[Freesurfer] PhD studentship at Durham University
Dear colleagues, Applications are invited for a fully funded PhD position (3 years) in the Department of Psychology at Durham University. The successful applicant will work with Paige Scalf in the Centre for Vision and Visual Cognition (CVVC) on the neural processes underlying vision, attention and working memory employing combinations of research methods and tools from psychology, neuroscience and functional neuroimaging (fMRI). The Department of Psychology and CVVC offer an exciting and friendly multidisciplinary research environment with ample opportunities for training and collaboration. The centre has access to excellent technical facilities including a 0T and 3T MRI scanner, as well as laboratories for brain stimulation (TMS, tdCS), motion analysis systems, behavioural experiments and eye-tracking. Dr Scalf has expertise in ultra-high resolution fMRI and time-resolved fMRI methodology. The candidate is expected to have a strong academic background. A preference is given to students with a background in psychology, neuroscience, math or computer science at the master’s level. Candidates who have knowledge of fMRI analysis packages (SPM, Matlab, Freesurfer, AFNI), statistical software (e.g., R or Stata) and programming skills (e.g.,python, C++, matlab ) will have a strong advantage. Applications are welcome from EU nationals. The position is expected to begin in October 2015. Applications should include a curriculum vitae and a cover letter. Three letters of academic reference, assessing the applicant’s research potential and personality, should be sent independently by the referees. Applications should be submitted electronically and all material, including reference letters, be sent to’psychology.off...@durham.ac.uk’ with reference to “PhD position vision/attention" in the e-mail header. Applications must be received by April 14th 2015. Informal inquiries can be sent via email to Paige Scalf, paige.sc...@durham.ac.uk ___ 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] Fully funded PhD studentship at Durham University
Dear colleagues, Applications are invited for a fully funded PhD position (3 years) in the Department of Psychology at Durham University. The successful applicant will work with Paige Scalf in the Centre for Vision and Visual Cognition (CVVC) on the neural processes underlying vision, attention and working memory employing combinations of research methods and tools from psychology, neuroscience and functional neuroimaging (fMRI). The Department of Psychology and CVVC offer an exciting and friendly multidisciplinary research environment with ample opportunities for training and collaboration. The centre has access to excellent technical facilities including a 0T and 3T MRI scanner, as well as laboratories for brain stimulation (TMS, tdCS), motion analysis systems, behavioural experiments and eye-tracking. Dr Scalf has expertise in ultra-high resolution fMRI and time-resolved fMRI methodology. The candidate is expected to have a strong academic background. A preference is given to students with a background in psychology, neuroscience, math or computer science at the master’s level. Candidates who have knowledge of fMRI analysis packages (SPM, Matlab, Freesurfer, AFNI), statistical software (e.g., R or Stata) and programming skills (e.g.,python, C++, matlab ) will have a strong advantage. Applications are welcome from students who are eligible for EU fee rates (UK, EU nationals). The position is expected to begin in October 2015. Applications should include a curriculum vitae and a cover letter. Three letters of academic reference, assessing the applicant’s research potential and personality, should be sent independently by the referees. Applications should be submitted electronically and all material, including reference letters, be sent to’psychology.off...@durham.ac.uk’ with reference to “PhD position vision/attention" in the e-mail header. Applications must be received by May 30th 2015. Informal inquiries can be sent via email to Paige Scalf, paige.sc...@durham.ac.uk http://scalflab.wix.com/visualcognitionlab https://www.dur.ac.uk/cvvc/research/ https://www.dur.ac.uk/cnru/ https://www.dur.ac.uk/psychology/research/neuroimagingcentre/ ___ 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] tksurfer viewing issues
Hello, I too am having trouble with tksurfer displaying the surfaces upside down and back to front, but believing that they are correctly oriented (i.e. Talairach coordinates change in the wrong direction wrt to the surface but in the correct direction wrt the display window). I"m also running a CentOs flavor. Did anyone manage to solve this issue? All the best, Paige ___ 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] tksurfer viewing issues
Hi Bruce, I'm analyzing phase encoded retinotopy, and it is not clear to me how to load complex overlays in freeview. Perhaps I am missing something? Best, Paige Hi Paige we have stopped development and most support of tksurfer. Can you use freeview instead or is there still some functionality that you need that is unique to tksurfer? cheers Bruce On Thu, 29 Sep 2016, Paige Scalf wrote: >* Hello, *> >* I too am having trouble with tksurfer displaying the surfaces upside down *>* and back to front, but believing that they are correctly oriented (i.e. *>* Talairach coordinates change in the wrong direction wrt to the surface but *>* in the correct direction wrt the display window). I"m also running a CentOs *>* flavor. Did anyone manage to solve this issue? *> >* All the best, *>* Paige* -- Paige E. Scalf, Ph.D. Lecturer Department of Psychology Durham University Psychology Department Durham University Science Laboratories South Road DURHAM DH1 3LE ___ 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] trio dicom files and mri_convert
Hello, I've been trying to use mri_convert (freesurfer-Darwin-tiger-stable-pub-v3.0.3) to reconstruct images from our Siemens Magnetom Trio. When I type: mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_ A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA Block1.img DB*.IMA and Block1.img are the input and output files respectively, I get the output detailed below (the salient error seems to be that mri_convert can't find a useful transformation matrix). Can you tell me what I can do to correct this problem? Many thanks in advance, Paige Scalf mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA Block1.img reading from DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA... Getting Series No Scanning Directory INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 INFO: Scanning for Series Number 3 INFO: found 107 files in series INFO: loading series header info. INFO: sorting. RunNo = 2 INFO: (120 110 50), nframes = 107, ismosaic=1 ERROR: incorreclty formatted version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B17 Maj = 0, Min=-1073775504, MinMin = 0 mojo:/Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 paige$ mri_convert -it dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA Block1.img mri_convert -it dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA Block1.img reading from DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA... Getting Series No Scanning Directory INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 INFO: Scanning for Series Number 3 INFO: found 107 files in series INFO: loading series header info. INFO: sorting. RunNo = 2 INFO: (120 110 50), nframes = 107, ismosaic=1 ERROR: incorreclty formatted version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B17 Maj = -1073770984, Min=22021328, MinMin = -1610546680 107 DICOM 3.0 files in list Found 107 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 107. reading DICOM image... - DICOM meta-header file name /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1/DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA Date and time study date 20100318 study time 160300.312000 series time 162802.453000 acquisition time162802.453000 Identification patient nameDB_A0A1_318 manufacturerSIEMENS Dimensions number of rows 880 number of columns 960 number of frames107 pixel width 2.1 pixel height2.1 slice thickness 2.1 field of view 1877.33 image number1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 25 repetition time 3000 inversion time not found echo number 1 flip angle 1.5708 bits allocated 16 Spatial information first image position-1027.46 -12.1727 952.833 last image position -1027.46 -12.1727 952.833 image orientation 1 0 0 0 -0.00174528 -0.98 - TR=3000.00, TE=25.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, 0.00174528, -0.99) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: -2.133 -0.000 nan nan; -0.000 0.004 nan nan; 0.000 -2.133 nan nan; 0.000 0.000 0.000 1.000; ___ 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] Freesurfer Digest, Vol 73, Issue 52
Well, I have retinotopy data (analyzed using FSL) that is flatmapped and registered (painfully by hand) using 3.0.3. I need the data for my current study, and I'm not sure how well it would survive transformation to the more recent version. If someone can tell me that the data I processed using 3.0.3 will still be usable/play nicely after an upgrade, I can do that. If that's not possible, I'd prefer to transplant files; multiple operational versions of software does get confusing, but that would also work as a last resort. Thanks, Paige On Fri, Mar 19, 2010 at 3:10 PM, Sebastian Moeller < sebastian.moel...@lur.rwth-aachen.de> wrote: > Hi Paige, > > I ran into a similar problem a few months ago. Freesurfer 3.0.5 could not > read data from a TIM trio with numaris B17. I solved this by transplanting > (copying) a number of files from freesurfer 4.4.0 (the recent one at the > time) into 3.0.5. unpacsdcmdir, mri_convert and a few more, that worked > okay, but I since switched to freesurfer 4.5.0 for good. If you have to > stick to 3.0.3 I can try to look up which files I had to replace in 3.0.5. > Or alternatively you can install v4.5.0 parallel to 3.0.3 and only use it to > import the DICOM data... > > best regards > Sebastian > > On Mar 19, 2010, at 12:37 PM, freesurfer-requ...@nmr.mgh.harvard.eduwrote: > > > Message: 7 > > Date: Fri, 19 Mar 2010 14:37:24 -0500 > > From: Paige Scalf > > Subject: [Freesurfer] trio dicom files and mri_convert > > To: freesurfer@nmr.mgh.harvard.edu > > Message-ID: > > <1113e70c1003191237y6f5723aeha927124dd30b5...@mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hello, > > > > I've been trying to use mri_convert > > (freesurfer-Darwin-tiger-stable-pub-v3.0.3) to reconstruct images from > our > > Siemens Magnetom Trio. When I type: > > > > mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_ > > A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA > Block1.img > > > > > > DB*.IMA and Block1.img are the input and output files respectively, I get > > the output detailed below (the salient error seems to be that > mri_convert > > can't find a useful transformation matrix). > > > > Can you tell me what I can do to correct this problem? > > Many thanks in advance, > > > > Paige Scalf > > > > > > mri_convert -it siemens_dicom -ot analyze4d > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA > > Block1.img > > reading from > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA... > > Getting Series No > > Scanning Directory > > INFO: Found 111 files in > /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 > > INFO: Scanning for Series Number 3 > > INFO: found 107 files in series > > INFO: loading series header info. > > > > INFO: sorting. > > RunNo = 2 > > INFO: (120 110 50), nframes = 107, ismosaic=1 > > ERROR: incorreclty formatted version string syngo MR B17 > > found in dicom tag 18,1020 (len = 3 != 6) > > Numaris Version: syngo MR B17 Maj = 0, Min=-1073775504, MinMin = 0 > > mojo:/Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 paige$ mri_convert > > -it dicom -ot analyze4d > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA > > Block1.img > > mri_convert -it dicom -ot analyze4d > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA > > Block1.img > > reading from > > > DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.50.21615932.IMA... > > Getting Series No > > Scanning Directory > > INFO: Found 111 files in > /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 > > INFO: Scanning for Series Number 3 > > INFO: found 107 files in series > > INFO: loading series header info. > > > > INFO: sorting. > > RunNo = 2 > > INFO: (120 110 50), nframes = 107, ismosaic=1 > > ERROR: incorreclty formatted version string syngo MR B17 > > found in dicom tag 18,1020 (len = 3 != 6) > > Numaris Version: syngo MR B17 Maj = -1073770984, Min=22021328, MinMin = > > -1610546680 > > 107 DICOM 3.0 files in list > > Found 107 DICOM Files > > WARNING: NumberOfFrames 0 != Found Count of slices 107. > > reading DICOM image... > > - > > DICOM meta-header > > > > file name > > > /Volumes/dub
[Freesurfer] job opportunity
Beginning August 15th, a two-year position is available for a highly motivated and talented postdoctoral fellow in the Department of Psychology at the University of Arizona. The goal of this research program is to study the neural processes that support vision, perception and attention using functional neuoimaging (including ultra high resolution and time resolved fMRI) and behavioral (including eye-tracking) methods. Candidates will be expected to support the research goals of the PI, but will also be given the opportunity to develop more independent lines of research. The candidate will be encouraged to take advantage of the highly collaborative departmental environment. The Department of Psychology is part of the School of Mind, Brain, and Behavior (MBB), and is a member of the College of Science, in keeping with its strong research-oriented approach and scientifically-derived knowledge base. Its faculty and students interact and collaborate with those of other MBB programs and departments—Neuroscience, Cognitive Science, and Speech, Language and Hearing Science—as well as with other academic units across campus. The fMRI facilities at the University of Arizona includes a GE 3.0T Signa scanner that is fully available for research use 5 days per week. The University of Arizona is a premier (NSF ranking: # 16) public research university located in Tucson, Arizona. The sun shines nearly every day in Tucson, which is surrounded by four mountain ranges that include the southernmost downhill ski resort in the USA. Tucson also supports great opportunities for hiking and cycling, and is one of the most bicycle friendly cities in the US. Candidates must have a PhD in neuroscience or a related field and the capacity to make a substantive intellectual contribution to the research program. Candidates with previous neuroimaging experience and strong programming skills will will be preferred. Of particular interest are those candidates with experience using python-based programs such as the Vision Egg and SciPy. For more information, contact Dr. Paige Scalf (psc...@gmail.com). Applications may be submitted to job #47659 at http://www.uacareertrack.com. ___ 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.
