[Freesurfer] GLM for volume
Dear all, In mris_preproc, I see that there's an option to choose volume for --meas, would this change anything in the subsequent GLM processes (mri_surf2surf, mri_glmfit)? I'm following the tutorial for group analysis, but I haven't seen any mention of measures apart from thickness, so is this even a valid question? For mri_surf2surf and mri_glmfit, what are the other options for areas apart from --cortex? Cheers, Linda ___ 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] tkregister2 error
Dear list, I'm having problems with the tkregister2 command, I input the following command: tkregister2 --mov ~/Desktop/input/*_d/mri/rawavg.mgz --noedit --s *_d --regheader --reg ~/Desktop/input/*_d/mri/register.dat Where I'm setting the directory of my subjects, and I get the following output /Desktop/input/*_d/mri/register.dat /usr/local/freesurfer/tktools/tkregister2.bin: No match. However, when I try a similar command with the sample data from bert (And after adjusting the subject folder settings) It works fine. I ran out of ideas on how to fix it, does anybody have any clue of what can I do? Thanks a lot for your help Regards ___ 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] save custom made path on surface as label
Hi Bruce, thanks for your reply. I was interested in computing the distance between two labels (or within a label), the idea was to export the this path label and e.g lh.orig into matlab and then determine the distance along the surface. Do we have tool for this issue in freesurfer? cheers, Erhan 2012/3/7 Bruce Fischl fis...@nmr.mgh.harvard.edu Yes, you probably need to generate a closed path, or a closed cut. I'm not sure if we support saving paths as label files. Anyone know? Bruce On Wed, 7 Mar 2012, Erhan Genc wrote: Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label file? cheers, erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax:+49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de http://www.brain.mpg.de/**research/singer-emeritus-** department/people/erhan-genc/http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-genc/ 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/**compliancelinehttp://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. -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax:+49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-genc/ ___ 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] Fwd: Total WM and GM Vol in FS 5.0.0
Hi Dhinakaran. I think we include this in one of the stats files. Allison or Doug would know. cheers Bruce On Fri, 9 Mar 2012, Dhinakaran Chinappen wrote: Hi Prof. Fischl and Dr.Greve, I was wondering if you all got this email below? I sent in to the FS listserv early yesterday. Would really appreciate your help on this matter of total WM and total GM. Much thanks, Dhinakaran. -- Forwarded message -- From: Dhinakaran Chinappen dchin...@seas.upenn.edu Date: Thu, Mar 8, 2012 at 1:20 PM Subject: Total WM and GM Vol in FS 5.0.0 To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Cc: Professor Lynnae Schwartz schwart...@email.chop.edu Hi all, I am using Freesurfer 5.0.0, before the outputs for cortical and subcortical GM and WM were made available in the final output files. What is the best way to calculate total gray matter volume (cortical and subcortical)? Is it through mris_anatomical_stats or mri_segstats? Also, are there commands to calculate total cortical and total subcortical volumes of GM separately? As for total white matter, is using the sum of the volumes of Left-Cerebral-White-Matter and Right-Cerebral-White-Matter considered acceptable practice? Or should I go to the command line and use mris_wm_volume? Thanks in advance for the clarification, Dhinakaran. -- ___ 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] tkregister2 error
Hi Daniel what subject are you trying to run on? I think it's complaining about one of the *_d parts of your command. Can you put the actual name in instead of a wildcard? cheers Bruce On Fri, 9 Mar 2012, Daniel Preciado wrote: Dear list, I'm having problems with the tkregister2 command, I input the following command: tkregister2 --mov ~/Desktop/input/*_d/mri/rawavg.mgz --noedit --s *_d --regh eader --reg ~/Desktop/input/*_d/mri/register.dat Where I'm setting the directory of my subjects, and I get the following outp ut /Desktop/input/*_d/mri/register.dat /usr/local/freesurfer/tktools/tkregister2.bin: No match. However, when I try a similar command with the sample data from bert (And af ter adjusting the subject folder settings) It works fine. I ran out of ideas on how to fix it, does anybody have any clue of what can I do? Thanks a lot for your help Regards ___ 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] save custom made path on surface as label
Hi Erhan this is what we typically use the spherical coordinate system for. Just compute the distance along the great circle connecting two points (for your example it would be the centroid of the labels, or possibly the max of the min over all pairs of points in the two labels, which would be the Hausdorff distance). cheers Bruce On Fri, 9 Mar 2012, Erhan Genc wrote: Hi Bruce, thanks for your reply. I was interested in computing the distance between two labels (or within a label), the idea was to export the this path label and e.g lh.orig into matlab and then determine the distance along the surface. Do we have tool for this issue in freesurfer? cheers, Erhan 2012/3/7 Bruce Fischl fis...@nmr.mgh.harvard.edu Yes, you probably need to generate a closed path, or a closed cut. I'm not sure if we support saving paths as label files. Anyone know? Bruce On Wed, 7 Mar 2012, Erhan Genc wrote: Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label file? cheers, erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-ge nc/ 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. -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-ge nc/ ___ 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] Group comparison
Hi All, I am trying to compare controls to patients. There is an interaction between group and age (i.e. the aging pattern is different for both groups). I did an interaction contrast and this was significant in the same areas that were significant in the original comparison. I can't switch to a DOSS model (because the slopes are different). Interestingly, I'm getting some areas increasing with age as well, but I'm not sure if these results are valid since some may argue I can't compare the group thicknesses if there is this interaction. There aren't topologic errors in my samples either. Given all this, I'm at a bit of a loss in terms of figuring out how to compare thicknesses between the groups. Can it still be done? Thank you, Allison ___ 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] DTI analysis: freesurfer vs DTI studio
Hi Ayaz: Both packages are equally good. The main difference, is that DTI studio runs on Windows while FreeSurfer is Linux/ Unix based. So it depends on your platform. It also depends on your research question/s. best, Alan BIDMC/ Boston On Thu, Mar 8, 2012 at 7:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ayaz I'm not all that familiar with DTI studio. Tracula, which is a package within FreeSurfer, automically generates models of 17 or so major white matter fascicles with no user intervention required. cheers Bruce On Thu, 8 Mar 2012, Ayaz, Muhammad wrote: Dear All, I am new to freesurfer DTI analysis. Can anybody explain what is the advantage of using freesurfer for DTI analysis over DTI studio? Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. ___ 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] DTI analysis: freesurfer vs DTI studio
Hi Ayaz, In addition to the platform differences, DTIstudio uses deterministic tractography algorithm (Fiber Assignment by Continuous Tracking (FACT) method), whereas the TRACULA uses prior information of anatomy surrounding the fiber tracts along with a more sensitive probabilistic crossing fibers algorithm (based on FSL's bedpostX). Hope this is helpful, Priti Hi Ayaz: Both packages are equally good. The main difference, is that DTI studio runs on Windows while FreeSurfer is Linux/ Unix based. So it depends on your platform. It also depends on your research question/s. best, Alan BIDMC/ Boston On Thu, Mar 8, 2012 at 7:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ayaz I'm not all that familiar with DTI studio. Tracula, which is a package within FreeSurfer, automically generates models of 17 or so major white matter fascicles with no user intervention required. cheers Bruce On Thu, 8 Mar 2012, Ayaz, Muhammad wrote: Dear All, I am new to freesurfer DTI analysis. Can anybody explain what is the advantage of using freesurfer for DTI analysis over DTI studio? Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system. ___ 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
Re: [Freesurfer] GLM for volume
No, it does not change anything. Just make sure to use the new mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc Linda Zhang wrote: Dear all, In mris_preproc, I see that there's an option to choose volume for --meas, would this change anything in the subsequent GLM processes (mri_surf2surf, mri_glmfit)? I'm following the tutorial for group analysis, but I haven't seen any mention of measures apart from thickness, so is this even a valid question? For mri_surf2surf and mri_glmfit, what are the other options for areas apart from --cortex? Cheers, Linda ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Fwd: Total WM and GM Vol in FS 5.0.0
All of those except total brain volume are included in the aseg.stats. You can get total brain volume by running mri_binarize --i aparc+aseg.mgz --o junk.mgh --count brainvol.dat brainvol.dat will be a text file with the brain volume in it. You can delete junk.mgh doug Bruce Fischl wrote: Hi Dhinakaran. I think we include this in one of the stats files. Allison or Doug would know. cheers Bruce On Fri, 9 Mar 2012, Dhinakaran Chinappen wrote: Hi Prof. Fischl and Dr.Greve, I was wondering if you all got this email below? I sent in to the FS listserv early yesterday. Would really appreciate your help on this matter of total WM and total GM. Much thanks, Dhinakaran. -- Forwarded message -- From: Dhinakaran Chinappen dchin...@seas.upenn.edu Date: Thu, Mar 8, 2012 at 1:20 PM Subject: Total WM and GM Vol in FS 5.0.0 To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Cc: Professor Lynnae Schwartz schwart...@email.chop.edu Hi all, I am using Freesurfer 5.0.0, before the outputs for cortical and subcortical GM and WM were made available in the final output files. What is the best way to calculate total gray matter volume (cortical and subcortical)? Is it through mris_anatomical_stats or mri_segstats? Also, are there commands to calculate total cortical and total subcortical volumes of GM separately? As for total white matter, is using the sum of the volumes of Left-Cerebral-White-Matter and Right-Cerebral-White-Matter considered acceptable practice? Or should I go to the command line and use mris_wm_volume? Thanks in advance for the clarification, Dhinakaran. -- -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] dt_recon with siemens skyra data
Hello all, I am trying to process siemen dti data from a skyra model in the dt_recon software. But the software fails in the conversion from Dicom. Anyone had experience with the DTI sequence from a skyra model? Any suggestion is welcome Thanks in advance John Ochoa Bioingeniería Universidad de Antioquia ___ 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] error in eating individual label values of area
Hi, I am trying to get the individual data points for a label I´ve made for an effect site on area. After making the label, I try to go to group and marked graphed vertices avg. It then just gives me this error message (pasted below)- this has happened on different boxes and w/ different effects. Is there some reason why I can´t do this on area? I am truly grateful for any idea on how to fix this! best, kristine element error110 already exists in .fsgdf-0.gwPlot element error110 already exists in .fsgdf-0.gwPlot while executing $gw element create error$nClass$nErrorIndex -data $lBar -color $color -symbol splus -label -pixels 5 (procedure FsgdfPlot_PlotData line 91) invoked from within FsgdfPlot_PlotData $iID (procedure FsgdfPlot_EndPointList line 5) invoked from within FsgdfPlot_EndPointList $gGDFID (procedure GDF_SendCurrentPoints line 23) invoked from within GDF_SendCurrentPoints (procedure GDF_PlotAvgMarkedVerts line 4) invoked from within GDF_PlotAvgMarkedVerts invoked from within .w.fwMenuBar.mbwTools.mw.cmw14 invoke active (uplevel body line 1) invoked from within uplevel #0 [list $w invoke active] (procedure tk::MenuInvoke line 47) invoked from within tk::MenuInvoke .w.fwMenuBar.mbwTools.mw.cmw14 1 (command bound to event) -- Kristine B Walhovd Professor University of Oslo Center for the Study of Human Cognition Department of Psychology PB 1094 Blindern 0317 Oslo 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.
