Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

processing OASIS database using freesurfer 5
by Gonzalo Rojas Costa 02 Aug '11

02 Aug '11

Hi: I need to reprocess some images of the OASIS database using freesurfer 5... Should I use only the command "recon-all -s OAS1_0074_MR1 -all", or I must add the option "-expert expert.opts" ?... In the first case freesurfer automatically use thresholds specified in expert.opts ?... Sincerely, Gonzalo Rojas Costa

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Re: [Freesurfer] Poor Intensity or Image Resolution?
by Bruce Fischl 02 Aug '11

02 Aug '11

Hi Antonella Are the sequence parameters the same? The way you convert should have no effect Bruce On Jul 27, 2011, at 11:51 AM, Antonella Kis <atorok9(a)yahoo.com> wrote: > Hi Bruce, > > I highly appreciate your great help/advice. > > Unfortunately, today I have another question: I finished running the recon-all for the new subjects for which I converted the dicom files in the NIFTI format as you advised me, using mri_convert. I was telling you that the .nii.gz file for this new subjects are very big , around 38 MB. Today I was analysing the volumes and I see there is a poor image in comparison with my other brains that were converted in a NIFTI format (having just 4 MB size) by someone else before me. > > My question is: is this poor image due to a different conversion way (I understood the other person used Mricron to convert the files) OR I need to do manually corrections adding control points for the intensity normalization. > > What is your suggestion/advise? > > Many thanks. > Antonella > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, July 26, 2011 5:53 PM > Subject: Re: [Freesurfer] Loading atlases > > Hi Antonella > > the atlas is not guaranteed to be correct. If it were we would just take the labels from it :) The only way to tell if it is correct is to look at the segmentations on top of the MR and see if they follow the visible boundary > > To get the surfaces you should do > > tkmedit SUBJECT1 brainmask.mgz lh.white \ > -aux T1.mgz -surfs \ > -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > cheers > Bruce > > > > On Tue, 26 Jul 2011, Antonella Kis wrote: > > > Hi, > > > > I would like to check if my subcortical segmentation is correct so I was running: > > > > tkmedit SUBJECT1 brainmask.mgz \ > > -aux T1.mgz -surfs \ > > -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > > > 1). Pial (red line), and white (yellow line) surfaces are shown and I wonder how I can add a green lie for my orig surface? > > 2). After I load the aparc+aseg.mgz is theer a way to load and overlay the original/correct atlas so I can see if my segmentation is correct? > > > > Thank you very much. > > Antonella > > > > > > > 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. > > > <P27.tiff>

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xopts script...
by Gonzalo Rojas Costa 02 Aug '11

02 Aug '11

Hi: In the web page "FSTutorial/TroubleshootingData - Free Surfer Wiki" appears "Try using an xopts script first to change the intensity thresholds being used"... What is a xopts script ?... How can I use a xopts script to change the intensity thresholds ?... Sincerely, Gonzalo Rojas Costa

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by laura de giglio via LinkedIn 02 Aug '11

02 Aug '11

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Fwd: Problem loading nii
by John Jan Drozd 01 Aug '11

01 Aug '11

But of course, Bruce says the .nii.gz format should have worked, so it does not need to be type mgz format. I would trust Bruce. Sorry for not cc'ing the mailing list earlier. Thanks, John John Drozd Post-Doctoral Fellow Robarts Research Institute University of Western Ontario London, Ontario, Canada http://publish.uwo.ca/~jdrozd2 Begin forwarded message: > From: John Jan Drozd <john.drozd(a)gmail.com> > Date: 1 August, 2011 5:10:07 PM EDT > To: "Tax, C.M.W." <c.m.w.tax(a)student.tue.nl> > Subject: Re: [Freesurfer] Problem loading nii > > Hi, > > I believe the image must be type mgz format for Freesurfer. (For FSL it needs to be type nii or nii.gz.) > > Try typing: > > gunzip t1.nii.gz > mri_convert t1.nii t1.mgz > tkmedit -f t1.mgz > > John > > John Drozd > Post-Doctoral Fellow > Robarts Research Institute > University of Western Ontario > London, Ontario, Canada > http://publish.uwo.ca/~jdrozd2 > > > On 2011-08-01, at 4:55 PM, "Tax, C.M.W." <c.m.w.tax(a)student.tue.nl> wrote: > >> Dear Sir/Madam, >> >> I would like to use freesurfer for cortical flattening, working with the nii format. When I try to load the nii.gz file as described on http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html, I get the following error: >> >> student@BMT-PC125:~$ tkmedit -f t1.nii.gz >> niiRead(): error opening file ./t1.nii.gz >> >> >> Error: Loading volume t1.nii.gz >> >> Couldn't read the anatomical volume. >> >> Tkmedit couldn't read the volume you specified. >> This could be because the image format wasn't recognized, >> or it couldn't find the proper header, >> or the file(s) were unreadable, >> or it was the wrong size. >> >> >> This image t1.nii.gz was obtained by converting DICOM images with dcm2nii. I also tried to load a example dataset downloaded from http://nifti.nimh.nih.gov/nifti-1/data, but still I get the same error. FSL was able to load both datasets without problems. >> >> Please could you help me with this problem? >> >> Thank you in advance, >> >> Kindest Regards >> >> _______________________________________________ >> 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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parts of brain not included in segmentation
by Branka Milivojevic 01 Aug '11

01 Aug '11

Hi, I'm a relatively new user of freesurfer, so I don't have much experience ... but I think I've also had problems with recon-all output. Posterior part of the brain has been omitted in a number of subjects. For one of the subjects I have tried to increase the area that is included in the brainmask, but the surfaces were still missing parts of the brain (I don't have output for the original problem). For the same subject, I have then tried to include control points (perhaps too many?), and then I ended up with a really large chunk of the occipital lobe missing.(surfsOnOrig.png & surfsOnBrainmask.png) surfsOnOrig_2.pmg and surfsOnBrainmask_2.png are from another subject, but you can see an example of how much occipital lobe is missing what happens when I run recon-all. (perhaps it is not too much to do a manual edit?) I think the problem might be a large difference in the white/gray contrast between occipipal lobe and the rest of the brain. Could you please tell me if this is fairly normal amount of brain to be missing and if there is anything that I could do to improve the situation. Thanks so much in advance. Cheers, Branka

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Re: [Freesurfer] trac-all -path errors
by Priti Srinivasan 01 Aug '11

01 Aug '11

Hi Ping, This is an issue with the mac build, that we are currently working on fixing. Anastasia, (cc'd) is working on a patch that you can download to resolve this issue. As far as the nb0 value is concerned you're correct, it assumes that the first 7 volumes are b0, but it uses that to compute an average b0 mask, so you should be fine using nb0 = 1. It will then use only the first volume (b0) to create the mask. Please refer to this thread for details on nb0 value in the configuration file: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018768.html -Priti > HI Priti, > > I've attached the trac-all.log. The "prior" had not finished, > complaining about memory allocation. > > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice Cannot allocate memory > > > The systems I tested were MAC OS X 10.5.8. with 2 x 2.66 Ghz Quad-Core processors and 16 GB memory, and MAC OS X 10.6 with 20 GB memory. Both of them failed with the same errors. > > In addition, I need to set nb0 = 1 in the configure file in order to run the "prior", although there are 7 b0 sparked in every 7 volumes. I think "nb0=7" means the first 7 volumes will be assumed to > non-diffusion weighted. Correct me if I am wrong. > Thanks. > > Ping > > > > On Fri, Jul 29, 2011 at 11:26 AM, Priti Srinivasan > <rspriti(a)nmr.mgh.harvard.edu> wrote: >> Hi Ping, >> The text files get created in the trac-all -prior stage. Maybe something >> went wrong in that step. Is this the case for all the tracts or just for >> this tract? If you can send us the trac-all.log file under the scripts directory it'll be easier to troubleshoot as to what went wrong. -Priti >>> Hi, >>> I got the error running "trac-all -path -c configure.txt" >>> ERROR: Could not open >>> ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt I can only find only image files in the "dlabel/diff" directory, but not text files. >>> Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? Thanks, >>> Ping >>> _______________________________________________ >>> 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] trac-all -path errors
by Moiyadi, Ammar 01 Aug '11

01 Aug '11

Hi, I am also getting the error where the txt files cannot be opened because they were not created beforehand. Where does the trac-all -prior step take place? Does it appear within the trac-all -prep script? Thank you, Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Friday, July 29, 2011 10:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 89, Issue 99 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. trac-all -path errors (Ping-Hong Yeh) 2. Re: trac-all -path errors (Priti Srinivasan) ---------------------------------------------------------------------- Message: 1 Date: Fri, 29 Jul 2011 11:09:28 -0400 From: Ping-Hong Yeh <pinghongyeh(a)gmail.com> Subject: [Freesurfer] trac-all -path errors To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAL1NnmP2+KdE5cNMVH4-qhnvSeMeQA7AjQ+cp-qPFtmGv3A+0Q(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi, I got the error running "trac-all -path -c configure.txt" ERROR: Could not open ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt I can only find only image files in the "dlabel/diff" directory, but not text files. Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? Thanks, Ping ------------------------------ Message: 2 Date: Fri, 29 Jul 2011 11:26:13 -0400 (EDT) From: "Priti Srinivasan" <rspriti(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] trac-all -path errors To: "Ping-Hong Yeh" <pinghongyeh(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <42727.132.183.139.239.1311953173.squirrel(a)mail.nmr.mgh.harvard.edu> Content-Type: text/plain;charset=iso-8859-1 Hi Ping, The text files get created in the trac-all -prior stage. Maybe something went wrong in that step. Is this the case for all the tracts or just for this tract? If you can send us the trac-all.log file under the scripts directory it'll be easier to troubleshoot as to what went wrong. -Priti > Hi, > > I got the error running "trac-all -path -c configure.txt" > > ERROR: Could not open > ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt > > > I can only find only image files in the "dlabel/diff" directory, but > not text files. > > Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? > > Thanks, > > Ping > _______________________________________________ > 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 End of Freesurfer Digest, Vol 89, Issue 99 ****************************************** 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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bbregister
by Michelle Umali 01 Aug '11

01 Aug '11

Hi Bruce, So for the following command: bbregister --s bert --mov func.nii --init-fsl --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf In the case of a retinotopy analysis, which files are register.dat and func.nii? Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: [Hide Quoted Text] Hi Michelle Try using bbregister. Cheers Bruce On Jul 31, 2011, at 6:54 PM, Michelle Umali <muu1(a)columbia.edu> wrote: Dear Freesurfers, During my retinotopy analysis, I was getting very strange fieldsign data (blue and red speckles) and my polar and eccentricity data was limited to the occipital pole. It was suggested that I check registration between the functional and anatomical. I was looking up tkregister2 help to figure this out but am still unsure how to register the polar and eccentricity data to the anatomical. Any help would be most appreciated. -Michelle Umali _______________________________________________ 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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Need help to run MRI data using Freesurfer in Mac OSx
by joanna floria 01 Aug '11

01 Aug '11

Hello Everyone, We just installed Freesurfer on Mac and the software got installed successfully. But when I am running my data, it just gets stuck in between and shows me the error. The command I used was: /Applications/freesurfer/bin/recon-all-s 002 -i /Users/kashou/Desktop/fMRI/Anesthetics/002/SPGR/MR000000 -all -notal-check The error: /Applications/freesurfer/subjects/002/mri \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin Nasser-Kashous-iMac.local 10.4.1 Darwin Kernel Version 10.4.1: Fri Jul 16 23:04:20 PDT 2010; root:xnu-1504.7.51~1/RELEASE_I386 i386 recon-all -s 002 exited with ERRORS Can anyone please help me out with the error? Thanks, Joanna

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Freesurfer August 2011