Freesurfer

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30132 discussions

Rejoindre mon réseau sur LinkedIn
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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mris_flatten problem
by Oya, Hiroyuki (UI Health Care) 01 Aug '11

01 Aug '11

Dear all, A patch created by mris_flatten looked odd (see attached image) . Any suggestion for this problem? Original patch (before flattening) seems good. Thank you. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Retinotopy Registration to Anatomical
by Michelle Umali 31 Jul '11

31 Jul '11

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

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Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
by sheraz＠nmr.mgh.harvard.edu 31 Jul '11

31 Jul '11

Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School Job Description A postdoctoral position is available with the TRANSCEND Research Program (www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org) which is affiliated with the Massachusetts General Hospital, Harvard Medical School and MIT. We are seeking a candidate with a strong basis in magnetic resonance imaging. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL as well as resting state fMRI), and on co-registering MEG with MRI. This position will involve analysis of existing multimodal imaging data and collection of new data. The emphasis of the postdoctoral fellowship will be analysis of existing datasets with secondary activity in piloting data for new studies. It will involve working closely with a multidisciplinary team and with children, and will also involve some research oriented analysis of data collected for clinical purposes. After initial phase-in, ample opportunity will also be provided to the candidate to self-explore and lead research. Datasets to be analyzed include: MRI (including DTI and 1H-spectroscopy) and MEG data on 6-12 and teenage matched autism spectrum and control subjects with phenotyping data MRI data ( (morphometry, DTI, spectroscopy) plus laboratory and phenotyping data) on 70 children with autism plus epilepsy and/or mitochondrial dysfunction, along with one or more overnight EEGs on each patient data from children ages 2-10 with and without autism. Overall objectives: To perform multimodal analyses of research and clinical research data, to develop new approaches for performing these analyses, and to design pipelines for data analysis. To write papers and grants which will be high priorities all along the way and will be actively supported by senior faculty. To take advantage of the world class faculty and facilities of the Martinos Center for Biomedical Imaging to perform the above activities to their maximal potential. The programs emphasis is on pathophysiologically grounded brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Requirements: Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Prior experience in MRI analysis is required. Experience with EEG will be an added advantage. Salary will be consistent with Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees and will range between $45,000 to $55,000 depending upon qualifications and experience. Compensation also includes full staff benefits, including health insurance, and vacation time. Contact: Interested applicants may send a CV to Dr. Martha R. Herbert at mherbert1(a)partners.org and cc transcend(a)partners.org.

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