Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

mri_convert error
by Pom Sailasuta 25 Feb '11

25 Feb '11

Hello, I got an error below using mri_convert, please help /////////////////////////////////////////// [Pom@pom-PC mri]$ mri_convert -it dicom -ot mgz /orig/i399386.MRDC.1 001.mgz mri_convert -it dicom -ot mgz /orig/i399386.MRDC.1 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /orig/i399386.MRDC.1... Starting DICOMRead2() ERROR: file /orig/i399386.MRDC.1 does not exist. /////////////////////////////////// I am in /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri folder and there is subfolder orig and definitely contains the first GE DICOM file i399386.MRDC.1 and all users has permission to red and write in the subjects dir. thanks for your input. pom

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Re: [Freesurfer] aparcstats2table error
by Alex Hanganu 25 Feb '11

25 Feb '11

Thank you for your quick answer. Chris - it's "/stats/" in the address. Doug - Thanks, mris_anatomical_stats works. For this it was also necessary to copy the .label file in each subjects - "/label/" directory Alex --- En date de : Jeu 24.2.11, Chris Hyatt <Chyatt(a)harthosp.org> a écrit : De: Chris Hyatt <Chyatt(a)harthosp.org> Objet: Re: [Freesurfer] aparcstats2table error À: "FS Mailing List" <Freesurfer(a)nmr.mgh.harvard.edu>, "Alex Hanganu" <hanganu.alexandru(a)yahoo.de> Date: Jeudi 24 février 2011, 18h48 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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Subcortical segmentation of a skull-stripped Analyze-formatted image
by andrewkrause＠ucla.edu 24 Feb '11

24 Feb '11

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

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Mapping label to subjects
by John Richey 24 Feb '11

24 Feb '11

Dear freesurfer experts, I have what I think is a fairly straighforward task, but the steps are not exactly clear to me. I wish to create a new label on the cortical surface and then map this label to each individual subject in order to extract roi data. I've successfully made my label on the cortical surface for the subject 'fsaverage', however it's not clear to me how to map this back to individual space (that is, to create the corresponding file in SUBJECTS_DIR/$SUBJ/labels/ ) Thanks in advance, any help would be greatly appreciated.

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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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Freesurfer February 2011