Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Shifting hdr information in .nii?
by Joakim Vinberg 12 Apr '11

12 Apr '11

A little off-topic maybe, but: I am working to load external data into analysis programs using .nii format files. I have inplanes acquired at an ACPC orientation, as well as data collected and specially pre-processed through a MATLAB pathway that unfortunately strips away all orientation information. I have been trying to find a way to use the header information from the inplanes to orient the data (unfortunately, automated alignment algorithms fail due to the nature of the data). Does anybody have any suggestions, or information on exactly which fields in the .nii header to shift? Thanks in advance for all of the help on a thorny problem! Joakim

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Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School
by sheraz＠nmr.mgh.harvard.edu 12 Apr '11

12 Apr '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 and statement of interest addressing background and specific pertinence of the candidates interest to Dr. Martha R. Herbert at mherbert1(a)partners.org and cc transcend(a)partners.org. Applications will be considered until the position is filled.

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fill problem in properly normalized volume
by Fred Dick 12 Apr '11

12 Apr '11

Dear all we have had some odd behavior in 4 fairly high quality datasets that have been very nicely normalized and deskulled with a good Talairach but then only half filled in wm.mgz and all surfs (to various semi-planes). Orientation seems correct in tkmedit as well. We were thinking that it might be a cutting plane problem but weren't sure how this would happen since all else is OK. Anyone else have this issue (and a solution?) Thanks, Fred

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Segmentation Fault
by Allie Rosen 12 Apr '11

12 Apr '11

Hi All, Upon trying to assembly my subjects into a single surface space, I got the following error: *ERROR: number of vertices in /media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness does not match surface (142271,140585) ERROR: reading curvature file * I then tried to perform recon-all -make all, but got this error: *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log* In the .log, I got this: *-7.5000 22.5000 15.0000 2793.2134 1Segmentation fault ERROR: 'imgreg_4dfp /usr/rapps/freesurfer/average/711-2C_as_mni_average_305 /usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139 ERROR: mpr2mni305 execution aborted* Which is a segmentation fault. Can anyone help me fix this? Thanks, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

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Dura, manual editing, mri_gcut
by roger.jou＠yale.edu 12 Apr '11

12 Apr '11

Hi all, Sorry for the newbie questions, but I was wondering if there were any general guidelines on how much remaining DURA MATER and ARACHNOID MATER is acceptable after running autorecon1. In general, should dura be completely removed and arachnoid be left as is? Also, is mri_gcut run automatically as part of autorecon1? If so, how would I rerun mri_gcut to help remove more dura and/or arachnoid? Finally, is manual editing recommended for removing remaining dura and/or arachnoid? If so, should I strive to remove absolutely all of it? Thanks you all in advance! Roger

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bbregister
by Saad Ramadan 12 Apr '11

12 Apr '11

Hi freesurfer-ers: when you run something like: *bbregister --s MySubject --t1 --mov t1_svs.nii --init-fsl --reg t1.reg.dat* ** I expect to generate a file "t1.reg.dat". bbregister is exiting normally with no error message. Where is this file? I cannot find it. Thanks in advance. Saad

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Error downloading old version of freesurfer
by Rune Eikeland 12 Apr '11

12 Apr '11

Hi, When I try to download an old version of freesurfer (4.3.1) from http://www.freesurfer.net/pub/dist/freesurfer/4.3.1/ I get the following error message: The connection was reset The connection to the server was reset while the page was loading. I get the same error message with all versions of 4.3.1. Will it be possible for someone to fix these links? Alternatively, is it possible to download this version for Leopard/Mac from some other location? Best regards, Rune

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unable to dload freesurfer old versions
by Nikhil Pratap Singh 11 Apr '11

11 Apr '11

Hi, I was trying to download freesurfer realease 4.3 from the archives but unable to do so. Is the website down? freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0-full.tar.gz <http://www.freesurfer.net/pub/dist/freesurfer/4.3.0/freesurfer-Linux-centos…> Best, Nikhil

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Re: [Freesurfer] functional ROI analysis problem
by Katie Bettencourt 11 Apr '11

11 Apr '11

Ok, I ran that and a couple questions. I ran it on 2 different subjects and got the exact same value, is that expected? Do I need to run it for each subject? Also, do I need to do this for event-related designs as well, or just block designs? I tried to run it on another analysis I did, an event-related one, but got this error: ??? Error using ==> times Matrix dimensions must agree. Katie > On Mon, Apr 11, 2011 at 12:22 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> You can run it anytime after the analysis. The 'X' file below is >> an actual file that is there (X.mat). The value that you get out >> of this procedure should be used to multiply the values you get >> out of roisummary-sess. >> >> >> doug >> >> >> >> Katie Bettencourt wrote: >> >> I'm working with Yaoda Xu. Thanks for the percent signal >> change fix, but I"m a little >> confused by what you wrote. When do I run that? after running >> roisummary-sess? Or after the analysis is run? >> >> >> Also, is the load('X' a placeholder where I need to put >> load('filename')? or will it just work as is? Obviously I >> change the session and analysis in the cd line. And is >> that a flat scale factor for all conditions for that >> subject? >> >> Katie >> >> On Fri, Apr 8, 2011 at 10:59 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> btw, I notice that you have a harvard email now (was BU). >> who are >> you working with there? >> doug >> >> Katie Bettencourt wrote: >> >> Hi all, >> >> I'm doing ROI analysis on functional data with an >> anatomical >> label, and while the activity looks strong and robust in >> tksurfer, the % signal changes I am getting are very >> low (and >> much lower than we've previously found), and I'm not sure >> what's going on. >> >> I'm running Freesurfer 4.5 on red hat linux. >> >> The design is a blocked design with 4 non-null conditions, >> baseline is fixation. Attached is a picture of the >> activity I >> get for 2 subjects for on of the conditions vs fixation >> (baseline) at a p<0.05 threshold with the ROI outlined in >> black as well as the output from roisummary-sess for >> these two >> subjects in that roi. I calculate % signal change based of >> the output from roisummary-sess, dividing each condition by >> the baseline in that file and then multiplying by 100. % >> signal changes are listed below, along with all >> commands run. >> >> % signal change: >> 110222SKJ_connected 110222SP_connected >> 0.000988998467052 0.000533852720367 >> 0.00105349836708 0.000556814127695 >> 0.000408499366826 0.000327200054419 >> 0.000440749316839 0.000436266739225 >> >> commands: >> mkanalysis-sess -analysis connect -TR 2 -paradigm >> connect.dat >> -designtype blocked -funcstem fmc -motioncor -runlistfile >> connect_runs.txt -inorm -tpexclude tpexclude.dat >> -nconditions >> 4 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur >> >> mkcontrast-sess -analysis connect -contrast >> connected_vs_unconnected -a 1 -c 2 >> mkcontrast-sess -analysis connect -contrast >> connected_vs_noise >> -a 1 -c 3 >> mkcontrast-sess -analysis connect -contrast >> connected_vs_phase >> -a 1 -c 4 >> mkcontrast-sess -analysis connect -contrast >> connected_vs_fix >> -a 1 -c 0 >> mkcontrast-sess -analysis connect -contrast >> unconnected_vs_noise -a 2 -c 3 >> mkcontrast-sess -analysis connect -contrast >> unconnected_vs_phase -a 2 -c 4 >> mkcontrast-sess -analysis connect -contrast >> unconnected_vs_fix >> -a 2 -c 0 >> mkcontrast-sess -analysis connect -contrast >> noise_vs_phase -a >> 3 -c 4 >> mkcontrast-sess -analysis connect -contrast >> noise_vs_fix -a 3 -c 0 >> mkcontrast-sess -analysis connect -contrast >> shape_vs_noise -a >> 1 -a 2 -c 3 >> mkcontrast-sess -analysis connect -contrast >> shape_vs_phase -a >> 2 -a 1 -c 4 >> mkcontrast-sess -analysis connect -contrast >> shape_vs_noisephase -a 2 -a 1 -c 3 -c 4 >> mkcontrast-sess -analysis connect -contrast act_vs_fix >> -a 2 -a >> 1 -a 3 -a 4 -c 0 >> >> selxavg3-sess -sf connect-sess -df connect.dir >> -analysis connect >> >> #run ROIs >> setenv anal connect >> foreach roi ( infIPS supIPS loc ) >> foreach h (lh rh) >> func2roi-sess -roidef ${roi}-${anal}-${h} -analysis $anal >> -anatlabel ips_loc/${roi}-${h} -sf connect-sess -df >> connect.dir >> roisummary-sess -sumfile ips-rois/${anal}_${roi}-${h}.dat >> -roidef ${roi}-${anal}-${h} -analysis ${anal} -sf >> connect-sess >> -df connect.dir >> python roi_reader.py -r ${roi} -a ${anal} -z ${h} -f >> ips-rois -c 4 >> end >> end >> >> Thanks, >> >> Katie >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> >> 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. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >

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Fwd: bbregister bug? with init-spm option--flips left and right
by Tyler Seibert 11 Apr '11

11 Apr '11

Screenshot2 attached ---------- Forwarded message ---------- From: Tyler Seibert <tseibert(a)ucsd.edu> Date: Thu, Mar 17, 2011 at 4:02 PM Subject: bbregister bug? with init-spm option--flips left and right To: freesurfer(a)nmr.mgh.harvard.edu Hello, I hope this is the correct email list--this is my first time posting (just subscribed). I have been using bbregister to calculate a tranformation matrix between a T2 image (T2brain.nii.gz) and the subject's T1.mgz for subsequent use with mri_vol2surf. I have found that the init-fsl option frequently gives very poor registrations (e.g., registered T2 is rotated 30+ degrees from T1). The init-spm option seemed to be working great. However, upon close inspection, I became suspicious this option was actually flipping the T2 so that the left hemisphere became right and vice versa. I am using FreeSurfer version 4.5 and have spm8 referenced in my matlab path. I used a directory ~/bbreg_test in my home directory for the test (linux), which consisted simply of running bbregister with init-fsl and init-spm options. The attached log file (log.txt) contains the commands I used. The terminal output from each test was saved in text files as well, also attached. I have also attached two screenshots of the tkregister2 output for these tests. In each screenshot the far left image is the registered T2 using init-spm, and the far right image is the registered T2 using init-fsl. As the init-fsl version is clearly wrong, the middle image in each screenshot is the init-fsl output again, but manually rotated several degrees to the left to better emphasize the mirror-image relationship between the init-spm (far left) and init-fsl (middle and far right) output images. Please let me know if there is anything further you need from me to investigate this or if there is any insight you can give me as far as how to avoid this error. I noticed at line 209 of the spm_test.txt log file there is a message stating that RAS coordinate system is assumed (see below, where I have copied lines 208-213 for convenience). This may very well be the problem, as the T2brain.nii.gz volume is in LAS, according to mri_info output. However, I do not see where I can override this RAS assumption. >> >> >> >> >> >> >> >> >> /home/tylers/apps/spm8/spm_coreg.m > >> >> >> >> >> INFO: Assuming RAS coordinate system > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using > /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/refvol.spmregister.img > as the target image > >> using > /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/movvol.spmregister.img > as the source image > >> >> >> >> >> >> >> >> >> >> >> >> >> >> > Thank you, -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego

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