[Freesurfer] PhD position: Neuroimaging (MRI) in Epilepsy, University of Liverpool
PhD Studentship in Specialised MRI in Medically Refractory Epilepsy £13,726 pa Stipend Department of Molecular Clinical Pharmacology, Institute of Translational Medicine Location: University Campus Ref: PhD-MRI-refractory-epilepsy/WWW Closing date for receipt of applications: Thu, 07 Nov 2013 17:00:00 GMT A PhD Studentship is available in the Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine at the University of Liverpool, supervised jointly between Dr. Simon Keller and Professor Tony Marson. This is an exciting project that involves collaboration with the Walton Centre NHS Foundation Trust (WCFT), which is a specialist neurosciences NHS hospital providing a high quality, integrated, multidisciplinary neurosciences service to the northwest of England and North Wales. The multidisciplinary Epilepsy Research Group at the University of Liverpool and WCFT has a long-standing international reputation for assessing outcomes in people with epilepsy. People with medically refractory epilepsy who do not have a discernable brain abnormality on routine magnetic resonance imaging (MRI) pose a significant challenge in the clinical management of their disorder. Neurosurgeons are more hesitant to operate on people without an identifiable structural abnormality, and for people who do undergo surgery, postsurgical outcome is significantly poorer compared to people with a focal brain abnormality (e.g. hippocampal sclerosis). The focus of this project will be to use specialised MRI approaches with sophisticated image analysis techniques for people with refractory epilepsy who were found to be MRI-negative during routine clinical imaging in an attempt to identify brain alterations that may underlie the epilepsy disorder. You will perform manual and automated quantitative MRI (e.g. high resolution hippocampal measurements, analysis of cortical thickness), diffusion tensor imaging (DTI) and resting-state functional MRI analyses on data prospectively acquired for people with epilepsy and healthy controls. There is also the opportunity to analyse neuroimaging data that has been previously acquired. You will be expected to present your work at internal departmental meetings, national and international conferences, and as peer-reviewed manuscripts in internationally renowned journals. Applications are sought from graduates (First or Upper Second) in Neuroscience, Biomedical Science, Psychology, Medicine, or an equivalent discipline. Experience with MRI analysis techniques, particularly in context of a postgraduate qualification, is desirable. This studentship includes PhD tuition fees (UK/EU students only) and is available for three years. To apply please send a copy of your CV with covering letter to: Dr. Simon Keller (simon.kel...@liv.ac.ukmailto:simon.kel...@liv.ac.uk). -- Dr. Simon S. Keller Lecturer and Senior Scientist Neuroimaging The Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool 2nd Floor, Neurological Science Clinical Sciences Centre Aintree University Hospitals and The Walton Centre NHS Foundation Trusts Lower Lane Liverpool L9 7LJ Tel: +44 (0)151 529 5943 simon.kel...@liverpool.ac.ukmailto:simon.kel...@liverpool.ac.uk www.liv.ac.uk/translational-medicine/staff/simon-keller/ ___ 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] R: Re: correction on question: offset in qdec GUI
Hi Freesurfers! Has any one got an answer to this query asked sometime ago: Hi list, I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And what I can do using it? Hi Bruce, I'm referring to offset in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano What the OFFSET next to the threshold max. is for? Kind regards Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ 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] How to generate histograms of intensities in one anatomical region?
Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in those regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot! Best,Yue Date: Fri, 1 Nov 2013 08:45:35 -0400 From: fis...@nmr.mgh.harvard.edu To: moonblue...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in one anatomical region? Hi Yue if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can also use mask_label to remove values outside of an ROI if that is what you are interested in. cheers Bruce On Fri, 1 Nov 2013, ?? wrote: Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab. I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction. Thanks! Best, Yue 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] How to generate histograms of intensities in one anatomical region?
Hi Yue tksurfer will only display cortical histograms. For subcortical regions you are probably best off using something like matlab (which would be pretty trivial) cheers Bruce On Fri, 1 Nov 2013, ?? wrote: Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in those regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot! Best, Yue Date: Fri, 1 Nov 2013 08:45:35 -0400 From: fis...@nmr.mgh.harvard.edu To: moonblue...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in one anatomical region? Hi Yue if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can also use mask_label to remove values outside of an ROI if that is what you are interested in. cheers Bruce On Fri, 1 Nov 2013, ?? wrote: Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab. I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction. Thanks! Best, Yue 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] ERROR: comparison in expression (FS with SGE)
I think the latest version of FSL has this sorted out (it doesn't change your machine's POSIXLY_CORRECT setting except briefly in the middle of fsl_sub). Peace, Matt. From: chenchunhuichina chenchunhuich...@gmail.com Date: Friday, November 1, 2013 2:55 AM To: Matt Glasser m...@ma-tea.com Cc: free surfer freesurfer@nmr.mgh.harvard.edu Subject: ERROR: comparison in expression (FS with SGE) Dear Matt and freesurfers, I am encounting this old problem, that is, using fsl_sub to launch FreeSurfer jobs in SGE and get this error message: (standard_in) 2: Error: comparison in expression and freesurfer stoped. But running freesurfer without fsl_sub is OK (using fsl_sub to launch other commonds also fine). Following Matt's message on this problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-May/023961.html, I added a line POSIXLY_CORRECT=0 in fsl_sub under the line set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*` which now looks like this ... set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*` POSIXLY_CORRECT=0 ... However, the error was still the same, and what's even worse is that seems the job was launched twice. So can Matt or anybody tell me why? Am I misunderstood Matt's message? or mybe version differences since Matt's solution came out one year ago? I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0, FMRIB Software Library, Release 5.0 (c) 2012 there are two fsLsub ./src/sgeutils/fsl_sub ./bin/fsl_sub which one should I edit or both? Any help is appreciated, Thank you all! 2013-11-01 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ___ 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] offset in QDEC
Dear Freesurfers and experts Can any one please tell me what the offset box next to the max. box (under Threshold) in QDEC GUI is for? When I change from e.g 0 to 1 or higher I get larger significant clusters. How and when is this feature used? I also notice this very question is on the archive list but not answered. Here is the quote Hi Bruce, I'm referring to offset in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano Thanks Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ 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] How to generate histograms of intensities in one anatomical region?
Hi Bruce, Thanks for responding so quickly. Sorry I probably don't describe my question clearly and my examples are bad. This is really new to me. So please correct me if I say something wrong. Let me explain again. Hopefully it will make some sense. What I want to do is first to segment out different cortical and subcorical regions(like frontal cortex, occipital cortex, posterior cingulate cortex, putamen etc.) and then generate histograms from these regions separately. The surfaces give me the histograms that only include the intensities on the edges of the regions, right? I am wondering if I can generate histograms from the area of one cortical region not just the boundaries. Thanks! Best,Yue Date: Fri, 1 Nov 2013 11:12:46 -0400 From: fis...@nmr.mgh.harvard.edu To: moonblue...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] How to generate histograms of intensities in one anatomical region? Hi Yue tksurfer will only display cortical histograms. For subcortical regions you are probably best off using something like matlab (which would be pretty trivial) cheers Bruce On Fri, 1 Nov 2013, ?? wrote: Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in those regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot! Best, Yue Date: Fri, 1 Nov 2013 08:45:35 -0400 From: fis...@nmr.mgh.harvard.edu To: moonblue...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in one anatomical region? Hi Yue if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can also use mask_label to remove values outside of an ROI if that is what you are interested in. cheers Bruce On Fri, 1 Nov 2013, ?? wrote: Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab. I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction. Thanks! Best, Yue 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] offset in QDEC
Hi Bruce, Thanks. Is it statistically sound to use e.g offset 1? My between-group results are not FDR corrected at offset 0, but if I change the offset to 1 results will be larger in size and FDR corrected! Any pitfalls with that? Cheers Hamza On 01/11/2013 15:53, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Hamza offset is the zero point of the colorscale. Usualy it is 0 so that atuff that is 0 is displayed in blue/cyan and stuff that is 0 in yellow/red cheers Bruce On Fri, 1 Nov 2013, Hamza Alshuft wrote: Dear Freesurfers and experts Can any one please tell me what the offset box next to the max. box (under Threshold) in QDEC GUI is for? When I change from e.g 0 to 1 or higher I get larger significant clusters. How and when is this feature used? I also notice this very question is on the archive list but not answered. Here is the quote Hi Bruce, I'm referring to offset in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is mor e larger. Stefano Thanks Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. 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. This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to generate histograms of intensities in one anatomical region?
Got you. I will check out ribbon and read more about mri_vol2surf. Thanks for your help! Yue Date: Fri, 1 Nov 2013 12:16:48 -0400 From: fis...@nmr.mgh.harvard.edu To: moonblue...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] How to generate histograms of intensities in one anatomical region? the surfaces can be used to sample in many different ways using options to mri_vol2surf. For example you could average over the ribbon then display the histogram of that. For subcortical structures the surfaces don't make sense, so you are better off just doing it in matlab cheers Bruce On Fri, 1 Nov 2013, ?? wrote: Hi Bruce, Thanks for responding so quickly. Sorry I probably don't describe my question clearly and my examples are bad. This is really new to me. So please correct me if I say something wrong. Let me explain again. Hopefully it will make some sense. What I want to do is first to segment out different cortical and subcorical regions(like frontal cortex, occipital cortex, posterior cingulate cortex, putamen etc.) and then generate histograms from these regions separately. The surfaces give me the histograms that only include the intensities on the edges of the regions, right? I am wondering if I can generate histograms from the area of one cortical region not just the boundaries. Thanks! Best, Yue Date: Fri, 1 Nov 2013 11:12:46 -0400 From: fis...@nmr.mgh.harvard.edu To: moonblue...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] How to generate histograms of intensities in one anatomical region? Hi Yue tksurfer will only display cortical histograms. For subcortical regions you are probably best off using something like matlab (which would be pretty trivial) cheers Bruce On Fri, 1 Nov 2013, ?? wrote: Hi Bruce, Thanks for the information. The surface works for me. These histograms generated from the surfaces, if I understand correctly, are based on the intensities along the boundaries of one region. Can I also generate histograms including the whole region? Like Pick putamen or caudate and generate histograms and statistic summaries based on all the pixels in those regions. Or can I generate binary masks of putamen or caudate from the labels then I can apply those masks and generate histograms in other softwares? Thanks a lot! Best, Yue Date: Fri, 1 Nov 2013 08:45:35 -0400 From: fis...@nmr.mgh.harvard.edu To: moonblue...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How to generate histograms of intensities in one anatomical region? Hi Yue if you sample them on to the surface with mri_vol2surf you can use the overlay histogram facility in tksurfer to do what you want. You can also use mask_label to remove values outside of an ROI if that is what you are interested in. cheers Bruce On Fri, 1 Nov 2013, ?? wrote: Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab. I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction. Thanks! Best, Yue 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
Re: [Freesurfer] funcroi calculating percent signal change
Hi Doug, Thanks, this seems to work! Quick question -- in the past we've done ROI analyses where we've functionally constrained our labels. When calculating percent signal change we would take the output from funcroi-table-sess divide it by the output of funcroi-table-sess with no -c flag (the baseline offset value) and multiply by 100. Is this also a correct method for calculating percent signal change? I've tried it for the current ROI I'm using and compared my calculated value to the value I got by adding -m cespct and the numbers I'm getting are not the same (ex. 0.0159 vs 0.01444 for one subject). Is -m cespct more accurate? Thanks! Best, Alex Hi Alex, if you use -m cespct it will report the mean percent signal change within the ROI. Does this work? doug On 10/31/2013 02:37 PM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions: funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated! Thanks, Alex -- 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] preferred method for generating appropriate bvecs for tracula
Once the file is in 3-column format:
cat yourfilename | awk '{print $1 -$2 $3}'
On Thu, 31 Oct 2013, Salil Soman wrote:
Hi Anastasia,
Thank you for this code piece. Is there a way to modify it so that set y's
sign gets flipped? (I have a dataset where its is acquired on GE (so the Y
row gets flipped)?
Thank you!
-Sal
On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
set x = `cat bvecs | awk '{if (NR==1) print}'`
set y = `cat bvecs | awk '{if (NR==2) print}'`
set z = `cat bvecs | awk '{if (NR==3) print}'`
@ k = 1
while ( $k = `head -1 bvecs|wc -w` )
echo $x[$k] $y[$k] $z[$k]
@ k = $k + 1
end
I'd make sure though dcm2nii doesn't L-R flip the gradient
vectors, I think there was a thread recently that suggested it
might.
On Wed, 7 Aug 2013, Salil Soman wrote:
Hi,
I have dicoms that I turn to nifti using dcm2nii
(with the default settings plus anonymization option
turned on [-a
y]). The bvec files it generates by default are 3
rows by n columns (where n is b0 number +
directions). I am under
the impression tracula requires this to be converted
to a n row by 3 column file. 1) is this correct, 2)
is there a
preferred way to perform this transformation on
linux systems?
Thanks you,
-Sal
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.
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
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Re: [Freesurfer] funcroi calculating percent signal change
Great, thanks for the clarification Doug! Best, Alex It depends on how are you defining percent contrast. What you are are slightly different methods. Using -m cespct is equivalent to computing 100*Sum(contrast_i/baseline_i)/N where i is a voxel in the ROI Your method is equivalent to computing 100*Sum(contrast_i)/Sum(baseline_i) So they will be close but not exact. Which one is better? Hard to say. I would tend toward -m cespect doug On 11/01/2013 01:43 PM, Alexandra Tanner wrote: Hi Doug, Thanks, this seems to work! Quick question -- in the past we've done ROI analyses where we've functionally constrained our labels. When calculating percent signal change we would take the output from funcroi-table-sess divide it by the output of funcroi-table-sess with no -c flag (the baseline offset value) and multiply by 100. Is this also a correct method for calculating percent signal change? I've tried it for the current ROI I'm using and compared my calculated value to the value I got by adding -m cespct and the numbers I'm getting are not the same (ex. 0.0159 vs 0.01444 for one subject). Is -m cespct more accurate? Thanks! Best, Alex Hi Alex, if you use -m cespct it will report the mean percent signal change within the ROI. Does this work? doug On 10/31/2013 02:37 PM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions: funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated! Thanks, Alex -- 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/ -- 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] Dilated ventricles
Hi Victor If you upload the subject I'll take a look Buce On Nov 1, 2013, at 5:43 PM, Victor Kovac kovac...@umn.edu wrote: Freesurfer experts, I have attached the recon-all log from the scan I included an image of in my previous email. Any suggestions on how to deal with dilated ventricles when the -bigventricles flag is not sufficing would be deeply appreciated. Thank you. Victor On Tue, Oct 29, 2013 at 12:02 PM, Victor Kovac kovac...@umn.edu wrote: Dear Freesurfer experts, I have run recon-all and included the -bigventrcles flag on a number of brains with ventriculomegaly. This fixed the segmentation errors in a few cases; however, there are still brains with dilated ventricles for which recon-all is not providing accurate segmentation (see attached image). Are there any other tricks I can attempt to solve this issue? I was considering doing manual pial and white matter edits in conjunction with filling the ventricles by using the Edit Voxels Tool. Would this be advisable? Thank you! Victor recon-all.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
