Re: [Freesurfer] Problem running recon-all with option -qcache
Hi Doug, Indeed, you are right, I forgot to run recon-all -autorecon3. It is not well documented that after running -autorecon2-wm one should also run -autorecon3. I had the impression that this portion was executed automatically by -autorecon2-wm. Ed On 2 Feb 2011, at 18:03, Douglas N Greve wrote: Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll need to re-run some portion of recon-all depending upon where in the stream it aborted. doug Ed Gronenschild wrote: Hi, A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was: number of vertices in ../subjectID/surf/lh.thickness does not match surface (141969,131763). It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness. I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected. What can I do to use the -qcache option? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] reg-feat2anat: a problem!
Hi Aga, are you using nifti? If analyze, that could be the problem. Do your functionals and anatomicals have a different sign to their determinants (you can check with mri_info). In principle, reg-feat2anat should handle this but in some cases it does not. The 5.1 version will handle it properly. If they do have the same sign, then look through the log file and find the flirt command. Run that command by itself (you may need to run reg-feat2anat with --nocleanup to keep it from deleting the files). If that fails, then contact the FSL people doug Agnieszka Burzynska wrote: Dear all, I am using the command reg-feat2anat to transform functional data pre-processed in FSL to the anatomical image in Freesurfer. As suggested, I check the registration with reg-feat2anat --feat run2.feat —manual. I have 3 runs of functional data for each subject. Surprisingly, some runs are registered well but others not (even of the same subject, so using the same reference anatomical images: see the attached image. Upper row: bad registration of one run and lower row: good registration of another run). I have no problem to manually correct the registrations, it works well, but as I have many subjects, I wonder if there may be a way to change some options of reg-feat2anat to make it work better? Can you see from the attached image what is the problem with my images? (I viewed the functional and anatomical data of a few subjects, some woth good and some with bad registration and see no difference or flip) Thanks a lot for your help! Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_convert with lists and orientations
I get this behavior with --out_orientation, but not with --in_orientation. Are you sure it happens with both? And are you sure you want to be changing the orientation? If you have a volume from a person in the scanner head-first supine, then the answer is almost surely no. doug Reza Farivar wrote: Hello, I'm encountering a strange problem with mri_convert. Basically, if I just ask it to convert a set of dicoms into a 4D NIFTI, it does this fine, but if I specify anything about the input and/or output orientation (using --in_orientation or --out_orientation), it only spits out 1 image, not the entire time series. Am I doing something wrong? Thanks, Reza || Reza Farivar, Ph.D. Research Fellow Harvard Medical School Massachusetts General Hospital Dept. of Radiology Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Problem running recon-all with option -qcache
Thanks for the suggestion Ed. I've just added the text below to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Troubleshooting. If you know of another place where it would be useful, please let us know. doug Note that after you run recon-all with the -autorecon2-wm flag, you will still need to run it with the -autorecon3 flag. You can run it with both -autorecon2-wm and -autorecon3, though if the changes you made did not fix the problem, then the time spent running autorecon3 will be wasted. Ed Gronenschild wrote: Hi Doug, Indeed, you are right, I forgot to run recon-all -autorecon3. It is not well documented that after running -autorecon2-wm one should also run -autorecon3. I had the impression that this portion was executed automatically by -autorecon2-wm. Ed On 2 Feb 2011, at 18:03, Douglas N Greve wrote: Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll need to re-run some portion of recon-all depending upon where in the stream it aborted. doug Ed Gronenschild wrote: Hi, A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was: number of vertices in ../subjectID/surf/lh.thickness does not match surface (141969,131763). It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness. I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected. What can I do to use the -qcache option? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Abblocked Setup
The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] abblocked Setup
Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] reg-feat2anat: a problem!
That is not a problem. By anatomical I meant the FreeSurfer anatomical (eg, orig.mgz) doug Agnieszka Burzynska wrote: Dear Doug, Thank you a lot! Our feat data is always nifti, but anatomical FSL data is sometimes in the analyze format. Is this already a problem? I will now check the rest. Thank you, cheers, Aga On 2/7/11 4:35 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Aga, are you using nifti? If analyze, that could be the problem. Do your functionals and anatomicals have a different sign to their determinants (you can check with mri_info). In principle, reg-feat2anat should handle this but in some cases it does not. The 5.1 version will handle it properly. If they do have the same sign, then look through the log file and find the flirt command. Run that command by itself (you may need to run reg-feat2anat with --nocleanup to keep it from deleting the files). If that fails, then contact the FSL people doug Agnieszka Burzynska wrote: Dear all, I am using the command reg-feat2anat to transform functional data pre-processed in FSL to the anatomical image in Freesurfer. As suggested, I check the registration with reg-feat2anat --feat run2.feat ‹manual. I have 3 runs of functional data for each subject. Surprisingly, some runs are registered well but others not (even of the same subject, so using the same reference anatomical images: see the attached image. Upper row: bad registration of one run and lower row: good registration of another run). I have no problem to manually correct the registrations, it works well, but as I have many subjects, I wonder if there may be a way to change some options of reg-feat2anat to make it work better? Can you see from the attached image what is the problem with my images? (I viewed the functional and anatomical data of a few subjects, some woth good and some with bad registration and see no difference or flip) Thanks a lot for your help! Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Abblocked Setup
Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Abblocked Setup
sfa-sess is depricated now (should not even be in there). Use selxavg3-sess. doug Chindhuri Selvadurai wrote: Hi Doug, For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this? We are using: freesurfer v5 our subjects directory: /cluster/manoach/milton/subjects command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh output that was given: # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30 The contrasts are going to be created automatically. These will be: fund - stands for fundamental - this is the F-test of the sine and cosine components, probably what you want fund-sin -- t-test of the sine component (this may also be useful) fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape) harm -- F test on the harmonics (probably not too useful) It is going to assume that the first condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] POSTDOCTORAL POSITION - Neuroimaging and Brain Plasticity
Please see the attached file. If interested, pelase submit your C.V. and relevant reprints, together with a cover letter describing current research interests and future research goals, and also arrange to have three letters of reference sent independently to: Dr. Sylvain Moreno Rotman Research Institute Baycrest 3560 Bathurst Street Toronto, Ontario, M6A 2E1, Canada E-mail: smor...@rotman-baycrest.on.ca Amir M. Tahmasebi, Ph.D. Postdoctoral Research Fellow Rotman Research Institute, University of Toronto, Toronto, Ontario CANADA Tel: (416) 785-2500, ext. 3130 Web: www.cs.queensu.ca/~tahmaseb Postdoc Fellowship - ad.pdf Description: Adobe PDF document ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Whole brain gray matter image
Hello FS Experts, I am trying to generate the whole brain gray matter image, I use aparc_aseg.mgz - wm.mgz for gray matter mask, then use this mask for gray matter. Is it correct? What is the difference between aseg.mgz and ribbon.mgz? Hope your help. Thanks. Aize ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] two vol fields for retinotopic analysis?
Dear freesurfer experts: I noticed that there are two 'vol' fields when I use MRIread. 1) mri.vol 2) mri.analyzehdr.vol My question is: I have two arrays, one with 3D coordinates and a second 1 dimensional array with corresponding phase values. Which 'vol' field do I put the 3D coordinates in and which do I put the phase values in? Many thanks! -jason. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Job Opening: Research Technician in Brain Imaging
The Solodkin/Small Brain Circuits Laboratory at the University of California, Irvine, will soon have an opening for a research technician in image processing. This job would be ideal for someone interested in applying basic skills in signal processing or applied mathematics to a variety of functional and structural neuroimaging studies related to human language processing and motor control, including healthy adults and children, and adults and children with neurological injuries or disease. Job tasks include: analyzing functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) data, performing statistical analyses of processed human data, working with cortical surface maps, managing and updating our imaging database, and helping to improve our processing procedures, including our use of high-performance cluster and grid computers. The ideal candidate will have a B.A. or B.S. degree in engineering, physics, mathematics, or computer science; knowledge of the UNIX operating system; programming experience; interest in biomedical applications; coursework in signal analysis and/or statistics. Variations from these ideals will certainly be entertained in an otherwise highly qualified candidate. Although this position is not yet formally posted, we are interested in hearing from qualified candidates now. If interested, please forward your CV/resume to msch...@uci.edu. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. ___ Freesurfer mailing list Freesurfer@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.
