Re: [Freesurfer] tracking edits
Thanks alot! Deirdre On Fri, May 8, 2015 at 3:23 PM, Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu wrote: Deirdre, the -show-edits flag in recon-all will print edits. N. On Thu, 2015-05-07 at 12:29 -0400, Deirdre O Shea wrote: Dear Freesurfer experts, I wondered how I might be able to track all the edits I make on each subject e.g., how many control points etc. But most specifically if there was a way to see how much ,numerically, the image has changed with manual correction following the initial FreeSurfer run. Thanks in advance, Deirdre ___ 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. ___ 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] Interaction contrast setup
I'm trying to see if two behavioral variables interact (they are factors 1 and 2) while controlling for the demographics also included in the fsgd file. I would also like to run an interaction with age and factor1. Here are the first few lines of my fsgd file. Thanks GroupDescriptorFile 1 Title STX Class Male Class Female Variables Age_demeaned Edu_demeaned Factor1 Factor2 Input F01_1 Female -5.0889 1.8556 0.9 0.93 Input F02_1 Male 1.9111 -0.1444 0.85 0.85 On Fri, May 8, 2015 at 3:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what are you trying to test an interaction between? Can you send the first lines of your fsgd file? On 05/07/2015 10:41 AM, Sarah Banducci wrote: Hi all- I have been trying to determine the most appropriate way to set up an interaction contrast for glmfit. For my purposes I'm interested in looking at the interaction two performance variables while covarying demographics. I have 2 classes set to male and female and the first columns in my fsgd file are demeaned age and education. I have found 3 ways people suggest setting up an interaction contrast: 1- Putting the contrast in one row: 0 0 0 0 -.5 -.5 .5 .5 2- Using two rows for the contrast: 0 0 0 0 .5 .5 0 0 0 0 0 0 0 0 .5 .5 3- Creating an actual interaction term where the values are multiplied together in a new column of the fsgd file 0 0 0 0 0 0 0 0 .5 .5 I would be grateful to know how people set up this contrast. Also I would like to know how you run it (positive or negative) and subsequently how you interpret the results. Thanks, Sarah Banducci ___ 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 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] Taking a measure of cluster width and length on flat surface
Hi Bruce Thanks for the information on the flat patch, thats great that the relationships are preserved! With that in mind do you know if freesurfer has any inbuilt functions to take the kind of measurements that I was describing? Or will my MATLAB based proposal be the best option do you think? Thanks again! Sarah From: Sarah Finnegan Sent: 11 May 2015 17:13 To: Freesurfer support list [freesurfer@nmr.mgh.harvard.edu] Subject: Taking a measure of cluster width and length on flat surface Dear all, I am looking to take two measures within the visual cortex. 1) A measure of width and length for each activation cluster overlaid onto the flattened cortical surface. 2) A measure of spacing between each cluster I can find how to take measures of area but I specifically want to know the width and length separately to correlate this to potential stripe systems. My plan was to fit an oval to each of these clusters and measure length through the cardinal axis and width through the minor, spacing would be calculated from a line fit to the minor axis of each cluster. Unfortunately I think the unfolding process will have changed the spacing relationships between clusters to make this inappropriate. I wonder if there is a command or established pipeline to take such measures? Thanks for your help! Sarah ___ 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] Data interest of the CorticalParcellation_Yeo2011
Hi Annie, mri_surf2surf is complaining that it cannot write out the annotation. Just to clarify, is your subject called test_run_allindex? In other words, is the variable s equal to test_run_allindex? Does the directory /home/annie/test_run_allindex/label/ exist? If not, then you first need to create the directory first, and then mri_surf2surf can write the resulting annotation file into the directory. Cheers, Thomas On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 poohann1...@gmail.com wrote: Hi Professor Yeo : We tried the code mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot However there came an error of could not write annot file /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot No such file or directory And we checked our individual subject's label there isn't lh.Yeo2011_7Networks_N1000.annot Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into our subjects/label first? What can we do ? Thank you very much! Best wishes, Annie 2015-05-05 8:36 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu: Hi Annie, Please cc the freesurfer list when you reply because there might be other people more qualified to answer your question. Based on what you are saying, I think you can first use mri_surf2surf (with the sval-annot flag) to transform the 2011 functional networks .annot file from fsaverage space to the subject's native surface space. Type mri_surf2surf --help to see examples. You can then use mris_anatomical_stats to compute thickness statistics. Cheers, Thomas On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 poohann1...@gmail.com wrote: Dear Pro. Yeo: Very appreciate for your reply ! We are trying to use your definition of the functional network regions to re-parcellate our images and get the regions of volume or cortical thickness for our study interest of structural network. However, we did not want to re-run the first recon-all again due to it's spending to much time. And we are still can't find the way to solve this problem. Thank you very much for helping us! Best wishes, Annie Chen 2015-05-02 8:25 GMT+08:00 Thomas Yeo ytho...@csail.mit.edu: Hi Yu-Chieh, I am cc-ing the freesurfer list who may help you with your issues. Can you explain what exactly you are trying do? The parcellation is released in different resolutions including fsaverage5. Why can't you just use the fsaverage5 parcellation? Cheers, Thomas On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 poohann1...@gmail.com wrote: Dear professor Yeo : My name is Yu-chieh Chen , I am a graduated student from National Taiwan University of medical school, and my supervisor is professor Susan Shur-Fen Gau from department of psychiatry, National Taiwan University Hospital College of Medicine. We are very interesting about your paper published in 2011 which using resting MRI to separate brain regions to functional networks. We'd like to use your percellation to re-separate the brain regions based on your released data in Freesurfer( http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). And use these volume of brain regions for our study, however, there comes the problem that we assumed that we can change the fsaverage into fsaverage5, thus we may get the new volume of the parcellation_Yeo. But it is not work. So I send this email for help. Last , I am very appreciate your kindness and very sorry for my inappropriate and rough. Thank you very much for read this email and sorry for occupied your time. Best wishes, Yu-chieh Chen ___ 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] Tracula reinit
Hi, The various tracts have different default numbers of control points, with a higher number for more curved paths. In a previous mail Dr. Yendiki recommended changing the number of control points if several attempts rerunning reinit don't produce a satisfactory result. Is it always better to have a larger number of control points, except for the increase (I assume) in processing time? Or will a larger number produce a worse result for less curved tracts? yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ 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] Taking a measure of cluster width and length on flat surface
Hi Sarah I don't think we have anything for ellipsoid fitting, although Oliver Hinds did some in his paper on V1. Should be straightforward enough in matlab. The data are in 2D mm coords cheers Bruce On Tue, 12 May 2015, Sarah Finnegan wrote: Hi Bruce Thanks for the information on the flat patch, thats great that the relationships are preserved! With that in mind do you know if freesurfer has any inbuilt functions to take the kind of measurements that I was describing? Or will my MATLAB based proposal be the best option do you think? Thanks again! Sarah From: Sarah Finnegan Sent: 11 May 2015 17:13 To: Freesurfer support list [freesurfer@nmr.mgh.harvard.edu] Subject: Taking a measure of cluster width and length on flat surface Dear all, I am looking to take two measures within the visual cortex. 1) A measure of width and length for each activation cluster overlaid onto the flattened cortical surface. 2) A measure of spacing between each cluster I can find how to take measures of area but I specifically want to know the width and length separately to correlate this to potential stripe systems. My plan was to fit an oval to each of these clusters and measure length through the cardinal axis and width through the minor, spacing would be calculated from a line fit to the minor axis of each cluster. Unfortunately I think the unfolding process will have changed the spacing relationships between clusters to make this inappropriate. I wonder if there is a command or established pipeline to take such measures? Thanks for your help! Sarah ___ 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] Data interest of the CorticalParcellation_Yeo2011
Hi Annie, I assume this means 5202 is your subject ID? Maybe you should check if /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot exist? If so, you can run mris_anatomical_stats to generate statistics for the parcellation. Cheers, Thomas On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 poohann1...@gmail.com wrote: Hi Professor Yeo : After I rechecked the directory and run again mri_surf2surf I got the result: Saving target data Converting to target annot Saving to target annot /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot The file of 5202/label didn't come out with lh.Yeo2011_7Networks_N1000.annot But it seems succeed, right? How can I get the stat of this parcellation ? Thank you very much! Best wishes, Annie 2015-05-12 6:06 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu: Hi Annie, mri_surf2surf is complaining that it cannot write out the annotation. Just to clarify, is your subject called test_run_allindex? In other words, is the variable s equal to test_run_allindex? Does the directory /home/annie/test_run_allindex/label/ exist? If not, then you first need to create the directory first, and then mri_surf2surf can write the resulting annotation file into the directory. Cheers, Thomas On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 poohann1...@gmail.com wrote: Hi Professor Yeo : We tried the code mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot However there came an error of could not write annot file /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot No such file or directory And we checked our individual subject's label there isn't lh.Yeo2011_7Networks_N1000.annot Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into our subjects/label first? What can we do ? Thank you very much! Best wishes, Annie 2015-05-05 8:36 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu: Hi Annie, Please cc the freesurfer list when you reply because there might be other people more qualified to answer your question. Based on what you are saying, I think you can first use mri_surf2surf (with the sval-annot flag) to transform the 2011 functional networks .annot file from fsaverage space to the subject's native surface space. Type mri_surf2surf --help to see examples. You can then use mris_anatomical_stats to compute thickness statistics. Cheers, Thomas On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 poohann1...@gmail.com wrote: Dear Pro. Yeo: Very appreciate for your reply ! We are trying to use your definition of the functional network regions to re-parcellate our images and get the regions of volume or cortical thickness for our study interest of structural network. However, we did not want to re-run the first recon-all again due to it's spending to much time. And we are still can't find the way to solve this problem. Thank you very much for helping us! Best wishes, Annie Chen 2015-05-02 8:25 GMT+08:00 Thomas Yeo ytho...@csail.mit.edu: Hi Yu-Chieh, I am cc-ing the freesurfer list who may help you with your issues. Can you explain what exactly you are trying do? The parcellation is released in different resolutions including fsaverage5. Why can't you just use the fsaverage5 parcellation? Cheers, Thomas On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 poohann1...@gmail.com wrote: Dear professor Yeo : My name is Yu-chieh Chen , I am a graduated student from National Taiwan University of medical school, and my supervisor is professor Susan Shur-Fen Gau from department of psychiatry, National Taiwan University Hospital College of Medicine. We are very interesting about your paper published in 2011 which using resting MRI to separate brain regions to functional networks. We'd like to use your percellation to re-separate the brain regions based on your released data in Freesurfer( http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). And use these volume of brain regions for our study, however, there comes the problem that we assumed that we can change the fsaverage into fsaverage5, thus we may get the new volume of the parcellation_Yeo. But it is not work. So I send this email for help. Last , I am very appreciate your kindness and very sorry for my inappropriate and rough. Thank you very much for read this email and sorry for occupied your time. Best wishes, Yu-chieh Chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Whitening in FSFAST
Hi Doug, I wanted to ask what kind of noise model FSFAST employs for whitening. Is it the one described in Worsley, neuroimage 2002? Is there a place on the wiki or elsewhere where I could find a description? Thanks, Caspar ___ 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] Freeview
Can you please provide me with the contents of your $FREESURFER_HOME/build-stamp.txt file? -Zeke On 05/11/2015 07:33 PM, Isabelle Deschamps wrote: Dear Freesurfer Users, I am trying to update the freeview file. However, I cannot find the folder $FREESURFER_HOME/Freeview.app/Contents/MacOS/Freeview When I go into my Freesurfer folder, I cannot find Freeview.app. Any help would be greatly appreciated. Thanks, Isabelle * Isabelle Deschamps, Chercheure postdoctorale, Faculté de Médecine Département de réadaptation Université Laval Pavillon Ferdinand-Vandry 1050 avenue de la Médecine Québec (Québec) G1V 0A6 Centre de Recherche de l'Institut universitaire en santé mentale de Québec (CRIUMSQ) 2601, chemin de la Canardière, bureau F-2424A Québec (Québec) G1J 2G3 Téléphone : 418 663-5000 poste 6857 ___ 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] Segmentation of hippocampal subfields / version 6.0 release date
Hi Josh, the module is already in the development version of FS, and will be released along with FS6 hopefully very soon. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Josh Gray jgray7...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 11, 2015 1:33:32 PM Subject: [Freesurfer] Segmentation of hippocampal subfields / version 6.0 release date Hello, I wanted to inquire about when you think that this new package for freesurfer 6.0 will be complete? I am interested in pursuing hippocampal segmentation, but it seems that I should not use the segmentation from your older program and I should wait, would you agree? Thank you, Josh -- Josh Gray Graduate Student Psychology Dept. - Clinical Program Experimental Clinical Psychopharmacology Laboratory University of Georgia ___ 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] Segmentation of hippocampal subfields / version 6.0 release date
Josh, You can get an FS version that is close to v6 here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev Any testing on top of the hippocampal fields functionality would be greatly appreciated! Nick On May 12, 2015, at 5:42 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote: Hi Josh, the module is already in the development version of FS, and will be released along with FS6 hopefully very soon. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Josh Gray jgray7...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 11, 2015 1:33:32 PM Subject: [Freesurfer] Segmentation of hippocampal subfields / version 6.0 release date Hello, I wanted to inquire about when you think that this new package for freesurfer 6.0 will be complete? I am interested in pursuing hippocampal segmentation, but it seems that I should not use the segmentation from your older program and I should wait, would you agree? Thank you, Josh -- Josh Gray Graduate Student Psychology Dept. - Clinical Program Experimental Clinical Psychopharmacology Laboratory University of Georgia ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
