[Freesurfer] question about TRACULA
Dear Madam/Sir, I am trying to applying TRACULA on my data but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after some processing I obtain the following error xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: .97: expected numeric value printf: .002040: expected numeric value printf: .001230: expected numeric value printf: 8.010424: not completely converted printf: -4.983286: not completely converted printf: -.000389: expected numeric value printf: -.759652: expected numeric value printf: -5.031242: not completely converted printf: 8.006841: not completely converted printf: 7.864457: not completely converted printf: 3.131627: not completely converted printf: -3.216084: not completely converted printf: -1.957800: not completely converted printf: 7.048668: not completely converted printf: 5.956787: not completely converted printf: -7.998542: not completely converted printf: 1.996216: not completely converted printf: 4.004804: not completely converted printf: 7.008384: not completely converted printf: -2.985687: not completely converted printf: 3.996015: not completely converted printf: -.986002: expected numeric value printf: -9.000231: not completely converted printf: .153834: expected numeric value printf: 7.937660: not completely converted printf: .875656: expected numeric value printf: 4.150514: not completely converted printf: -2.115330: not completely converted printf: 8.962086: not completely converted printf: 2.050965: not completely converted printf: 5.758588: not completely converted printf: 8.092588: not completely converted printf: -4.165180: not completely converted printf: 4.753098: not completely converted printf: 5.079427: not completely converted printf: -6.132490: not completely converted printf: -4.21: not completely converted printf: 4.007709: not completely converted printf: 6.995579: not completely converted printf: -4.879465: not completely converted printf: -7.066532: not completely converted printf: 1.120257: not completely converted printf: -5.186508: not completely converted printf: -2.066011: not completely converted printf: -7.863320: not completely converted printf: -5.008038: not completely converted printf: 5.995846: not completely converted printf: 3.996178: not completely converted printf: 5.717007: not completely converted printf: 5.121524: not completely converted printf: -7.147437: not completely converted printf: 1.743757: not completely converted printf: 7.060581: not completely converted printf: -9.005971: not completely converted printf: -4.251174: not completely converted printf: 5.953915: not completely converted printf: -4.845450: not completely converted printf: -4.010977: not completely converted printf: -8.049025: not completely converted printf: -2.850488: not completely converted printf: 4.005690: not completely converted printf: -7.995851: not completely converted printf: 1.010371: not completely converted printf: -5.118400: not completely converted printf: -4.070279: not completely converted printf: -6.872761: not completely converted printf: 8.143535: not completely converted printf: 4.835332: not completely converted printf: 1.817269: not completely converted printf: 2.268035: not completely converted printf: -2.989943: not completely converted printf: 7.931980: not completely converted printf: -4.199139: not completely converted printf: -3.025800: not completely converted printf: -8.900100: not completely converted grep: /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dcminfo.dat: No such file or directory fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi input output xmin xsize ymin ysize zmin zsize fslroi input output tmin tsize fslroi input output xmin xsize ymin ysize zmin zsize tmin tsize Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Could you please give me some help? Thanks a lot Best Regards Lucia Billeci_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___ 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
Re: [Freesurfer] question about TRACULA
Hi Lucia - The error occurs when the text file with the gradient vectors is being processed. Can you please attach that file? Thanks, a.y On Fri, 20 Sep 2013, Lucia Billeci wrote: Dear Madam/Sir, I am trying to applying TRACULA on my data but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after some processing I obtain the following error xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: .97: expected numeric value printf: .002040: expected numeric value printf: .001230: expected numeric value printf: 8.010424: not completely converted printf: -4.983286: not completely converted printf: -.000389: expected numeric value printf: -.759652: expected numeric value printf: -5.031242: not completely converted printf: 8.006841: not completely converted printf: 7.864457: not completely converted printf: 3.131627: not completely converted printf: -3.216084: not completely converted printf: -1.957800: not completely converted printf: 7.048668: not completely converted printf: 5.956787: not completely converted printf: -7.998542: not completely converted printf: 1.996216: not completely converted printf: 4.004804: not completely converted printf: 7.008384: not completely converted printf: -2.985687: not completely converted printf: 3.996015: not completely converted printf: -.986002: expected numeric value printf: -9.000231: not completely converted printf: .153834: expected numeric value printf: 7.937660: not completely converted printf: .875656: expected numeric value printf: 4.150514: not completely converted printf: -2.115330: not completely converted printf: 8.962086: not completely converted printf: 2.050965: not completely converted printf: 5.758588: not completely converted printf: 8.092588: not completely converted printf: -4.165180: not completely converted printf: 4.753098: not completely converted printf: 5.079427: not completely converted printf: -6.132490: not completely converted printf: -4.21: not completely converted printf: 4.007709: not completely converted printf: 6.995579: not completely converted printf: -4.879465: not completely converted printf: -7.066532: not completely converted printf: 1.120257: not completely converted printf: -5.186508: not completely converted printf: -2.066011: not completely converted printf: -7.863320: not completely converted printf: -5.008038: not completely converted printf: 5.995846: not completely converted printf: 3.996178: not completely converted printf: 5.717007: not completely converted printf: 5.121524: not completely converted printf: -7.147437: not completely converted printf: 1.743757: not completely converted printf: 7.060581: not completely converted printf: -9.005971: not completely converted printf: -4.251174: not completely converted printf: 5.953915: not completely converted printf: -4.845450: not completely converted printf: -4.010977: not completely converted printf: -8.049025: not completely converted printf: -2.850488: not completely converted printf: 4.005690: not completely converted printf: -7.995851: not completely converted printf: 1.010371: not completely converted printf: -5.118400: not completely converted printf: -4.070279: not completely converted printf: -6.872761: not completely converted printf: 8.143535: not completely converted printf: 4.835332: not completely converted printf: 1.817269: not completely converted printf: 2.268035: not completely converted printf: -2.989943: not completely converted printf: 7.931980: not completely converted printf: -4.199139: not completely converted printf: -3.025800: not completely converted printf: -8.900100: not completely converted grep: /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dcminfo.dat: No such file or directory fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi input output xmin xsize ymin ysize zmin zsize fslroi input output tmin tsize fslroi input output xmin xsize ymin ysize zmin zsize tmin tsize Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Could you please give me some help? Thanks a lot Best Regards Lucia Billeci_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___ 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
Re: [Freesurfer] Qdec analysis -- Don't use DOSS with QDEC
Hi Elisa, don't use the DOSS feature in QDEC. Sorry, I sent out an email about 6mo ago on this, but it is not easy to let people know about a bug once the bug is out there. doug On 09/19/2013 11:30 AM, E. Scariati wrote: Dear Freesurfer experts, I would like to study the relationship between cortical thickness and one clinical variable with qdec, but correcting for age and gender. Given that I have only one group and 2 covariates (one continuous, one dichotomic) I don't know how I should set the design of my analysis in qdec, especially for the gender variable. I have tried two different ways (both DOSS design): 1) selecting Discrete = gender; Continuous = clinical measure; Nuisance factor = age and looking at the contrast called : Does the correlation between thickness and clinical measure accounting for gender differ from 0? nuisance factor : age 2) selecting : continuous = clinical measure; Nuisance Factor = age, gender (coded as 1 and 2) and looking at the contrast called : Does the correlation between thickness and clinical measure differ from 0, nuisance factor : age, gender But the two contrasts give very different results, which I find very surprising. I exported cortical thickness at the peak significance of the clusters and tried to run a GLM myself in SPSS and it seems that coding gender as a continuous variable with two values (1 and 2) provides the most realistic results. However, I saw many times on the mailing list that you recommend to use gender as a discrete variable, so I am very confused. Could you explain me the difference between these contrasts and help me to identify which one will accurately identify the correlation between cortical thickness and my clinical variable correcting for the effect of age and gender. Thank you in advance for your answer, Best regards Elisa ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] ACFFWHM for surface-based analyses in FSFAST?
Hi Caspar, I have not looked at it much. The temporal whitening has so little effect (at least at the group level), that I cannot imagine that it will make much difference. doug On 09/19/2013 09:36 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, mkanalysis-sess seems to default to a FWHM of 20 for the smooting of the ACF (in version 5.1). I was wondering whether it makes sense to use the same FWHM for volume and surface based analyses of functional data in FSFAST? I seem to remember that the autocorrelations differ between, e.g., grey and white matter, which might be a reason to use a different FWHM on the surface? Thank you very much, Caspar ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Qdec analysis -- Don't use DOSS with QDEC
Hi Marie, On 9/20/13 4:30 PM, Marie Schaer wrote: Hi Doug, I'm jumping in the discussion because I was a bit scared with your previous email mentioning that this DOSS bug affects all FreeSurfer's versions. Does that also affect statistical analyses computed with mri_glmfit using the command line? Do you have an insight whether the bias introduced by the bug is important or not? (as others may also be, I'm becoming a bit anxious about previously published results…) It does not affect the command-line version, only in QDEC. It was basically not creating a contrast matrix that matched the hypothesis question under some circumstances. Finally, to get back to Elisa's question: do you have some suggestion in the mean time to assess the relationship between cortical thickness and a clinical measure correcting for age and gender? Using DODS? With or without demeaning the covariates and nuisance? Sorry for the abundance of questions, and, as always, thanks a lot for your answer! Marie I would probably do it with DODS and just test the mean across the two groups, eg, Class M Class F Variables ClinicalVar Age [0 0 .5 .5 0 0] This would account for possible differences in slope between M and F. In the end, I think it will give you about the same as if use DOSS. If you have a small sample size, you could use DOSS because DODS will cost you 2 more DOF doug On Sep 20, 2013, at 6:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Elisa, don't use the DOSS feature in QDEC. Sorry, I sent out an email about 6mo ago on this, but it is not easy to let people know about a bug once the bug is out there. doug On 09/19/2013 11:30 AM, E. Scariati wrote: Dear Freesurfer experts, I would like to study the relationship between cortical thickness and one clinical variable with qdec, but correcting for age and gender. Given that I have only one group and 2 covariates (one continuous, one dichotomic) I don't know how I should set the design of my analysis in qdec, especially for the gender variable. I have tried two different ways (both DOSS design): 1) selecting Discrete = gender; Continuous = clinical measure; Nuisance factor = age and looking at the contrast called : Does the correlation between thickness and clinical measure accounting for gender differ from 0? nuisance factor : age 2) selecting : continuous = clinical measure; Nuisance Factor = age, gender (coded as 1 and 2) and looking at the contrast called : Does the correlation between thickness and clinical measure differ from 0, nuisance factor : age, gender But the two contrasts give very different results, which I find very surprising. I exported cortical thickness at the peak significance of the clusters and tried to run a GLM myself in SPSS and it seems that coding gender as a continuous variable with two values (1 and 2) provides the most realistic results. However, I saw many times on the mailing list that you recommend to use gender as a discrete variable, so I am very confused. Could you explain me the difference between these contrasts and help me to identify which one will accurately identify the correlation between cortical thickness and my clinical variable correcting for the effect of age and gender. Thank you in advance for your answer, Best regards Elisa ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec analysis -- Don't use DOSS with QDEC
Hi Doug, I'm jumping in the discussion because I was a bit scared with your previous email mentioning that this DOSS bug affects all FreeSurfer's versions. Does that also affect statistical analyses computed with mri_glmfit using the command line? Do you have an insight whether the bias introduced by the bug is important or not? (as others may also be, I'm becoming a bit anxious about previously published results…) Finally, to get back to Elisa's question: do you have some suggestion in the mean time to assess the relationship between cortical thickness and a clinical measure correcting for age and gender? Using DODS? With or without demeaning the covariates and nuisance? Sorry for the abundance of questions, and, as always, thanks a lot for your answer! Marie On Sep 20, 2013, at 6:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Elisa, don't use the DOSS feature in QDEC. Sorry, I sent out an email about 6mo ago on this, but it is not easy to let people know about a bug once the bug is out there. doug On 09/19/2013 11:30 AM, E. Scariati wrote: Dear Freesurfer experts, I would like to study the relationship between cortical thickness and one clinical variable with qdec, but correcting for age and gender. Given that I have only one group and 2 covariates (one continuous, one dichotomic) I don't know how I should set the design of my analysis in qdec, especially for the gender variable. I have tried two different ways (both DOSS design): 1) selecting Discrete = gender; Continuous = clinical measure; Nuisance factor = age and looking at the contrast called : Does the correlation between thickness and clinical measure accounting for gender differ from 0? nuisance factor : age 2) selecting : continuous = clinical measure; Nuisance Factor = age, gender (coded as 1 and 2) and looking at the contrast called : Does the correlation between thickness and clinical measure differ from 0, nuisance factor : age, gender But the two contrasts give very different results, which I find very surprising. I exported cortical thickness at the peak significance of the clusters and tried to run a GLM myself in SPSS and it seems that coding gender as a continuous variable with two values (1 and 2) provides the most realistic results. However, I saw many times on the mailing list that you recommend to use gender as a discrete variable, so I am very confused. Could you explain me the difference between these contrasts and help me to identify which one will accurately identify the correlation between cortical thickness and my clinical variable correcting for the effect of age and gender. Thank you in advance for your answer, Best regards Elisa ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST SEPTEMBER 27, 2013)
Dear Colleagues, The Neurobureau http://www.neurobureau.org is excited to announce a stipend program for Brainhack 2013 http://www.brainhack.org (October 23-26 in Sevres, France (just outside of Paris). The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist. The stipend program will provide at least 6 stipends for partial or full registration fees [if 24 attendees apply, you have a 25% chance of getting a stipend]. The exact breakdown of stipends provided will depend on the number of applicants and the cost of attending the conference for those applicants. The application for stipend requires: (1) A poster abstract (2) A 1-2 page Brainhack project proposal (pdf format) (3) NIH Biosketch/CV (pdf format) The Brainhack 2013 Organizing Committee will decide which applications will receive stipends based on their abstract and proposed brainhack projects. Details on Brainhack 2013 can be found herehttp://www.brainhack.org/?page_id=27784 . The deadline to apply for one of the stipends is 11:59PM EST on September 27th. All decisions will be made by October 3rd and must be accepted within 24 hours of being awarded. If you have any questions please contact myself (mclaren.don...@gmail.com) or one of the organizers. Click here to apply. http://www.brainhack.org/?page_id=40668 Good luck. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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] ACFFWHM for surface-based analyses in FSFAST?
Hi Doug, thanks for the response. I will also be looking at some single subject data, that's why I am asking. Do you have a hunch? Caspar On Friday, September 20, 2013, Douglas N Greve wrote: Hi Caspar, I have not looked at it much. The temporal whitening has so little effect (at least at the group level), that I cannot imagine that it will make much difference. doug On 09/19/2013 09:36 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, mkanalysis-sess seems to default to a FWHM of 20 for the smooting of the ACF (in version 5.1). I was wondering whether it makes sense to use the same FWHM for volume and surface based analyses of functional data in FSFAST? I seem to remember that the autocorrelations differ between, e.g., grey and white matter, which might be a reason to use a different FWHM on the surface? Thank you very much, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu javascript:; Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; 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 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] ACFFWHM for surface-based analyses in FSFAST?
I think even in single subject data it will not be much of an effect. I looked at it a little bit when I first programmed it. doug On 9/20/13 6:55 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thanks for the response. I will also be looking at some single subject data, that's why I am asking. Do you have a hunch? Caspar On Friday, September 20, 2013, Douglas N Greve wrote: Hi Caspar, I have not looked at it much. The temporal whitening has so little effect (at least at the group level), that I cannot imagine that it will make much difference. doug On 09/19/2013 09:36 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, mkanalysis-sess seems to default to a FWHM of 20 for the smooting of the ACF (in version 5.1). I was wondering whether it makes sense to use the same FWHM for volume and surface based analyses of functional data in FSFAST? I seem to remember that the autocorrelations differ between, e.g., grey and white matter, which might be a reason to use a different FWHM on the surface? Thank you very much, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu javascript:; 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; 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 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] Ph.D. student openings
Hi, I am looking to recruit talented students to develop novel image analysis and machine learning algorithms for the Human Connectome Project data. This is my research webpage: https://sites.google.com/site/yeoyeo02/. See more information below. Regards, Thomas Application Deadline: Nov 1st, 2013 in order to start in Fall 2014 Requirements: Bachelor's or Master's degree in computer science, electrical engineering, statistics or related fields. Ideal candidates should be highly motivated, and have research experience and/or excellent grades. Compensation: Graduate Student Fellowship Institutes: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings). Successful candidates may be required to travel between Singapore and the U.S. for certain projects. Contact: Interested candidates should email Thomas (ytho...@csail.mit.edu) with CV and/or questions. ___ 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] postdoc opening
Hi, I am looking to hire talented postdocs to develop novel image analysis and machine learning algorithms for the Human Connectome Project data. This is my research webpage: https://sites.google.com/site/yeoyeo02/. See more information below. Regards, Thomas Requirements: Ph.D. in computer science, electrical engineering, statistics or related fields. Candidates should have previously published research in image processing or statistical analysis, preferably in biomedical applications. Compensation: Competitive and commensurate with experience Institutes: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings). Successful candidates may be required to travel between Singapore and the U.S. for certain projects. Contact: Interested candidates should email Thomas (ytho...@csail.mit.edu) with CV and/or questions. To apply, please send cover letter, CV and names/contact information of 3 people who can provide letters of reference. ___ 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.
