Freesurfer

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30088 discussions

Nu_correct error
by Palzes, Vanessa 24 Feb '11

24 Feb '11

Hi all, I've been consistently getting a couple of different errors early on during -autorecon1: .ncvarput: ncid 4: Bad file descriptor mivarput1: MINC package entry point sharpen_volume: crashed while running minclookup (termination status=768) nu_estimate_np_and_em: crashed while running sharpen_volume (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct ncavarput: ncid 5: Bad file descriptor miicv_put: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct It's strange because sometimes it will work if I just restart recon-all -all, but other times it keeps crashing. Anyone knows what this could be? Thanks, Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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Re: [Freesurfer] aparcstats2table error
by Chris Hyatt 24 Feb '11

24 Feb '11

You have /stat/ rather than /stats/ in the address. Have you checked that? >>> Alex Hanganu <hanganu.alexandru(a)yahoo.de> 2/24/2011 12:22 PM >>> Dear Chris, Doug, We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness. The cmd used: aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label --meas thickness --t ROI.txt ERROR: cannot find .../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR Can you please tell us what might be the problem ? Sincerely, Alex.

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aparcstats2table error
by Alex Hanganu 24 Feb '11

24 Feb '11

Dear Chris, Doug, We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness. The cmd used: aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label --meas thickness --t ROI.txt ERROR: cannot find .../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR Can you please tell us what might be the problem ? Sincerely, Alex.

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Converting an ascii file to a freesurfer volume file
by Tina Jeon 23 Feb '11

23 Feb '11

Hello freesurfers, I am trying to convert a partially inflated surface .ply file created in afni to a freesurfer volume so that I can visualize the surfaces via tksurfer. Is there freesurfer command that converts text to volume, in essence the converse of mris_convert? And if not can you suggest a way that I can open the text file using a different graphical interface? Thank you in advance, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center ________________________________ UT Southwestern Medical Center The future of medicine, today.

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{Disarmed} structural sequence for Siemens Verio 3T
by houman.ebrahimi 23 Feb '11

23 Feb '11

Is there a list of recommended MPRAGE parameters for a Siemens Verio 3T machine? The structural protocols on this page: http://www.nmr.mgh.harvard.edu/~andre/ are for a Sonata (1.5T). I'm not sure what "Gleek 3T" means and again refers to a Sonata. Thanks for your help. Houman

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Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image
by Nick Schmansky 23 Feb '11

23 Feb '11

mri_convert --help has info on specifying orientation, with suitable warnings about the need for you to make sure you know which way is correct. n. On Wed, 2011-02-23 at 14:55 -0800, andrewkrause(a)ucla.edu wrote: > Thanks for the reply. For the orientation, I know from working with > the sources of the average that it's in neurological (left = left) > orientation. Is there a way to let mri_convert know this (it looks > like ANALYZE is usually radiological so I don't know if this is what > is assumed)? Unfortunately I don't know if it's possible to make the > average in nifti format instead, since everything is currently set up > using ANALYZE (i.e. the scans it's averaging are already in ANALYZE). > > -- Andrew > > Quoting Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>: > > > add the flag -notal-check to the end of recon-all command to skip the > > check. > > > > if you can make your average using nifti format you're better off as > > analyze doesnt retain orientation (l/r) info. > > > > you may have to manually register the brain following this: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > n. > > > > > > On Wed, 2011-02-23 at 13:38 -0800, andrewkrause(a)ucla.edu wrote: > >> Hello, > >> > >> I'm a complete newbie to FreeSurfer, so I appreciate any and all help > >> you can provide. I am trying to use FreeSurfer to automatically create > >> some masks of subcortical structures, but am having trouble getting > >> the whole process started. > >> > >> When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is > >> my subject name) it quits with the error > >> > >> "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > >> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" > >> > >> > >> I am trying to do this to a skull-stripped brain originally in Analyze > >> format (there are no DICOMs since it's actually an average of many > >> skull-stripped scans), to which I've already registered all of the > >> scans I want to study. I used mri_convert to convert the .img file > >> into a .mgz file, but compared to the bert example, the background > >> (non-brain area) is a light gray instead of black. I don't know if > >> this is where the error is occuring, and if it is, how to correct it. > >> If it helps, the scan I'm trying to create masks from has been > >> registered to the ICBM brain template. > >> > >> Let me know what other information you need and thanks for the help, > >> -- Andrew > >> _______________________________________________ > >> 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] installation problem in ubuntu
by Pedro Paulo de Magalhães Oliveira Junior 23 Feb '11

23 Feb '11

try the command: sudo apt-get install tcl -- PPJ Please: cc the freesurfer list when answering 2011/2/22 Carolina Valencia <cvalencia(a)linkdx.com.co> > Hi Pedro, > > Finally, I could install it with the license file and the environment is > properly set without warnings. > But trying to test it, following the instruction on the wiki page I have a > problem > > cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz > /usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio. > > in the .bashrc I copy the right location of the freesurfer folder > FREESURFER_HOME=/home/cvalencia/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > > 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > >> run this command >> >> sudo rm -rf $FREESURFER_HOME >> >> >> >> 2011/2/21 Carolina Valencia <cvalencia(a)linkdx.com.co> >> >>> Thanks Pedro, >>> >>> How I uninstall that version to re-install the correct version? >>> I look for some answers and try >>> >>> rm -rf $FREESURFER_HOME >>> >>> It says that I don't have permission,how I can unistall it, if i'm the >>> admin user? >>> >>> Thanks in advance, >>> >>> Carolina >>> >>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br >>> > >>> >>>> It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS >>>> >>>> >>>> 2011/2/21 Carolina Valencia <cvalencia(a)linkdx.com.co> >>>> >>>> >>>>> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae >>>>> #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux >>>>> >>>>> Thanks, >>>>> >>>>> >>>>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < >>>>> ppj(a)netfilter.com.br> >>>>> >>>>> Please send the result of the command: >>>>>> >>>>>> uname -a >>>>>> >>>>>> >>>>>> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < >>>>>> cvalencia(a)linkdx.com.co> wrote: >>>>>> >>>>>>> Hi Bruce, >>>>>>> >>>>>>> I'm experimenting problems with the installation on Ubuntu too. >>>>>>> There's is warning in the welcome message, it seems that something is >>>>>>> missing: >>>>>>> >>>>>>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- >>>>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>>>>> WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist >>>>>>> FREESURFER_HOME /home/cvalencia/Descargas/freesurfer >>>>>>> FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast >>>>>>> FSF_OUTPUT_FORMAT nii >>>>>>> SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects >>>>>>> MNI_DIR /home/cvalencia/Descargas/freesurfer/mni >>>>>>> FSL_DIR /usr/share/fsl/4.1 >>>>>>> >>>>>>> >>>>>>> I try to test it and it shows >>>>>>> cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit >>>>>>> /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de >>>>>>> ejecutable incorrecto. Binary file not executable. >>>>>>> >>>>>>> Thanks a lot, >>>>>>> >>>>>>> Carolina >>>>>>> >>>>>>> 2011/2/18 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>>>>> >>>>>>>> Hi Jie, >>>>>>>> >>>>>>>> what hardware are you using? Is it a 64 bit operating system? >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> >>>>>>>> On Sat, 19 Feb 2011, Liukarl wrote: >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Hello, Freesurfer experts: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> I am new to freesurfer and try to >>>>>>>>> install the newest version of freesurfer in Ubuntu system. I >>>>>>>>> closely >>>>>>>>> followed the instructions, and the only difference is that I >>>>>>>>> installed it in my Documents, instead of local folder. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Below is the output after “source >>>>>>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh” >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -------- >>>>>>>>> freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- >>>>>>>>> >>>>>>>>> Setting up environment for >>>>>>>>> FreeSurfer/FS-FAST (and FSL) >>>>>>>>> >>>>>>>>> FREESURFER_HOME >>>>>>>>> /home/jie/Documents/freesurfer/ >>>>>>>>> >>>>>>>>> FSFAST_HOME >>>>>>>>> /home/jie/Documents/freesurfer//fsfast >>>>>>>>> >>>>>>>>> FSF_OUTPUT_FORMAT nii >>>>>>>>> >>>>>>>>> SUBJECTS_DIR >>>>>>>>> /home/jie/Documents/freesurfer//subjects >>>>>>>>> >>>>>>>>> MNI_DIR >>>>>>>>> /home/jie/Documents/freesurfer//mni >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Everything seems fine and I also added >>>>>>>>> the .license file to the freesurfer folder. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> But when I test it by “tkmedit bert >>>>>>>>> orig.mgz”, it reponds “Illegal instruction” >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> If I type in “recon-all”, it will >>>>>>>>> show >>>>>>>>> >>>>>>>>> “ Required Arguments: >>>>>>>>> >>>>>>>>> -subjid <subjid> >>>>>>>>> >>>>>>>>> -<process directive>…... >>>>>>>>> ” >>>>>>>>> and the other arguments. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> How to fix the problem and make >>>>>>>>> Fressurfer run? Any help is appreciated. Thanks a lot! >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Jie >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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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ASL tag-control order
by Rita Loiotile 23 Feb '11

23 Feb '11

Hi, How can I tell what the tag-control order of collection was for my ASL images? They were all acquired in Bay 3. I can get you other parameters if you need...

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question about qdec analysis
by 汪贵宏 23 Feb '11

23 Feb '11

Hi everybody, I am new user of Freesurfer,I simply take five procedures to process my data ,after I read the wiki on the website. The five procedures including: 1. mri_convert one-dicom-file-from-series blobby.nii.gz 2.recon-all -i blobby.nii.gz -subjid blobby –all 3.recon-all -s <subjid> -qcache 4.make_average_subject. 5.qdec Now, my questions are: 1.In our e-mail ,you often talk about recon-all, why did I never across question about it ? 2. I tried to run the qdec-tool, but experienced some problems . I got different thickness in one area. In detail: 1. When I open theqdec.table.dat ,the thickness is different from the thickness got from the display in Find Clusters and Goto Max, I really do not know why? 2. Did I get the same results from two differentqdec.table.dat , one qdec.table.dat has 34 Continuous Variables but the other had only one Continuous Variable ? 3.Why did the display from qdec smaller than the examples in the wiki on the website? Such as the pictures follow. I guess part of my problem is that I'm having trouble understanding exactly how to use the freesurfer. Can you try to give me a sort of layman's explanation? Thanks for your answer! wang

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TKSurfer question
by Weisinger, Brian (NIH/NIMH) [F] 23 Feb '11

23 Feb '11

Is there a way to get a general generic TK_Surfer output without using a subject? Thanks, Brian Weisinger

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