Freesurfer November 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
59 discussions

recon-all did not complete
by Abi Gopal 20 Nov '06

20 Nov '06

Hello all Below is my information: rhinal cat $FREESURFER_HOME/build-stamp.txt source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_data which recon-all cd /space/rhinal/2/users/gopal/lynch_data I am not having an error per se, but recon-all keeps crashing before it is complete. If i look at the files that were created in order of date modified, the last file created in the surf folder (before it crashed) is rh_defect labels. files such as rh.sphere and rh.thickness were not created (although the corresponding lh files were). Do I have to run the entire recon-all program again? Or can I just run recon-all -s lynch -autorecon3? I am just trying to figure out if there is a quicker way to create the remaining files other than running the entire recon-all process, which will take another 30 hrs. I appreciate any suggestions. Thanks very much Abi

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WG: [Freesurfer] recon-all with more than one subject
by Juergen Haenggi 20 Nov '06

20 Nov '06

Dear Freesurfer users I tried to run a loop for the recon-all command over subjects in order to use computational resources optimally. But the following error occured: I used the following command: foreach s (Patient01 Patient02 Patient03) recon-all $s -all end The error message is: s: undefined variable Any idea what is wrong in the command? Thanks a lot in advance Best regards Juergen > > Dear Avram > > thanks for your advise. I had try it, but there is an error message. > > I used the following command: > > foreach s (Patient01 Patient02 Patient03) recon-all $s -all end > > The error message is: > > s: undefined variable > > Any idea what is wrong in the command? > > Thanks a lot in advance > Best regards > Juergen > > ---------------------------------------------- > Juergen Haenggi, Ph.D. student > Neuropsychology and Imaging > Division of Psychiatry Research > Psychiatric University Hospital > University of Zurich, Switzerland > P.O. Box 1931 > Lenggstrasse 31, 8032 Zurich > 0041 44 384 26 10 (office phone) > 0041 76 445 86 84 (mobile phone) > 0041 44 384 26 86 (fax) > H 115 (office room number) > juergen.haenggi(a)bli.unizh.ch (division email) > http://www.dpr.unizh.ch/ (division website) > http://www.juergenhaenggi.ch (private website) > ---------------------------------------------- > > > > -----Ursprüngliche Nachricht----- > > Von: Avram Holmes [mailto:holmes@fas.harvard.edu] > > Gesendet: Donnerstag, 19. Oktober 2006 15:10 > > An: Juergen Haenggi > > Betreff: Re: [Freesurfer] recon-all with more than one subject > > > > Juergen, > > > > You could use a 'foreach' loop > > > > e.g., "foreach s (subject1 subject2)" then enter your recon-all > > command with a "$s" in the place of the subject name. Then > type "end". > > > > This makes a loop that will run through each of the subjects > > individually. > > > > Avram > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Avram Holmes > > Department of Psychology > > Harvard University > > 1210 William James Hall Phone:(617) 495-0790 > > 33 Kirkland Street Fax:(617) 495-3728 > > Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > > > > > On Thu, 19 Oct 2006, Bruce Fischl wrote: > > > > > Hi Juergen, > > > > > > why would you want to do such a thing? Just run recon-all > multiple > > > times with different subjects. > > > > > > cheers > > > Bruce > > > On Thu, 19 Oct 2006, Juergen Haenggi wrote: > > > > > >> Dear Freesurfer users > > >> > > >> is there any possibility to run recon-all with more than > > one subject? > > >> what is the option to use several subjects within one > > recon-all command? > > >> can one use more than one -s option in one recon-all command? > > >> > > >> thanks in advance > > >> best regards > > >> Juergen > > >> > > >> ---------------------------------------------- > > >> Juergen Haenggi, Ph.D. student > > >> Neuropsychology and Imaging > > >> Division of Psychiatry Research > > >> Psychiatric University Hospital > > >> University of Zurich, Switzerland > > >> P.O. Box 1931 > > >> Lenggstrasse 31, 8032 Zurich > > >> 0041 44 384 26 10 (office phone) > > >> 0041 76 445 86 84 (mobile phone) > > >> 0041 44 384 26 86 (fax) > > >> H 115 (office room number) > > >> juergen.haenggi(a)bli.unizh.ch (division email) > > >> http://www.dpr.unizh.ch/ (division website) > > >> http://www.juergenhaenggi.ch (private website) > > >> ---------------------------------------------- > > >> > > >> > > >> _______________________________________________ > > >> 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 > > > > > >

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func2sph-sess registration question - where should individual subject's register.dat files be?
by raij＠nmr.mgh.harvard.edu 17 Nov '06

17 Nov '06

Hi, I did not see this documented anywhere so I figured it would be best to double check. Any group analysis relies on that the individual functional and structural data have first been aligned, and there is therefore a register.dat file in the individual subject's directory. This is usually saved at $STUDY_DIR/$SESSION_DIR/bold/register.dat Now, when I run a group analysis, the functional (or structural) space of each individual subject is re-mapped onto the structural space of the target brain. This process must have access to the correct subject-specific register.dat files for each individual subject. In the case of a spherical surface group analysis, I would do this re-mapping by func2sph-sess that I run inside the $STUDY_DIR. The command would have the format func2sph-sess -analysis <analysisname> -sf sessid -df sesspar -trgsubject fsaverage -projfrac 0.3 where the contents of the "sessid" file would list all my $SESSION_DIRs (i.e., different subjects). Question: Where does func2sph-sess look for the individual level register.dat files? I assume it will automatically find them at $STUDY_DIR/$SESSION_DIR/bold/register.dat Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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GM segmentation
by Gallo, Antonio (NIH/NINDS) [F] 17 Nov '06

17 Nov '06

Dear All, I have a question regarding the pial surface in medial temporal lobes since segmentation fails to catch up some GM. Do you have any suggestions (do control point to add GM exist?) to fix this underextimation of GM ? Many Thanks, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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visualizing ASL images
by Abi Gopal 17 Nov '06

17 Nov '06

Hello all I'm new to the freesurfer mailing list, so I was hoping I could get some advice here. As part of my research, I have been acquiring arterial spin-labeling (ASL) images of subjects with cortical dysplasia (a type of brain malformation). However, I've been having problems visualizing the ASL images individually. Specifically, when I extract the ASL images in .DCM form, all 12 of them show up on a single picture. Do you know of any way to extract them individually, so that I can view a single slice on each page? I really appreciate any help you can give me. Thanks Abi -- Abilash A. Gopal Doris Duke Research Fellow, Harvard Medical School MD Candidate 2008, Tufts Medical School

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edit wm or pial?
by Reschke, Cole 16 Nov '06

16 Nov '06

Looking near the center of the picture, you will notice that the pial surface crosses the white matter. This is one of two slices where this happens. Is this a case where I edit the pial surface or the white matter, or both? Cole Reschke Data Manager, PET Center Banner Alzheimer Institute Banner Good Samaritan Medical Center Phone: (602) 239-4868

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annotation2label problem
by Cameron Ellis 16 Nov '06

16 Nov '06

Hi Everyone, When running mri_annotation2label for an individual subject one label is not extracted. The processing text says: 0 empty skipping. Does anyone know why this is happening and if I can get this label extracted? Do I need to re-run part of the autorecon process? Thanks, Cameron

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sig.mgh = -log(p)?
by Eric Moulton 16 Nov '06

16 Nov '06

The -log 10(p) image contains negative values, and when we convert these these values into p-values, we get p-values greater than 1. Is there possibly something wrong with the image? The sig.mgh histogram looks like a t-distribution (viewing with tksurfer...Configure Overlay Display...also after converting to ANALYZE format as viewed by fslview:Image Histogram). Thanks, Eric Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772 Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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Re: [Freesurfer] mri_convert and GE dicom
by Doug Greve 15 Nov '06

15 Nov '06

So, to be perfectly clear, the problem is *not* with the FreeSurfer tools. The problem is with fslview. While it reads the orientation information, it does not act upon it in order to reorient the images in a reasonable way. FSL has rather strict requirements on how the pixels must be arranged in order to use the tools (see www.fmrib.ox.ac.uk/fslfaq) -- this is above and beyond simple left-right orientation. Interleaved axial images from a Siemens scanner will, by default, not be arranged correctly. FSL provides tools to flip and reorient the data (this cannot be done with mri_convert). Try viewing the volumes in tkmedit (which is geometry-aware). If tkmedit displays them incorrectly, I will happily fix the problem. doug On Wed, 15 Nov 2006, David M Schnyer wrote: > Well, good point. When I bring it into FSLview the brain is not oriented as > expected. For example the lower left window has axial scans that are upside > down. Interestingly, the labels show the correct directions since A is > pointing down and P is pointing up but I have run into trouble in the past > running images like this through the FSL stream. Anyway, I will put these > images somewhere local where you can get at them when I get in tomorrow. > thanks, > > david > > Doug Greve wrote: > >> >> How do you know it's the wrong orientation? Is the data local to the >> our network? >> >> >> >> >> >> On Wed, 15 Nov 2006, David M Schnyer wrote: >> >>> I have been trying out the dev version of mri_convert on some GE dicom >>> images. This is functional data. If I leave the orientation alone and just >>> convert from Dicom to nifti then I get a timeseries volume in the wrong >>> orientation. OK, so I add the flag --out_orientation RAS. Here I get a >>> volume in the right orientation but the timeseries is gone. Now, it isn't >>> really gone, in that the file is the correct size but FSL no longer sees >>> it as a timeseries. Anyone dealt with something like this? >>> >>> thanks, >>> >>> david >>> >>> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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mri_convert and GE dicom
by David M Schnyer 15 Nov '06

15 Nov '06

I have been trying out the dev version of mri_convert on some GE dicom images. This is functional data. If I leave the orientation alone and just convert from Dicom to nifti then I get a timeseries volume in the wrong orientation. OK, so I add the flag --out_orientation RAS. Here I get a volume in the right orientation but the timeseries is gone. Now, it isn't really gone, in that the file is the correct size but FSL no longer sees it as a timeseries. Anyone dealt with something like this? thanks, david -- David Schnyer, Ph.D. Imaging Research Center & Department of Psychology University of Texas, Austin tel: (512) 471-8505 fax: (512) 232-4202 http://irc.utexas.edu/index.html

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Freesurfer November 2006