[Freesurfer] Per-vertex regressors
Hi all, I want to use the --prv (per vertex regressors) option in mri_glmfit, but there is very little information in the Wiki and I couldn't find any relevant info in the mailing list. I have two .mgz files, one contains the dependent variable, the other is the source of my pvr. I tried loading one column from the second file and appending it to the design matrix in Matlab for each vertex (in a loop), but it's too time consuming to be feasible. Someone tipped me about the pvr option in mri_glmfit but from the Wiki (see below) it seems I would have to load the regressors individually here as well..? What is pvr1, pvr2 etc. in the example below? Text files? That's either going to be one very long command line or I have to use a loop here too (probably in Matlab). Is there any way to tell mri_glmfit. for each vertex in the dependent variable file, take the corresponding vector from the pvr-file and append it to the design matrix? [from the WIki:] --pvr pvr1 --prv pvr2 ... Per-voxel (or vertex) regressors (PVR). Normally, the design matrix is 'global', ie, the same matrix is used at each voxel. This option allows the user to specify voxel-specific regressors to append to the design matrix. Note: the contrast matrices must include columns for these components. Thank you! -- yours, Lars M. Rimol, PhD Division of Mental Health and Addiction Institute of Clinical Medicine University of Oslo P.O. Box 85 Vinderen, 0319 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.
[Freesurfer] left/right WM vols
Dear FreeSurfer expertsI'm trying to study WM-lesions of my data. As I saw in previous messages to the forum and papers, it is contained in the aseg.mgz as the WM-hypointensities volume (label-ID 77), but it has only one value from the whole brain in the aseg.mgz, the left/right fields appear empty in the aseg.stats, and I would be interested in subtract this volume value, or volume label image for each hemisphere. Is it possible on FS? May thanks in advanced,Gabriel. ___ 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] Truncate positive values in tksurfer
Dear FS experts How can I force tksurfer to truncate the positive values and not the negative ones? Thanks in advance Best regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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] issue about LME Matlab tools
Hi Ting Just use the default procedure. We limited the number of iterations for the estimation procedure to 20 for the mass-univariate analysis. If the model for the covariance is correct, that is to say, you have correctly specified the set of random effects that is supported by your data then the estimation at each vertex usually converges in a few iterations (between 5 and 9). In your case, you have only two repeated measures in your data. In that scenario, you should only use a single random effect for the intercept term (or maybe for the head_motion time-varying covariate, see who produces better convergence results). You cannot use a model with two random effects when you only have two repeated measures because you don't have enough degrees of freedoms in your data. For example, if you had to estimate a completely unstructured covariance then you would only need to estimate three covariance parameters for two repeated measures, on the other hand if you impose structure on the covariance using the mixed effects model with two random effects then you are estimating four covariance components which will impose too much structure on the covariance and the estimation algorithm will fail to converge most of the time. Finally, even when the set of random effects is correctly specified the iterative estimation procedure may not converge at several vertices (eg. 10% or may be more of the total number of vertices under analysis). Hope this helps. Best -Jorge De: ting xu xutin...@gmail.com Para: freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 12 de diciembre de 2012 9:22 Asunto: [Freesurfer] issue about LME Matlab tools Dear all, A few questions come to me when I used LME Matlab toolbox. Then Jorge kindly answered my questions and he also asked me to post our discussion to Freesurfer list so everyone knows what's going on here :) Cheers, Ting --- Subject: Re: Re: issue about LME Matlab tools Sent: Tue, Dec 11, 2012 21:41:26 Hi Ting Please could you post this question to the Freesurfer list, so other people can benefit from this discussion? I'll answer you ASAP. Best -Jorge -- Subject: Re: Re: issue about LME Matlab tools Sent: Wed, Dec 12, 2012 6:44:36 AM Hi Jorge, Thank you for your explanation in more details. I followed your suggestion, set the convergence epsilon to 10^-5. It truly improved. I am now running the whole brain data, estimations in several voxels were not converge after 50 iterations. Given that iterations takes more computational time, how many iterations do you recommend and what do you usually do if it still not converge? Thank you again:) Warmly regards, Ting -- Subject: Re: issue about LME Matlab tools Sent: Wed, Dec 12, 2012 00:50:35 Hi Ting You needed more iterations to make the algorithm stop closer to the optimal values. Try: statsFS= lme_fit_FS(X,[1 2],Y,ni,10^-5); or the EM algorithm statsEM = lme_fit_EM(X,[1 2],Y,ni,10^-10); Neither of these algorithms can be guaranty to converge but I have found the FS algorithm to be the most robust and fast. For the mass-univariate setting we limited the number of iterations for the FS algorithm to only 20 due to computational time. Note that for only two repeated measures (as in your data) compound symmetry (a model with a single random effect for the intercept term) likely holds for the covariance matrix among the repeated measures. Although a likelihood ratio test here comparing the model with one random effects against the model with two random effects is barely significant it will not likely survive a multiple comparisons correction. You can not impose structure on D in our toolbox nor it is recommended for general longitudinal data. Let me know any doubt you might have. Best -Jorge -- Subject: issue about LME Matlab tools Sent: Tue, Dec 11, 2012 14:47:14 Dear Dr. Sabuncu Your recent work Statistical Analysis of Longitudinal Neuroimage Date with Linear Mixed Effects Models provided us a great matlab toolbox to apply Mixed Model, especially for imaging data. Now, I am investigating the intraclass correlation based on this toolbox. Sometime I found the function lme_fit_FS could not get the accurate estimations. I think the problem may be relevant to the initial value from OLS method, in the case that the within-subject variability estimated from lme_fit_init is very close to zero. I attached an example. Y is test-retest imaging data for one voxel, X is design matrix including intercept, head_motion, age, gender. I set random effect for intercept and head_motion. I also attached result from SAS and the model is ok. stats = lme_fit_FS(X,[1,2],Y,ni); Here I'm wondering is there any way to
Re: [Freesurfer] Truncate positive values in tksurfer
Under View-Configure-Overlay select both Truncate and Inverse under display options. doug On 12/12/12 8:19 AM, Jürgen Hänggi wrote: Dear FS experts How can I force tksurfer to truncate the positive values and not the negative ones? Thanks in advance Best regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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] Chunks of missing WM
Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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] Chunks of missing WM
OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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] WM-hypointensities
Dear Freesurfers,I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it.Can any one help me?Best Regards,Gabriel. ___ 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] WM-hypointensities
Hi Gabriel we don't lateralize them by default, so look for WM_hypointensities (77) instead. It would be pretty easy to lateralize them based on neighboring labels. cheers Bruce On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers, I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it. Can any one help me? Best Regards, Gabriel. ___ 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] clarifications about running bedpost instead of tracl-all step 2
Hello, thank you for your help with the first steps of running Tracula. I was trying to run trac-all step 3 (paths), but was getting an error with the mergedph1samples file. I saw on the mailbase that you have suggested to run bedpost directly to fix this I have 3 questions about this: 1) do I need to delete any of the (temporary?) files or folders created by trac-all step 2 before running bedpost 2) should I run bedpost INSTEAD of trac-all step 2 for the remaining subjects? 3) you have suggested on the list to run bedpost as: bedpostx /usr/local/freesurfer/subjects/C001/dmri is this the same dmri folder as created by tracula step 1 (for each subject) Thank you so much for your help with this - I really appreciate it best wishes Prerona On 10 December 2012 19:54, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I'm guessing that this shows up in the scripts/trac-all.log of a particular subject? Then it applies to that subject. On Mon, 10 Dec 2012, s0675204 wrote: Hello My trac- preproc has completed. However, I am confused about the status message. It says: #- trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012 ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387 Does this mean it was completed succesfully for everyone or everyone but that 00387 person? Is there any way I can verify this? thank you so much for your help best wishes, Prerona On 8 December 2012 13:38, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: In your dmrirc, you define multiple subjects, but only one bvecfile and one bvalfile that are used for all subjects. On Sat, 8 Dec 2012, s0675204 wrote: the values are the same but each subject has an individual bvec bval file. so it depends on how the script will read it? On 8 December 2012 00:03, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Are the bvecs/bvals not the same for all subjects? On Fri, 7 Dec 2012, s0675204 wrote: oh! i thought this was how these were meant to be! i will do that. sadly i left the lab and came home for the day but i will try it as soon as i am back and let you know! thank you so much! do we have to do this for each subject or just one time? On 7 December 2012 23:51, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I see. Can you try formatting them in columns (1 column for the bvals and 3 columns for the bvecs)? On Fri, 7 Dec 2012, s0675204 wrote: yes! these are the original files well these are the files i pointed to in my config file. and i think the script copies them over to the dmrirc folder? best wishes, Prerona On 7 December 2012 23:38, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Yes, I can see that each of the bvecs/bvals files is one long line. Was that the case for the original files that you specified in the dmrirc? On Fri, 7 Dec 2012, s0675204 wrote: Hi Anastasia I had attached the files, but maybe they did not go through to the mailing list? So I am sending them to your email id. Hope this is okay best wishes, Prerona -- Forwarded message -- From: s0675204 s0675...@sms.ed.ac.uk Date: 7 December 2012 19:44 Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited with ERRORS To: freesurfer@nmr.mgh.harvard.edu Hello I think I spoke to soon! It ended with errors again. I get the error message: bvecs and bvals don't have the same number of entries I saw on some older messages on the mail-base you said that we need to check that the number of entries in the bvals is same as and bvecs is 3 times as much as the number of volumes. I have checked that this is the case I am wondering if it is some formatting problem? there are no spaces at the end of the file. and there are no end of line markers either. Please could you advise me? I have attached the files and also pasted the contents below My config file is still the same (as pasted below) except I tried changing nb0 to 2 (# Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 2) best wishes, Prerona = bvals: 0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 bvecs: 0 0.99864840507507 0.01463935524225 0.01274211052805 0.85177010297775 0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873 0.51641523838043 0.46147873997688 0.54209464788436 0.44143822789192 0.52723878622055 0.4250853061676 0.51590526103973 0.43744987249374 0.50455766916275 0.05208261311054 0.06073396280407 0.00979638285934 0 0.99864840507507 0.01463935524225 0.01274211052805 0.85177010297775 0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873 0.51641523838043 0.46147873997688
Re: [Freesurfer] WM-hypointensities
Yes I did loo at the total WH-hypointensities(77), and substract them without a problem.What do you mean with lateralize them based on neighboring labels? How can I perform such thing on FS?Actually I'm interested in knowing to wich specific label o region they are.Bests,GabrielEl 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:Hi Gabrielwe don't lateralize them by default, so look for WM_hypointensities (77) instead. It would be pretty easy to lateralize them based on neighboring labels.cheersBruceOn Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote:Dear Freesurfers,I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty inthe aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it.Can any one help me?Best Regards,Gabriel.The information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] clarifications about running bedpost instead of tracl-all step 2
1) Can't hurt to delete. 2) Yes. 3) Yes. On Wed, 12 Dec 2012, s0675204 wrote: Hello, thank you for your help with the first steps of running Tracula. I was trying to run trac-all step 3 (paths), but was getting an error with the mergedph1samples file. I saw on the mailbase that you have suggested to run bedpost directly to fix this I have 3 questions about this: 1) do I need to delete any of the (temporary?) files or folders created by trac-all step 2 before running bedpost 2) should I run bedpost INSTEAD of trac-all step 2 for the remaining subjects? 3) you have suggested on the list to run bedpost as: bedpostx /usr/local/freesurfer/subjects/C001/dmri is this the same dmri folder as created by tracula step 1 (for each subject) Thank you so much for your help with this - I really appreciate it best wishes Prerona On 10 December 2012 19:54, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I'm guessing that this shows up in the scripts/trac-all.log of a particular subject? Then it applies to that subject. On Mon, 10 Dec 2012, s0675204 wrote: Hello My trac- preproc has completed. However, I am confused about the status message. It says: #- trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012 ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387 Does this mean it was completed succesfully for everyone or everyone but that 00387 person? Is there any way I can verify this? thank you so much for your help best wishes, Prerona On 8 December 2012 13:38, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: In your dmrirc, you define multiple subjects, but only one bvecfile and one bvalfile that are used for all subjects. On Sat, 8 Dec 2012, s0675204 wrote: the values are the same but each subject has an individual bvec bval file. so it depends on how the script will read it? On 8 December 2012 00:03, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Are the bvecs/bvals not the same for all subjects? On Fri, 7 Dec 2012, s0675204 wrote: oh! i thought this was how these were meant to be! i will do that. sadly i left the lab and came home for the day but i will try it as soon as i am back and let you know! thank you so much! do we have to do this for each subject or just one time? On 7 December 2012 23:51, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I see. Can you try formatting them in columns (1 column for the bvals and 3 columns for the bvecs)? On Fri, 7 Dec 2012, s0675204 wrote: yes! these are the original files well these are the files i pointed to in my config file. and i think the script copies them over to the dmrirc folder? best wishes, Prerona On 7 December 2012 23:38, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Yes, I can see that each of the bvecs/bvals files is one long line. Was that the case for the original files that you specified in the dmrirc? On Fri, 7 Dec 2012, s0675204 wrote: Hi Anastasia I had attached the files, but maybe they did not go through to the mailing list? So I am sending them to your email id. Hope this is okay best wishes, Prerona -- Forwarded message -- From: s0675204 s0675...@sms.ed.ac.uk Date: 7 December 2012 19:44 Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited with ERRORS To: freesurfer@nmr.mgh.harvard.edu Hello I think I spoke to soon! It ended with errors again. I get the error message: bvecs and bvals don't have the same number of entries I saw on some older messages on the mail-base you said that we need to check that the number of entries in the bvals is same as and bvecs is 3 times as much as the number of volumes. I have checked that this is the case I am wondering if it is some formatting problem? there are no spaces at the end of the file. and there are no end of line markers either. Please could you advise me? I have attached the files and also pasted the contents below My config file is still the same (as pasted below) except I tried changing nb0 to 2 (# Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 2) best wishes, Prerona = bvals: 0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 bvecs: 0 0.99864840507507 0.01463935524225 0.01274211052805 0.85177010297775 0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873 0.51641523838043 0.46147873997688 0.54209464788436 0.44143822789192 0.52723878622055 0.4250853061676 0.51590526103973 0.43744987249374 0.50455766916275 0.05208261311054 0.06073396280407 0.00979638285934 0 0.99864840507507 0.01463935524225 0.01274211052805 0.85177010297775 0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873 0.51641523838043 0.46147873997688 0.54209464788436
Re: [Freesurfer] Per-vertex regressors
Hi Lars, the way it works is that each pvr that you spec on the cmd line indicates another column in the design matrix. If you want multiple columns then add multiple --pvr options (thus pvr1, pvr2, etc). If you do not spec an X matrix or fsgd file, then it will assume that you want a column of 1s at each vertex. You need to create contrast matrices that have enough columns to cover all the columns in the design matrix, both fixed/global and per-vertex. doug On 12/12/2012 04:43 AM, Lars M. Rimol wrote: Hi all, I want to use the --prv (per vertex regressors) option in mri_glmfit, but there is very little information in the Wiki and I couldn't find any relevant info in the mailing list. I have two .mgz files, one contains the dependent variable, the other is the source of my pvr. I tried loading one column from the second file and appending it to the design matrix in Matlab for each vertex (in a loop), but it's too time consuming to be feasible. Someone tipped me about the pvr option in mri_glmfit but from the Wiki (see below) it seems I would have to load the regressors individually here as well..? What is pvr1, pvr2 etc. in the example below? Text files? That's either going to be one very long command line or I have to use a loop here too (probably in Matlab). Is there any way to tell mri_glmfit. for each vertex in the dependent variable file, take the corresponding vector from the pvr-file and append it to the design matrix? [from the WIki:] --pvr pvr1 --prv pvr2 ... Per-voxel (or vertex) regressors (PVR). Normally, the design matrix is 'global', ie, the same matrix is used at each voxel. This option allows the user to specify voxel-specific regressors to append to the design matrix. Note: the contrast matrices must include columns for these components. Thank you! -- yours, Lars M. Rimol, PhD Division of Mental Health and Addiction Institute of Clinical Medicine University of Oslo P.O. Box 85 Vinderen, 0319 Oslo, Norway ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM-hypointensities
Thanks bruce, for your answer,Does it exist a tool on FS or matlab to do such asignment of voxels from the WM-hypointensities (77) to the neighbouring labels?If so, does it can use whoever the aseg.mgz,the aparc+aseg or the wmparc.mgz to do this asignment?Thanks,GabrielEl 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:Hi Gabrielwe don't lateralize them by default, so look for WM_hypointensities (77) instead. It would be pretty easy to lateralize them based on neighboring labels.cheersBruceOn Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers, I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it. Can any one help me? Best Regards, Gabriel. ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] WM-hypointensities
then I would either use TRACULA (if you have DWI) or the wmparc to generate ROIs. I meant that you could count whether there are more lh or rh wm labels neighboring each one to figure out which hemi they are in cheers Bruce On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Yes I did loo at the total WH-hypointensities(77), and substract them without a problem. What do you mean with lateralize them based on neighboring labels? How can I perform such thing on FS? Actually I'm interested in knowing to wich specific label o region they are. Bests, Gabriel El 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió: Hi Gabriel we don't lateralize them by default, so look for WM_hypointensities (77) instead. It would be pretty easy to lateralize them based on neighboring labels. cheers Bruce On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers, I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it. Can any one help me? Best Regards, Gabriel. 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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] WM-hypointensities
wmparc should do it I think, although we don't have any tools for doing so it wouldn't be very hard in matlab On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Thanks bruce, for your answer, Does it exist a tool on FS or matlab to do such asignment of voxels from the WM-hypointensities (77) to the neighbouring labels? If so, does it can use whoever the aseg.mgz,the aparc+aseg or the wmparc.mgz to do this asignment? Thanks, Gabriel El 12/12/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió: Hi Gabriel we don't lateralize them by default, so look for WM_hypointensities (77) instead. It would be pretty easy to lateralize them based on neighboring labels. cheers Bruce On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers, I'm looking for a way to compute the left and right WM-hypointensities, as volume values or images. They always appear empty in the aseg.stats, and the corresponding segs No 78 79 do not appear in the aseg.mgz, and I'm a bit lost with it. Can any one help me? Best Regards, Gabriel. ___ 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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] Registering cortical surfaces
Dear FreeSurfer experts, I apologize in advance if my questions seem naive or too simple: I am completely new to FreeSurfer and I am still attempting to understand how to make good use of its potential. I believe I want to use it in an unusual way. I have been given two cortical surfaces, both in the form of genus 0 triangular meshes. The two meshes are stored as OFF files, but I can easily generate other formats (PLY, OBJ, simple ASCII, ...). For both surfaces I also have informations on some sulci, in the form of list of vertices, in ASCII format. I would like to map (register) one mesh onto the other: it seems that FreeSurfer would allow me to do this with the following steps: - inflate the two surfaces - map them onto the sphere - register one surface (on the sphere) onto the second surface (on the sphere). How do I make this work? I have looked at SurfaceRegAndTemplates, but the process described relates to specific FreeSurfer files. I will obviously need to convert my OFF files into a format that FreeSurfer can recognize, and vice versa convert the sphere representations (Source mesh, S, target mesh, T, and S on T) into an ascii format that I can analyze. Could someone give me an overview of how I should proceed, with pointers on which procedures I should use from FreeSurfer. Thanking you in advance for your help, Best regards, -Patrice ___ 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.
