[Freesurfer] Fwd: Connectome Research Coordinator (Senior), University of Pennsylvania
Dear colleagues, The Penn Frontotemporal Degeneration Center at the University of Pennsylvania (http://ftd.med.upenn.edu/) is seeking a research coordinator for the multi-site FTD Connectome study. Please see the details below; applications should be directed to http://jobs.hr.upenn.edu/postings/18756. Thanks, Jeff Phillips Postdoctoral Fellow Penn FTD Center University of Pennsylvania Duties: The primary responsibility of the successful candidate will be the coordination of a multi-site consortium using a novel approach to neuroimaging of neurodegenerative diseases. The lead site is Penn, and participating sites include Mayo Clinic, UCSF, MGH and Northwestern. All sites have specialized neuroimaging equipment, and we will be using advanced neuroimaging tools developed locally and in collaboration with the Human Connectome Project (HCP) to analyze the acquired data. The successful candidate also will be responsible for managing the Penn site. This project is coordinated with two other multi-site registries involving these same sites that are recruiting participants for this neuroimaging project (and other studies). Participants will include: 1. healthy control subjects; 2. individuals who have a frontotemporal degeneration (FTD) spectrum disorder such as primary progressive aphasia, progressive supranuclear palsy, or FTD with amyotrophic lateral sclerosis; and 3. individuals who are carrying a mutation that has resulted in an FTD spectrum disorder or are at risk for developing a FTD-spectrum disorder. Coordination will include weekly meetings with project coordinators at the other participating sites, developing reports for monthly meetings with NIH and principal investigators at other sites, monitoring imaging data flow to our coordinating site, monitoring the database that tracks participants, monitoring data flow from Penn to the HCP coordinating center, and managing requests for data from investigators. Other administrative responsibilities will include help managing the consortium budget. Local site responsibilities will include assistance with on-going recruitment processes, helping to collect imaging data, managing the local budget, supervising local technical and research staff, and participating in imaging analyses. Also included are implementation of Connectome imaging analysis and operation of the Prisma MRI scanner. Position is contingent on continued funding. Qualifications: A Bachelor’s degree and to 3 to 5 years of experience, or equivalent combination of education and experience, are required. Masters degree or PhD in neuroscience, psychology, linguistics, biology, biomedical engineering or related fields and 2 years to 3 years of experience strongly preferred. Past research and project coordination experience working in a similar lab setting is highly desirable. Experience with the following is preferred: Linux/Unix, brain imaging data analysis, MATLAB, computer programming, statistical analysis, research project management, or neuropsychological assessment. The candidate must be able to work independently and have strong organizational and interpersonal skills. Apply at http://jobs.hr.upenn.edu/postings/18756 ___ 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] accounting for BOLD response lag in FS retinotopy analysis
Hello all, I am performing my first retinotopy analysis, and I'd like to get some more information about the model created by paradigm files in the retinotopy analysis. Specifically, I am unsure whether to include or exclude fixation periods from the ends of my retinotopy runs. I imagine the analysis must somehow take into account the slow drop-off of the BOLD response--can you tell me if/how it does so? Since the analysis asks for the number of cycles, but not the duration of each cycle, I worry that including extra timepoints will just result in FS concluding that my stimulation period is longer than it actually is. If there exists an example design matrix for the retinotopy analysis, that would also be useful. Thanks, Jeff Phillips University of Pittsburgh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] retinotopy and alternating stimulus direction within-run
Hello all, I am wondering if the FS FAST retinotopy analysis can deal with within-run alternations of stimulus direction. I have collected data in which eccentricity and polar angle were manipulated in separate runs, but within each run, a cycle of stimulation in one direction was followed by a cycle in the opposite direction. For example, 32 s of clockwise-rotating wedges were followed by 32 s of counterclockwise wedges, etc. I realize now that this may not have been a wise choice--does FS FAST have some paradigm file option for alternating stimulation? If not, is my best solution to cut and splice my runs, dividing each into two mini-runs of single-direction stimulation? Thanks, Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] failed Talairach quality check; alternatives?
Hi all, I have an MPRAGE which consistently fails the Talairach quality check (see attached error) in autorecon1. (A 32-channel coil was used in this scan, and I suspect that might be a cause of the failure.) Per the wiki's suggestion, I have tried to manually fix the transform in tkregister2 and rerun reconstruction, but despite multiple attempts, I haven't been able to get a transform which satisfies the quality check. From similar list posts, I thought it might be possible for me to Talairach in an external program (BET, AFNI, etc.) and create a transform file that FreeSurfer can read. If this is possible, could you give me an overview of the process, or point me to existing documentation? Thanks, Jeff Phillips # #...@# Talairach Failure Detection Wed Jan 21 17:20:33 EST 2009 /data/projects/32ch_121908/121908-2/121908-2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5118, pval=0.1531 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /data/projects/32ch_121908/121908-2/121908-2/mri/transforms/talairach_avi.log TalAviQA: 0.95701 z-score: -4 ERROR: Talairach QA check failed! z-score = -4 <= -4 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux thinking.lrdc.pitt.edu 2.6.18-53.1.13.el5 #1 SMP Mon Feb 11 13:27:27 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Jan 21 17:20:34 EST 2009 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] drawing ROIs in surface space
Hello all, I am trying to hand draw ROIs from a functional overlay. The wiki mentions a Cut Area tool in tksurfer, which sounds ideal for getting rid of the area outside my ROI, but it's nowhere to be found in the tksurfer GUI for our installation, Centos 4 x86 64 bit. Has this tool been renamed or subsumed under some other tool? If there is an easier way for me to draw ROIs? Thanks, Jeff Phillips University of Pittsburgh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: drawing ROIs in surface space
Alright, perhaps I should revise my question--it seems like labels are the way to go for specifying ROIs. If that's the case, how do I convert a label file into a volume-space image? Thanks again, Jeff On Sat, Mar 7, 2009 at 2:09 PM, Jeff Phillips wrote: > Hello all, > > I am trying to hand draw ROIs from a functional overlay. The wiki mentions > a Cut Area tool in tksurfer, which sounds ideal for getting rid of the area > outside my ROI, but it's nowhere to be found in the tksurfer GUI for our > installation, Centos 4 x86 64 bit. Has this tool been renamed or subsumed > under some other tool? If there is an easier way for me to draw ROIs? > > Thanks, > > Jeff Phillips > University of Pittsburgh > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Can fieldsigns be added across sessions?
Hi all, I would like to add fieldsigns across multiple retinotopy sessions in the same subject, in order to get a metric of the reliability of the mapping. However, when I tried to do this in one subject, I found that fieldsigns from two sessions largely canceled one another out. This led to a discussion in our lab of whether the fieldsign 1) has a consistent meaning across sessions and subjects, or 2) whether the fieldsign in a given region, say V1, may switch from positive to negative due to noise or between-subject differences. For example, a colleague speculated that paint-sess could start with +1 at an arbitrary starting point on the edge of an occipital patch, then flip the sign whenever the polar angle/eccentricity gradients reversed themselves. Thus, V5 might be +1, V4 = -1, V3 = +1, V2 = -1, and V1 would be +1. However, if noise in a given session resulted in a failure to detect V4, then V1 would end up being the opposite fieldsign, -1. Is this correct? If so, then I might be shooting myself in the foot by adding fieldsign maps from different sessions. I would really appreciate any insight about how the fieldsign is assigned, and whether circumstances like the ones I describe could cause it to flip for a given functional region. Thanks, Jeff Phillips ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Can fieldsigns be added across sessions?
Hi Don, Thanks for your comments. I will try operating on the eccentricity and polar angle maps first--however, if I calculate a fieldsign from average maps, I presume that the fieldsign map will not be similarly graded, but rather binary. I'll have to think about how to adapt that to our purposes. I'm confident that the stimulus order was not reversed between sessions. One difference which did exist was that the first session involved unidirectional stimulation (i.e., only clockwise wedges and only expanding rings), while the second session involved bidirectional stimulation in alternating runs (i.e., both clockwise/counterclockwise and expanding/contracting rings). Would this difference create any problems? More generally, I'm still a bit confused about the calculation of the fieldsign. The wiki notes that "positive" and "negative" are arbitrarily defined--in other words, these terms don't bear any relation to clockwise/counterclockwise stimulation. It also appears (but please correct me if I'm wrong) that the meanings of these terms are not linked across the polar angle and eccentricity manipulations--that is, I haven't read of any rule that says if you call clockwise wedges positive, then expanding rings must also be termed positive. I thought that knowing this directionality would be important to interpreting the cross-product. I have been unable to find a document, wiki page, etc. which explains some of these details--if you happen to know of one, I would appreciate the reference. Thanks, Jeff On Fri, May 8, 2009 at 3:32 PM, Don Hagler wrote: > I think you should average your polar angle and eccentricity maps across > session and then calculate fieldsign from that. You do a complex average (a > separate average for real and imaginary components). > > By the way, the sign of the fieldsign measure should have a fixed meaning; > the orientation of the cross product of the gradients of polar angle and > eccenctricity, relative to the cortical surface. Are you sure you didn't > reverse the stimulus order or something? Was the projector's image upside > down or flipped left/right? > > -- > Date: Thu, 7 May 2009 18:47:32 -0400 > From: jeffrey.s.phill...@gmail.com > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Can fieldsigns be added across sessions? > > > Hi all, > > I would like to add fieldsigns across multiple retinotopy sessions in the > same subject, in order to get a metric of the reliability of the mapping. > However, when I tried to do this in one subject, I found that fieldsigns > from two sessions largely canceled one another out. This led to a > discussion in our lab of whether the fieldsign 1) has a consistent meaning > across sessions and subjects, or 2) whether the fieldsign in a given region, > say V1, may switch from positive to negative due to noise or between-subject > differences. For example, a colleague speculated that paint-sess could > start with +1 at an arbitrary starting point on the edge of an occipital > patch, then flip the sign whenever the polar angle/eccentricity gradients > reversed themselves. Thus, V5 might be +1, V4 = -1, V3 = +1, V2 = -1, and > V1 would be +1. However, if noise in a given session resulted in a failure > to detect V4, then V1 would end up being the opposite fieldsign, -1. Is > this correct? If so, then I might be shooting myself in the foot by adding > fieldsign maps from different sessions. I would really appreciate any > insight about how the fieldsign is assigned, and whether circumstances like > the ones I describe could cause it to flip for a given functional region. > > Thanks, > > Jeff Phillips > > -- > Windows Live™: Keep your life in sync. Check it > out.<http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Can fieldsigns be added across sessions?
Sorry, one additional question: per your suggestion, I can handle adding/averaging the real and imaginary component masks, but what syntax can I use in paint-sess to convert those composite masks into fieldsign maps? Thanks, Jeff On Mon, May 11, 2009 at 12:40 PM, Jeff Phillips < jeffrey.s.phill...@gmail.com> wrote: > Hi Don, > > Thanks for your comments. I will try operating on the eccentricity and > polar angle maps first--however, if I calculate a fieldsign from average > maps, I presume that the fieldsign map will not be similarly graded, but > rather binary. I'll have to think about how to adapt that to our purposes. > > > I'm confident that the stimulus order was not reversed between sessions. > One difference which did exist was that the first session involved > unidirectional stimulation (i.e., only clockwise wedges and only expanding > rings), while the second session involved bidirectional stimulation in > alternating runs (i.e., both clockwise/counterclockwise and > expanding/contracting rings). Would this difference create any problems? > > More generally, I'm still a bit confused about the calculation of the > fieldsign. The wiki notes that "positive" and "negative" are arbitrarily > defined--in other words, these terms don't bear any relation to > clockwise/counterclockwise stimulation. It also appears (but please correct > me if I'm wrong) that the meanings of these terms are not linked across the > polar angle and eccentricity manipulations--that is, I haven't read of any > rule that says if you call clockwise wedges positive, then expanding rings > must also be termed positive. I thought that knowing this directionality > would be important to interpreting the cross-product. > > I have been unable to find a document, wiki page, etc. which explains some > of these details--if you happen to know of one, I would appreciate the > reference. > > Thanks, > > Jeff > > > On Fri, May 8, 2009 at 3:32 PM, Don Hagler wrote: > >> I think you should average your polar angle and eccentricity maps across >> session and then calculate fieldsign from that. You do a complex average (a >> separate average for real and imaginary components). >> >> By the way, the sign of the fieldsign measure should have a fixed meaning; >> the orientation of the cross product of the gradients of polar angle and >> eccenctricity, relative to the cortical surface. Are you sure you didn't >> reverse the stimulus order or something? Was the projector's image upside >> down or flipped left/right? >> >> -- >> Date: Thu, 7 May 2009 18:47:32 -0400 >> From: jeffrey.s.phill...@gmail.com >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: [Freesurfer] Can fieldsigns be added across sessions? >> >> >> Hi all, >> >> I would like to add fieldsigns across multiple retinotopy sessions in the >> same subject, in order to get a metric of the reliability of the mapping. >> However, when I tried to do this in one subject, I found that fieldsigns >> from two sessions largely canceled one another out. This led to a >> discussion in our lab of whether the fieldsign 1) has a consistent meaning >> across sessions and subjects, or 2) whether the fieldsign in a given region, >> say V1, may switch from positive to negative due to noise or between-subject >> differences. For example, a colleague speculated that paint-sess could >> start with +1 at an arbitrary starting point on the edge of an occipital >> patch, then flip the sign whenever the polar angle/eccentricity gradients >> reversed themselves. Thus, V5 might be +1, V4 = -1, V3 = +1, V2 = -1, and >> V1 would be +1. However, if noise in a given session resulted in a failure >> to detect V4, then V1 would end up being the opposite fieldsign, -1. Is >> this correct? If so, then I might be shooting myself in the foot by adding >> fieldsign maps from different sessions. I would really appreciate any >> insight about how the fieldsign is assigned, and whether circumstances like >> the ones I describe could cause it to flip for a given functional region. >> >> Thanks, >> >> Jeff Phillips >> >> -- >> Windows Live™: Keep your life in sync. Check it >> out.<http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009> >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Can fieldsigns be added across sessions?
he > same subject, in order to get a metric of the reliability of the mapping. > However, when I tried to do this in one subject, I found that fieldsigns > from two sessions largely canceled one another out. This led to a > discussion in our lab of whether the fieldsign 1) has a consistent meaning > across sessions and subjects, or 2) whether the fieldsign in a given region, > say V1, may switch from positive to negative due to noise or between-subject > differences. For example, a colleague speculated that paint-sess could > start with +1 at an arbitrary starting point on the edge of an occipital > patch, then flip the sign whenever the polar angle/eccentricity gradients > reversed themselves. Thus, V5 might be +1, V4 = -1, V3 = +1, V2 = -1, and > V1 would be +1. However, if noise in a given session resulted in a failure > to detect V4, then V1 would end up being the opposite fieldsign, -1. Is > this correct? If so, then I might be shooting myself in the foot by adding > fieldsign maps from different sessions. I would really appreciate any > insight about how the fieldsign is assigned, and whether circumstances like > the ones I describe could cause it to flip for a given functional region. > > Thanks, > > Jeff Phillips > > -- > Windows Live™: Keep your life in sync. Check it > out.<http://windowslive.com/explore?ocid=TXT_TAGLM_BR_life_in_synch_052009> > > > > -- > Hotmail® has a new way to see what's up with your friends. Check it > out.<http://windowslive.com/Tutorial/Hotmail/WhatsNew?ocid=TXT_TAGLM_WL_HM_Tutorial_WhatsNew1_052009> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Can fieldsigns be added across sessions?
;>From: jeffrey.s.phill...@gmail.com >><mailto:jeffrey.s.phill...@gmail.com> >>To: dhagle...@hotmail.com <mailto:dhagle...@hotmail.com> >>CC: freesurfer@nmr.mgh.harvard.edu >><mailto:freesurfer@nmr.mgh.harvard.edu> >> >> >> >>Hi Don, >> >>Thanks for your comments. I will try operating on the >>eccentricity and polar angle maps first--however, if I calculate a >>fieldsign from average maps, I presume that the fieldsign map will >>not be similarly graded, but rather binary. I'll have to think >>about how to adapt that to our purposes. >>I'm confident that the stimulus order was not reversed between >>sessions. One difference which did exist was that the first >>session involved unidirectional stimulation (i.e., only clockwise >>wedges and only expanding rings), while the second session >>involved bidirectional stimulation in alternating runs (i.e., both >>clockwise/counterclockwise and expanding/contracting rings).Would >> this difference create any problems? >> >>More generally, I'm still a bit confused about the calculation of >>the fieldsign. The wiki notes that "positive" and "negative" are >>arbitrarily defined--in other words, these terms don't bear any >>relation to clockwise/counterclockwise stimulation. It also >>appears (but please correct me if I'm wrong) that the meanings of >>these terms are not linked across the polar angle and eccentricity >>manipulations--that is, I haven't read of any rule that says if >>you call clockwise wedges positive, then expanding rings must also >>be termed positive. I thought that knowing this directionality >>would be important to interpreting the cross-product. >>I have been unable to find a document, wiki page, etc. which >>explains some of these details--if you happen to know of one, I >>would appreciate the reference. >> >>Thanks, >> >>Jeff >> >>On Fri, May 8, 2009 at 3:32 PM, Don Hagler ><mailto:dhagle...@hotmail.com>> wrote: >> >>I think you should average your polar angle and eccentricity >>maps across session and then calculate fieldsign from that. >> You do a complex average (a separate average for real and >>imaginary components). >> >>By the way, the sign of the fieldsign measure should have a >>fixed meaning; the orientation of the cross product of the >>gradients of polar angle and eccenctricity, relative to the >>cortical surface. Are you sure you didn't reverse the >>stimulus order or something? Was the projector's image upside >>down or flipped left/right? >> >> >> >>Date: Thu, 7 May 2009 18:47:32 -0400 >>From: jeffrey.s.phill...@gmail.com >><mailto:jeffrey.s.phill...@gmail.com> >>To: freesurfer@nmr.mgh.harvard.edu >><mailto:freesurfer@nmr.mgh.harvard.edu> >> >>Subject: [Freesurfer] Can fieldsigns be added across sessions? >> >> >>Hi all, >> >>I would like to add fieldsigns across multiple retinotopy >>sessions in the same subject, in order to get a metric of the >>reliability of the mapping. However, when I tried to do this >>in one subject, I found that fieldsigns from two sessions >>largely canceled one another out. This led to a discussion in >>our lab of whether the fieldsign 1) has a consistent meaning >>across sessions and subjects, or 2) whether the fieldsign in a >>given region, say V1, may switch from positive to negative due >>to noise or between-subject differences. For example, a >>colleague speculated that paint-sess could start with +1 at an >>arbitrary starting point on the edge of an occipital patch, >>then flip the sign whenever the polar angle/eccentricity >>gradients reversed themselves. Thus, V5 might be +1, V4 = -1, >>V3 = +1, V2 = -1, and V1 would be +1. However, if noise in a >>given session resulted in a failure to detect V4, then V1 >>would end up being the opposite fieldsign, -1. Is this >>correct? If so, then I might be shooting myself in the foot >>by adding fieldsign
Re: [Freesurfer] Can fieldsigns be added across sessions?
Hi Doug and Jon, I wanted to follow up on your last e-mail--can you tell me how you were able to set an "anchor point" in the calcarine fissure? If you can recall why it seemed necessary to set the calcarine fissure fieldsign to +1, I would greatly appreciate it. This sounds potentially useful to us, as it seems like some combination of low statistical power and the operation of the fieldsign algorithm could be causing the between-session inconsistencies in our maps. Thanks, Jeff On Mon, May 11, 2009 at 8:45 PM, Douglas N Greve wrote: > > > Jeff Phillips wrote: > >> Hi Doug, >> >> Thanks for responding, and I think I need to restate our original >> question(s). What we are trying to do is to get a metric of the reliability >> of retinotopic mapping--i.e., across multiple sessions, how often are >> regional borders replicated? To that end, we have been splitting up our >> data, treating pairs of eccen/polar stimulation runs (1 run eccen, 1 run >> polar) as separate sessions, and then summing the fieldsign maps which we >> get for each session. Thus, if we have 5 "sessions", we could ideally sum >> their fieldsigns and find that most vertices/voxels had a 5-out-of-5 score. >> I realize that our power over each session (i.e., over just two runs) is >> very low, but ignoring that very important issue for the time being, does it >> make sense to sum (not average) our fieldsign maps in this way? >> > Seems reasonable. > >> >> Relatedly, can you think of a scenario in which the V1 fieldsign could be >> opposite between two sessions, even if the direction of stimulation is the >> same (and consistently named in paradigm files)? >> > That seems unlikely, but I vaguely remember that I thought it would be a > good idea to have the software adjust the sign such that the calcarine > always had +1, implying that I ran into a situation where there was a flip, > but I can't remember what that situation was. Jon, do you know? > > doug > >> >> Thanks, >> >> Jeff >> >> On Mon, May 11, 2009 at 6:10 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >>Hi Y'all, sorry for not chiming in sooner. Jeff, if you have >>multiple eccen or polar runs, you should just be able to set them >>up as runs in the fsfast directory structure (ie, as dirs with >>0-padded, 3digit run numbers), and it should find them and combine >>them properly. And you can include the directionality in the >>paradigm file, as you have suggested. >> >>doug >> >>Don Hagler wrote: >> >>I am not familiar with fsfast, so someone with intimate >>knowledge of the code (Doug?) could help more. But if you can >>specify the stimulus order in your paradigm files, then you >>should not have to do any phase reversals yourself. It seems >>strange (i.e. bug-like) that your fieldsign comes out >>different for the two sessions in this situation. When you >>view the resulting polar angle and eccentricity maps in >>tksurfer, are the colors reversed as well? >> >> >> >>Date: Mon, 11 May 2009 15:01:53 -0400 >>Subject: Re: [Freesurfer] Can fieldsigns be added across sessions? >>From: jeffrey.s.phill...@gmail.com >><mailto:jeffrey.s.phill...@gmail.com> >>To: dhagle...@hotmail.com <mailto:dhagle...@hotmail.com> >>CC: freesurfer@nmr.mgh.harvard.edu >><mailto:freesurfer@nmr.mgh.harvard.edu> >> >>Hi Don, >> >>Thanks for writing back again. Let me clarify: in our last >>session, we had a scanning menu like this: >> >>1 run polar/clockwise >>1 run eccen/expanding >>1 run polar/counter-clockwise >>1 run eccen/contracting >> >>The difference in direction was reflected in our paradigm >>files (*.par), with clockwise & expanding runs categorized as >>positive, and the others as negative. I have assumed that if >>the paradigm files specify this difference, it will not be >>necessary to manually flip the signs for negative runs. Is >>this correct? >> >>Jeff >> >>On Mon, May 11, 2009 at 2:45 PM, Don Hagler >>mailto:dhagle...@hotmail.com> >><mailto:dhagle...@hotmail.com <mailto:dhagle...@hotmail.com>&
[Freesurfer] Neuroimaging Data Engineer position at University of Pennsylvania
External Email - Use Caution The Frontotemporal Degeneration Center (FTDC; https://secure-web.cisco.com/1hStz2eH3jXe2_6SYQbWkdC4nCQBiJDXOrnEBPo72L63UY7rB2-N8m1zBp1jE_-DoYqPJvIE6XYmTxiuyYhs197BH5hyVRiEzoRyTY51WXFu326LzbX9SKg1bKnL3T2RyTxSjptKAzupLdEbC-NJo1co-NU7M-d-1V1QEHKWMIhHC-qxzcY_19Ah-7eQFdgf0Kp47I6hLtDc6V_GiFr-a93BpJ28g61aT3UNUgZPsavxPNJYIhliKTcz53AR2dUULyzDyr_VqGyneYFU46rlUZN3HSRlOYhqDUHuZUePmWvYBZJba0dR0JOpouHQtvSkBggMcMSnSGhfnfrzQiYjJVg/https%3A%2F%2Fwww.med.upenn.edu%2Fftd) at the University of Pennsylvania in Philadelphia, PA is looking for a neuroimaging data engineer to work on processing and analysis of multimodal MRI and PET data from our longitudinal neurodegenerative disease cohort. This is a great opportunity for an individual with imaging experience who wants to do unique imaging research as a staff scientist. Primary responsibilities include processing, analyzing and archiving neuroimaging datasets and facilitating integration of neuroimaging and clinical data repositories using the Integrated Neurodegenerative Disease Database (INDD) and cloud-based commercial platform FlyWheel. Neuroimaging datasets will include magnetic resonance imaging (MRI) and positron emission tomography (PET) series. The candidate will both implement existing pipelines and help develop novel pipelines. An additional primary responsibility will involve the training and co-supervision of neuroimaging analyses and general computing skills of junior lab personnel, including coordinators and research specialists. The candidate will also manage, receive, send, review, organize, process, and harmonize secondary data acquired via external collaborations and/or from publicly available data repositories, such as the Alzheimer’s Disease Neuroimaging Initiative. A third responsibility will be to perform basic statistical and bioinformatics analyses of imaging data to support the research of senior ADRC and FTDC staff and faculty. There will be publication opportunities for mentored research projects. Minimum qualifications include a bachelor's degree and two years of data analyst experience or an equivalent combination of education and experience. Required knowledge includes process and data modeling, data architectural development methodology and working knowledge of databases. Experience using data analysis tool and databases. Demonstrated competence in systems analysis and design and the ability to quickly learn and apply new technologies. Preferred qualifications include a master’s degree or PhD, plus 3-5 years’ experience in a computational (e.g., Computer Science, Bioinformatics) or biological (e.g., Biology, Neuroscience, Genomics) field or equivalent experience. Experience required with neuroimaging software (ANTs, FreeSurfer, SPM), programming/scripting (PERL, Python), open-source software development (Github), and working statistical knowledge (R, STATA, SPSS). Familiarity with neurodegenerative disease and/or psychiatric disorders is a plus. Must possess good organizational and time management skills, good written and verbal communications skills; ability to work independently and supervise others; be able to multi-task. Willingness to learn and keep current with technology and the rules and regulations involving clinical research a must. This position is continent upon grant funding. The FTDC enjoys close collaborations with the broader Penn neurology and neuroscience community, including the Alzheimer's Disease Research Center (ADRC), Center for Neurodegenerative Disease Research, Center for Cognitive Neuroscience, and Institute on Aging. For more details and to apply, please visit: https://secure-web.cisco.com/1OVx8sXmfwGjbGatlnZFYBlPhguVk1gBfDdFupynpMWI3fmv3u2GiOtxpaDrSnKEqy3GCGCWsUJK_Zhp8yFJsk7PMIc_vYcFIehOzANf3GcmIlpQpSRVECdAkulr0LVYLAAxLlqxJIXQLUz26nDWfR5Nto4O8HdGkVX87bOG44rkr34gP6KIjIFJk25hW3SS_3p_AhZJCxWJaz8F_7U20SmsFxE6KFCy6plBA3VUPoA-95addn5ULiWk6kKheoCHiq3tPoh9DRT8y4_K4RrU7QBUZcajHvHZW6JRGueSujB6JNEkZUui0iuZnuJav-OSs3ZPWjmUXXFmID5vTLCpdyQ/https%3A%2F%2Fwd1.myworkdaysite.com%2Fen-US%2Frecruiting%2Fupenn%2Fcareers-at-penn%2Fjob%2FNeuroimaging-Data-Engineer--Hybrid-Eligible---Department-of-Neurology-_JR00058376-1 Informal inquiries may be directed to Dr. Corey McMillan ( cmcmi...@pennmedicine.upenn.edu) or Dr. Jeff Phillips ( jef...@pennmedicine.upenn.edu). Jeff Phillips Research Assistant Professor of Neurology Penn Frontotemporal Degeneration Center University of Pennsylvania Philadelphia, PA ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceli
[Freesurfer] Clinical Research Coordinator position at Penn FTD Center, Univ. of Pennsylvania, Philadelphia
External Email - Use Caution Dear colleagues, The Penn Frontotemporal Degeneration Center is seeking a Clinical Research Coordinator to manage our ongoing NIA-funded PET and MRI studies of atypical, early-onset Alzheimer's disease and frontotemporal dementia patients. This position is ideal for aspiring researchers looking to gain experience with neuroimaging, Alzheimer's disease and related dementias, and clinical trial management. Please share this link with your talented trainees or colleagues--I'm happy to respond to direct inquiries: https://secure-web.cisco.com/12wO4MVCs84118ysL8fy6xvbYNtL9LzfpZBTronQnSEbQR_vPQFY3RBHeEm7ZMbmjpYwsKtaGjWXoqW-qPS6wbiyPZKVGT5G0UQwYESEob_zw8dYx18UbwEvLNrGm7hcKhwRkttxcJjPYkrbFXkN6IdGDMRX8xVvUC66lZIXbx0Wgm3lmXTKsYE7uxSPAnhdRvlFtW4fy9xWdWuWQ0zhQ6NjtODFFCTZ9CMuXwOEN3nHJSuCIIDDu7f9VMrbIj6yeoQc74SieOB4A3FPLevilwxQG8ZpBmUlKFMNMbfTIiWzU3qcMks49oNa0sDiDWtLnKeAP5tgsE5sFMTeVMuLdxQ/https%3A%2F%2Fwd1.myworkdaysite.com%2Fen-US%2Frecruiting%2Fupenn%2Fcareers-at-penn%2Fjob%2FClinical-Research-Coordinator-A--Hybrid-Eligible--Department-of-Neurology-_JR00068570-1 Thanks so much, Jeff Phillips Research Assistant Professor of Neurology Penn Frontotemporal Degeneration Center Philadelphia, PA ___ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
