Re: [Freesurfer] longitudinal stream - template
Hi Martin, Thank you for your answer, but my idea was to compare the atrophy rates when using scans at 6 months (0 - 6 months) and scans at 12 months (0 - 12 months). If my templates are built with more time points, the results will be biased, right? Regards, Yolanda 2013/3/18 Martin Reuter mreu...@nmr.mgh.harvard.edu: Hi Yolanda, actually it is advantageous if the template is build from more time points. You don't need to process the images again, just do your statistical analysis with the time points you are interested in. But: why restrict the statistics to a subset of the data? If you are interested in yearly change, you can compute that from all time points. If you are interested in seeing if the atrophy rate increases over time, use a piecewise linear model (node at 6 months) and see if the slopes increase, etc. Removing time points from the statistics is usually a bad idea as you loose power. Best, Martin On 03/18/2013 01:15 PM, Yolanda Vives wrote: Dear FreeSurfer experts, I have run a longitudinal study considering multiple time points (7 scans/subject on average) with FS 5.1. However, I am interested in the percent changes between two time points only (between 0 and 6 months and between 0 and 1 year). Should I run the longitudinal stream from step 2 (template) two more times (1.- considering only 0 and 6 months scans and 2.- considering only 0 and 12 months scans) or is it correct even if my templates were built with all the time scans together? Thank you for your help, Yolanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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] Very different results between 5.1.0 and 5.2.0
Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in particular. Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. They are significantly different, t(160) = 56.71. The correlation between the two versions is r = .33 Is this something possible?? I can't see what went wrong in my procedures. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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] longitudinal analysis
Hello Martin, Thank you for your swift reply. I failed to make myself clear, and will try describing my study again. First, an important point: the study is not longitudinal per se, but I am interested in applying the methods of longitudinal analysis. I only have one time point, all the scans have been collected within the same session. I am studying a large group of subjects whom each underwent a scan session with 4 scans. Each of these scans were graded for quality on a scale from 1-4. An example of what I then did was to process each subject twice, once with the scan of quality ”1”, and a second time averaging the scans of quality ”1” and ”2”, thus resulting in two groups between which each subject is compared to itself. Now I am attempting to set up a longitudinal analysis with this data. I have processed through the longitudinal stream, and I guess my question starts at the point of post-processing: How, if feasible, can I transfer the idea of “across group comparison between time point and time point 2” to “across group comparison between 1 scan and 2 scans” in setting up the QDEC table and continuing from there? I hope this make sense, your help is greatly appreciated. Best regards, Joy-Loi On 2013-03-18 19:13, Martin Reuter wrote: Hi Joy-Loi, so you have 2 time points? the first with a single scan, the second with two within-session scans that you want to average? I don't understand exactly what you are trying to do. To test differences in reliability you'd have to scan a bunch of subjects twice in a session and then twice in another session. Then you can look at reliability when using only one scan (e.g. the first) or when averaging both scans in both time points. 'varying quality' with respect to motion also scares me a little. There can be individual outliers that severely affect your mean response (unless you have lots of subjects). Anyway for these things you would process your results through the longitudinal stream (this allows you also to be unbiased with respect to the time point). There are several design questions to consider (e.g. does it make sense to include all virtual time points into the same base, or run everything twice: one base for the averaged images , another for the single images and then compare etc. ) Either way this is not a standard analysis and you'd be pretty much on your own with how to set it up. Best, Martin On 03/18/2013 09:02 AM, Joy-Loi Chepkoech wrote: Hello FreeSurfer experts, I am currently trying to systematically investigate the differences in cortical and subcortical estimates that occur when performing recon-all on one scan, or when averaging across scans of varying quality with regard to movement. I have a list of subjects that each have been processed (recon-all) twice (once with one scan and once with two scans), and would like to run some FreeSurfer statistical analysis on them. Is it feasible to set up a longitudinal analysis similar to the one described here: (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)? If it is, could someone assist me in setting this analysis up? (I have tried following the tutorial, where I on each subject set 0 years for one scan, and 1 year for two scans in the QDEC table, but the results from the QDEC analysis don't seem to agree with previous SPSS results that I have). Thank you, Joy-Loi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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] longitudinal analysis
Hi Joy-Loi, yes, you can do that using the free surfer tools (e.g. check if 'atrophy', i.e. change across the two methods, is different from zero, meaning if there is a bias). Any of the statistical methods described here: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics can do that. You will find that results differ, but you will not know if they differ because of the - different quality of the scans - difference in processing (averaging 2 scans) - or simply the noise one would always expect from the scanner (imaging / positioning etc). It would be interesting to distinguish those sources of variability. But for that you'd need a second time point I think. Best, Martin On Mar 19, 2013, at 10:47 AM, Joy-Loi Chepkoech j.l.chepko...@psykologi.uio.no wrote: Hello Martin, Thank you for your swift reply. I failed to make myself clear, and will try describing my study again. First, an important point: the study is not longitudinal per se, but I am interested in applying the methods of longitudinal analysis. I only have one time point, all the scans have been collected within the same session. I am studying a large group of subjects whom each underwent a scan session with 4 scans. Each of these scans were graded for quality on a scale from 1-4. An example of what I then did was to process each subject twice, once with the scan of quality ”1”, and a second time averaging the scans of quality ”1” and ”2”, thus resulting in two groups between which each subject is compared to itself. Now I am attempting to set up a longitudinal analysis with this data. I have processed through the longitudinal stream, and I guess my question starts at the point of post-processing: How, if feasible, can I transfer the idea of “across group comparison between time point and time point 2” to “across group comparison between 1 scan and 2 scans” in setting up the QDEC table and continuing from there? I hope this make sense, your help is greatly appreciated. Best regards, Joy-Loi On 2013-03-18 19:13, Martin Reuter wrote: Hi Joy-Loi, so you have 2 time points? the first with a single scan, the second with two within-session scans that you want to average? I don't understand exactly what you are trying to do. To test differences in reliability you'd have to scan a bunch of subjects twice in a session and then twice in another session. Then you can look at reliability when using only one scan (e.g. the first) or when averaging both scans in both time points. 'varying quality' with respect to motion also scares me a little. There can be individual outliers that severely affect your mean response (unless you have lots of subjects). Anyway for these things you would process your results through the longitudinal stream (this allows you also to be unbiased with respect to the time point). There are several design questions to consider (e.g. does it make sense to include all virtual time points into the same base, or run everything twice: one base for the averaged images , another for the single images and then compare etc. ) Either way this is not a standard analysis and you'd be pretty much on your own with how to set it up. Best, Martin On 03/18/2013 09:02 AM, Joy-Loi Chepkoech wrote: Hello FreeSurfer experts, I am currently trying to systematically investigate the differences in cortical and subcortical estimates that occur when performing recon-all on one scan, or when averaging across scans of varying quality with regard to movement. I have a list of subjects that each have been processed (recon-all) twice (once with one scan and once with two scans), and would like to run some FreeSurfer statistical analysis on them. Is it feasible to set up a longitudinal analysis similar to the one described here: (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)? If it is, could someone assist me in setting this analysis up? (I have tried following the tutorial, where I on each subject set 0 years for one scan, and 1 year for two scans in the QDEC table, but the results from the QDEC analysis don't seem to agree with previous SPSS results that I have). Thank you, Joy-Loi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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
Re: [Freesurfer] Correspondence of Talairach coordinates from one subject to other
Hi Doug, I tried to do what you recommended but I am encountering an inconsistency. (Note: I obtain the same results in R (with ginv() ) and Matlab (with pinv() ) ) Could you please have a look at the code and the values please? I don't know what else to do right now... (it is possible to copy paste everything in Matlab) *** TalXFM = [1.040797, 0.011370, -0.069615, -0.863770;0.031794, 0.939578, 0.254677 ,-32.126083; 0.048458, -0.236663 ,1.101207, -20.946930]; Norig = [-1.0 , -0.0 , -0.0 , 130.38606 ;-0.0 , 0.0 , 1.0, -109.95447 ;-0.0, -1.0 , 0.0 , 150.14441 ; 0.0,0.0 , 0.0 , 1.0]; Torig = [-1.0 , 0.0 , 0.0 , 128.0; 0.0 , 0.0 , 1.0, -128.0; 0.0 , -1.0 , 0.0 , 128.0; 0.0 , 0.0 , 0.0 , 1.0]; W = TalXFM * Norig * inv(Torig); Volume_RAS = [1, -30, 1, 1]; MNI_Talairach = W * Volume_RAS' % Coincides with Tkmedit % MNI_Talairach = (0.9133; -37.3562; 7.5331) Volume_RAS = pinv(W)*MNI_Talairach % DOES NOT COINCIDE % Volume_RAS = (0.4324; -2.9014; 8.7350; 3.8992) shouldn't be [1, -30, 1, 1]; ? Is the transformation two-way? Should it be? Many thanks again for your help, Gari On Wed, Mar 13, 2013 at 10:15 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: Hi Gary, you would use the MNI305 space as the common space. Eg, Case 2 shows you how to go from RAS of a subject to MNI305 space. You would reverse that to go from MNI305 space to another subject's RAS space thus allowing a RAS-RAS transform. If you have a surface overlay for a subject, you can use mri_surf2surf to transfer it to another subject. doug On 3/12/13 11:54 PM, Garikoitz Lerma-Usabiaga wrote: Thanks Doug, I've seen the page, but I understand that everything is within the same subject. I want to find the equivalencies between subjects. I mean, the plane y = 30 in fsaverage, will correspond to a plane with a bigger Y for a larger head (could be defined anatomically, the most outer point of the hippocampus, for example. When finding equivalencies for surface ROIs from one subject to another we used label2label for example. If I have an overlay in volume space, how should I move it to another subject? Thanks again, Gari On 12/03/2013, at 20:29, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Gary, check out this wiki page and let me know if you still have questions http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems doug On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote: Hi! how can I translate a coordinate in talairach space of one subject (Colin27), to every subject in a study? For example, I would like to know where is the coordinate Y = +30 Talairach of Colin27 in Subject_00, Subject_01, etc. Should I use vol2vol to create a volume for every subject? Is there any direct method with register matrices or something like that? Thank you very much, Gari ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. ___ 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] longitudinal stream - template
Hi Yolanda, if you want to simulate a study where one obtains 2 time points (6 months apart) or 2 time points (12 months apart) and then compare the results, you would need to run these two independently through free surfers longitudinal stream (one time including 0 and 6 month, the other time including 0 and 12 months). If you are interested in measuring if for whatever reason there is a change in the slope at 6 months (e.g. a nonlinear trajectory) you can do the piecewise linear model that I described below on the full dataset. Best, Martin On Mar 19, 2013, at 4:26 AM, Yolanda Vives yvi...@pic.es wrote: Hi Martin, Thank you for your answer, but my idea was to compare the atrophy rates when using scans at 6 months (0 - 6 months) and scans at 12 months (0 - 12 months). If my templates are built with more time points, the results will be biased, right? Regards, Yolanda 2013/3/18 Martin Reuter mreu...@nmr.mgh.harvard.edu: Hi Yolanda, actually it is advantageous if the template is build from more time points. You don't need to process the images again, just do your statistical analysis with the time points you are interested in. But: why restrict the statistics to a subset of the data? If you are interested in yearly change, you can compute that from all time points. If you are interested in seeing if the atrophy rate increases over time, use a piecewise linear model (node at 6 months) and see if the slopes increase, etc. Removing time points from the statistics is usually a bad idea as you loose power. Best, Martin On 03/18/2013 01:15 PM, Yolanda Vives wrote: Dear FreeSurfer experts, I have run a longitudinal study considering multiple time points (7 scans/subject on average) with FS 5.1. However, I am interested in the percent changes between two time points only (between 0 and 6 months and between 0 and 1 year). Should I run the longitudinal stream from step 2 (template) two more times (1.- considering only 0 and 6 months scans and 2.- considering only 0 and 12 months scans) or is it correct even if my templates were built with all the time scans together? Thank you for your help, Yolanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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. - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] multi-echo mprage
Hi All, I have some multi-echo mprage images from a sequence and protocol set up to emulate Andre's 2008 paper. What's are the best-practices for using data from this type of sequence in Freesurfer? Related side questions: I have used the suggested morphometry protocols on the FS wiki (1mm iso resolution, same FOV, bandwidth matched, etc) 1) are people who are using this method using 4 echoes of alternating polarity, or 4 echoes of the same polarity? 2) for some subjects I have also acquired a 3D T2. Any recommendations on using these data together? Thanks, Souheil Souheil Inati, PhD Staff Scientist Functional MRI Facility NIMH/NIH/DHHS souheil.in...@nih.gov 301-402-9409 ___ 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] multi-echo mprage
Hi Souheil we usually compute the RMS across echoes and give that to recon-all as a normal mprage. It's a reasonable (although of course not optimal) weighting since the earlier echoes have more signal and more contrast. For the T2s, there's a new post-hoc procedure for deformaing the surfaces to match them (-T2pial or something like that in recon-all) cheers Bruce On Tue, 19 Mar 2013, Inati, Souheil (NIH/NIMH) [E] wrote: Hi All, I have some multi-echo mprage images from a sequence and protocol set up to emulate Andre's 2008 paper. What's are the best-practices for using data from this type of sequence in Freesurfer? Related side questions: I have used the suggested morphometry protocols on the FS wiki (1mm iso resolution, same FOV, bandwidth matched, etc) 1) are people who are using this method using 4 echoes of alternating polarity, or 4 echoes of the same polarity? 2) for some subjects I have also acquired a 3D T2. Any recommendations on using these data together? Thanks, Souheil Souheil Inati, PhD Staff Scientist Functional MRI Facility NIMH/NIH/DHHS souheil.in...@nih.gov 301-402-9409 ___ 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.
Re: [Freesurfer] multi-echo mprage
Hi Souheil I would run the two sets of scans separately; I would expect a T2 bias in the sample if they are run together with ones that have no T2. Perhaps see how T2 images influence the output (maybe have a .fsgd file with T2/noT2 as two levels) to see if there are significnt differences- no? Hth, shantanu On Tue, March 19, 2013 1:22 pm, Bruce Fischl wrote: Hi Souheil we usually compute the RMS across echoes and give that to recon-all as a normal mprage. It's a reasonable (although of course not optimal) weighting since the earlier echoes have more signal and more contrast. For the T2s, there's a new post-hoc procedure for deformaing the surfaces to match them (-T2pial or something like that in recon-all) cheers Bruce On Tue, 19 Mar 2013, Inati, Souheil (NIH/NIMH) [E] wrote: Hi All, I have some multi-echo mprage images from a sequence and protocol set up to emulate Andre's 2008 paper. What's are the best-practices for using data from this type of sequence in Freesurfer? Related side questions: I have used the suggested morphometry protocols on the FS wiki (1mm iso resolution, same FOV, bandwidth matched, etc) 1) are people who are using this method using 4 echoes of alternating polarity, or 4 echoes of the same polarity? 2) for some subjects I have also acquired a 3D T2. Any recommendations on using these data together? Thanks, Souheil Souheil Inati, PhD Staff Scientist Functional MRI Facility NIMH/NIH/DHHS souheil.in...@nih.gov 301-402-9409 ___ 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 -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ 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] make a volume template from the surface-based template for non-human primates
can you send your mris_fill command line? And maybe the lh.white surface you are trying to fill? Bruce On Tue, 19 Mar 2013, Longchuan Li wrote: Hi, Bruce This is the lh.white that gives me the empty volume when I use mris_fill to sample it to the volume space. Could you help diagnose what is causing it? Thank you very much in advance! Lognchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, March 17, 2013 11:47 AM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan I'm not sure what space the volume average is constructed in - Doug would know. Probably talairach, in which case it won't match the surfaces well. Can you send along your mris_fill command line? It shouldn't produce an empty volume. There's no reason to look at the inflated surfaces in the volume though - they have no volumetric meaning. cheers Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, Bruce Sorry for the late reply as I was trying to figure it out by myself. I mean the average of the subjects in the volume space that were used for generating the surface template. Actually I kind of found a volume average in the mri folder named as T1.mgz that seems to correspond to the surface template for the non-human primates. Perhaps because my ?h.white and ?.pial surface files do not have the identical origins as that of the volume template, when I used the function mri_surf2vol to project the mgh surface file to the volume average, I always got the outputs telling me there is 0 hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the volume using mri_fill and I got an empty volume. I then tried to project ?h.inflated to the volume space using the mri_fill and this time, I got a mask in the output volume space. Therefore, i suspect that there is a mismatch of the origins between the ?h.white and the volume template in the mri folder. Could you please show me what are the best strategies to correctly project the mgh file to the volume template in the 'mri' folder? Many thanks Longchuan ___ _ From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 15, 2013 4:56 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan what kind of volume template do you mean? Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks in advance! Longchuan 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 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] Medial orbitofrontal QA question
Thanks very much, Doug and Bruce! This e-mail and any attachments to it (the Communication) are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 19 March 2013 00:00 To: Alice Burnett Cc: freesurfer@nmr.mgh.harvard.edu; rahul desikan Subject: Re: [Freesurfer] Medial orbitofrontal QA question Hi Alice, you might also see what Rahul (ccd) thinks if you send an image. cheers Bruce On Mon, 18 Mar 2013, Alice Burnett wrote: Hi FreeSurfer experts, I have been working with a dataset we have run through FreeSurfer 5.0 and am interested in the medial orbitofrontal region (Desikan atlas). We have an unexpected surface area finding, so we want to rule out any systematic error in the generation of the area measurements. We followed the wiki instructions for processing and checked and edited all images as necessary, so the pial and white surface placement looks OK. I'm wondering, would you have any particular recommendations for QA checking the mOFC or things we should be looking out for? Thanks so much! Alice This e-mail and any attachments to it (the Communication) are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ 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 email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any question, please contact MCRI IT Helpdesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Medial orbitofrontal QA question
actually, I think you need to look up his email at UCSD as his MGH one bounced Bruce On Wed, 20 Mar 2013, Alice Burnett wrote: Thanks very much, Doug and Bruce! This e-mail and any attachments to it (the Communication) are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 19 March 2013 00:00 To: Alice Burnett Cc: freesurfer@nmr.mgh.harvard.edu; rahul desikan Subject: Re: [Freesurfer] Medial orbitofrontal QA question Hi Alice, you might also see what Rahul (ccd) thinks if you send an image. cheers Bruce On Mon, 18 Mar 2013, Alice Burnett wrote: Hi FreeSurfer experts, I have been working with a dataset we have run through FreeSurfer 5.0 and am interested in the medial orbitofrontal region (Desikan atlas). We have an unexpected surface area finding, so we want to rule out any systematic error in the generation of the area measurements. We followed the wiki instructions for processing and checked and edited all images as necessary, so the pial and white surface placement looks OK. I'm wondering, would you have any particular recommendations for QA checking the mOFC or things we should be looking out for? Thanks so much! Alice This e-mail and any attachments to it (the Communication) are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ 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 email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any question, please contact MCRI IT Helpdesk for further assistance. __ __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Brainsuite -- FreeSurfer
Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs -- write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz.That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way. VP___ 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] Brainsuite -- FreeSurfer
I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer VP From: pval...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite -- FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400 Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs -- write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz.That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way. VP ___ 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] make a volume template from the surface-based template for non-human primates
Hi, Bruce The command line I used is: mris_fill -r 1 -c rh.white rh.white.nii.gz I attached the rh.white in my previous mail. Could you see it in the attachment? Thank you! Longchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, March 19, 2013 8:10 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates can you send your mris_fill command line? And maybe the lh.white surface you are trying to fill? Bruce On Tue, 19 Mar 2013, Longchuan Li wrote: Hi, Bruce This is the lh.white that gives me the empty volume when I use mris_fill to sample it to the volume space. Could you help diagnose what is causing it? Thank you very much in advance! Lognchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, March 17, 2013 11:47 AM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan I'm not sure what space the volume average is constructed in - Doug would know. Probably talairach, in which case it won't match the surfaces well. Can you send along your mris_fill command line? It shouldn't produce an empty volume. There's no reason to look at the inflated surfaces in the volume though - they have no volumetric meaning. cheers Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, Bruce Sorry for the late reply as I was trying to figure it out by myself. I mean the average of the subjects in the volume space that were used for generating the surface template. Actually I kind of found a volume average in the mri folder named as T1.mgz that seems to correspond to the surface template for the non-human primates. Perhaps because my ?h.white and ?.pial surface files do not have the identical origins as that of the volume template, when I used the function mri_surf2vol to project the mgh surface file to the volume average, I always got the outputs telling me there is 0 hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the volume using mri_fill and I got an empty volume. I then tried to project ?h.inflated to the volume space using the mri_fill and this time, I got a mask in the output volume space. Therefore, i suspect that there is a mismatch of the origins between the ?h.white and the volume template in the mri folder. Could you please show me what are the best strategies to correctly project the mgh file to the volume template in the 'mri' folder? Many thanks Longchuan ___ _ From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 15, 2013 4:56 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan what kind of volume template do you mean? Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks in advance! Longchuan 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.
