tutorial: >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >> >> Step7.3: Specifying Number Of low-b Images The last step to set up if >> not >> using original DICOMs would be to specify the number of low-b images >> with >> the following variable: >> >> set nb0 = *No. of low-b images* >> >> ** - To be replaced with the actual number from the acquisition. >> >> >> >> >> >> >> On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote: >>> Hi list, >>> I'm running TRACULA. I do not have problem when I have 16 DTI direction >>> and b=0 is the first volume: I put nb0=1. >>> For some subjects I have 16 direction but b=0 is the last of volume in >>> dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative >>> to >>> position of b=0 in the bvals.txt or to total number (quantitative) of >>> b=0 >>> in the bvals.txt? >>> Thanks, >>> >>> Stefano >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> - >> Juan Eugenio Iglesias, PhD >> http://www.jeiglesias.com >> igles...@nmr.mgh.harvard.edu >> Athinoula A. Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > > > - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] nb0 question
Hi Juan, The number of b0 images can be more than 1; it is specified when you acquire the image. Hth, Shantanu On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote: > Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter > where in the table it is. From the tutorial: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > Step7.3: Specifying Number Of low-b Images The last step to set up if not > using original DICOMs would be to specify the number of low-b images with > the following variable: > > set nb0 = *No. of low-b images* > > ** - To be replaced with the actual number from the acquisition. > > > > > > > On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote: >> Hi list, >> I'm running TRACULA. I do not have problem when I have 16 DTI direction >> and b=0 is the first volume: I put nb0=1. >> For some subjects I have 16 direction but b=0 is the last of volume in >> dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative >> to >> position of b=0 in the bvals.txt or to total number (quantitative) of >> b=0 >> in the bvals.txt? >> Thanks, >> >> Stefano >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > - > Juan Eugenio Iglesias, PhD > http://www.jeiglesias.com > igles...@nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] nb0 question
Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter where in the table it is. From the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Step7.3: Specifying Number Of low-b Images The last step to set up if not using original DICOMs would be to specify the number of low-b images with the following variable: set nb0 = *No. of low-b images* ** - To be replaced with the actual number from the acquisition. On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote: > Hi list, > I'm running TRACULA. I do not have problem when I have 16 DTI direction > and b=0 is the first volume: I put nb0=1. > For some subjects I have 16 direction but b=0 is the last of volume in > dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to > position of b=0 in the bvals.txt or to total number (quantitative) of b=0 > in the bvals.txt? > Thanks, > > Stefano > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] longitudinal sulci depth change
Hello, I was wondering if I could get some clarification regarding the longitudinal measure of rate of change in sulci depth. In our study we have a patient population that participated in an intervention and a similar group of wait list controls. We have scans for pre and post intervention timepoints. I have ran the longitudinal analysis in QDEC looking at the thickness change measures, however I was also interested in the sulc measures. I was able to get the analysis to run with the new measures long.sulc-rate etc. However I am having a hard time conceptualizing the meaning of the results. Does a negative rate change indicate either a deepening or a shallowing of the sulci? Is the opposite the case for gyral regions? Any advice would be greatly appreciated. -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Pial boundaries
I am afraid I can't... Can you give any advise without pictures? Thank you in advance. Melina 2013/2/21 Bruce Fischl > Can you send us an image? > > > > On Feb 21, 2013, at 7:24 AM, melinaki p-t wrote: > > > Hello, > > > > I would like to ask if there are any commands or any manual edits I can > use to fix the pial boundaries even if the white matter boundaries are fine. > > The white matter boundaries follow the white matter pretty good but > there is some grey matter missing at some areas. Its not a massive problem > though. > > Thank you in advance. > > Melina > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] DEFECT 57
Hi Chikku That is a giant defect - almost the size of an entire hemi. Something is badly wrong. Check the aseg and filled volumes to see what's going on, and the ?h.orig.nofix Bruce On Feb 21, 2013, at 5:35 AM, Varghese Chikku wrote: > Hi all, > One of my subject exited with error after 5 days of processing. > This is what it said, > CORRECTING DEFECT 57 (vertices=101022, convex hull=10822) > Excessive topologic defect encountered: could not allocate 536232126 > edges for retessellation > Cannot allocate memory > Darwin chikkus-MacBook-Pro.local 12.2.1 Darwin Kernel Version 12.2.1: > Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 > x86_64 > > recon-all -s onco4 exited with ERRORS at Fri Feb 15 12:17:05 CET 2013 > > My question is this much edges normal and how much memory i need > allocate to process this. > > Many Thanks > Chikku > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Pial boundaries
Can you send us an image? On Feb 21, 2013, at 7:24 AM, melinaki p-t wrote: > Hello, > > I would like to ask if there are any commands or any manual edits I can use > to fix the pial boundaries even if the white matter boundaries are fine. > The white matter boundaries follow the white matter pretty good but there is > some grey matter missing at some areas. Its not a massive problem though. > Thank you in advance. > Melina > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Registration & segmentation with FSL - obtaining correlation matrix..
On Feb 20, 2013, at 3:02 PM, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat
& aseg2feat)
When I extract the values (as per the matlab code below), I see NaNs in certain
regions. Of the 19 datasets that I have analyzed I have see NaNs for the
following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am having some trouble.
I run reg-feat2anat & aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can be fixed).
Question: Is there any alternative to getting this correlation matrix?
i.e every ROI against every other ROI?
Thanks,
S
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[Freesurfer] nb0 question
Hi list, I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 is the first volume: I put nb0=1. For some subjects I have 16 direction but b=0 is the last of volume in dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to position of b=0 in the bvals.txt or to total number (quantitative) of b=0 in the bvals.txt? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Generate mask from surface in diffusion space
Dear freesurfers I'm using bbregister and mri_surf2surf to transform intermediate cortical surfaces and mid surfaces normals to diffusion space. Next I'm trying to generate volumes from these surfaces (in the same diffusion space), however the generated volumes are much thicker then the generated surfaces. for example to generate surface normals I used the following: mri_surf2surf --s subjectid --hemi lh --sval-nxyz white_surface_in_diffusion --tval lhwhitediffusion_n.mgh mri_surf2vol --surfval lhwhitediffusion_n.mgh --hemi lh --surf white --reg mri/register.dat --outvol lh_white_n.img --template lowb.img Any idea what am I doing wrong? Thanks! Shani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Pial boundaries
Hello, I would like to ask if there are any commands or any manual edits I can use to fix the pial boundaries even if the white matter boundaries are fine. The white matter boundaries follow the white matter pretty good but there is some grey matter missing at some areas. Its not a massive problem though. Thank you in advance. Melina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] DEFECT 57
Hi all, One of my subject exited with error after 5 days of processing. This is what it said, CORRECTING DEFECT 57 (vertices=101022, convex hull=10822) Excessive topologic defect encountered: could not allocate 536232126 edges for retessellation Cannot allocate memory Darwin chikkus-MacBook-Pro.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 recon-all -s onco4 exited with ERRORS at Fri Feb 15 12:17:05 CET 2013 My question is this much edges normal and how much memory i need allocate to process this. Many Thanks Chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
