Re: [Freesurfer] mri_glmfit-sim with pre-cached fails
Doug, For the PCA residuals we found 37% for the first component. The same analysis has been done for FreeSurfer v4.5.0, and we found a residual FWHM of 15.27 and 30% for the first PCA component. The time courses showed some outliers for both versions, very much dependent on the position on the surface, i.e., each time different subjects were outside the confidence limits. Summarizing: v4.5.0: residualFWHM = 15.27; 1st PCA 30% v5.0.0: residualFWHM = 34.00; 1st PCA 37% (number of subjects is 53). So, it is a puzzle why the residual FWHM is that large for v5.0.0. Ed On 1 Oct 2012, at 9:15, Ed Gronenschild wrote: On 28 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 27 Date: Fri, 28 Sep 2012 10:03:47 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fmri_glmfit-sim with pre-cached fails To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5065ae43.7060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hmmm, that's a lot, but I'm very surprised that the final FWHM is over 30. How many subjects do you have? There might be one that is messed up. You can check this by loading the y.mgh as a time course in tksurfer. It will give you a graph with each subject. Finally, you can run mri_glmfit with the --pca option to get a PCA of the residuals. This will create a folder called pca-eres. Look at the stats.dat and see how much variance is explained by the first component (first row, 4th column). doug On 09/28/2012 03:31 AM, Ed Gronenschild wrote: Hi Doug, For mri_glmfit I used a cortical thickness smoothed with a FWHM of 20, resulting from using the -qcache option in recon-all. Ed On 27 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 16 Date: Thu, 27 Sep 2012 11:29:06 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 506470c2.5060...@nmr.mgh.harvard.edu mailto:506470c2.5060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking that no one would ever go above it, or maybe should never go above it. I can create tables at higher smoothing levels, but 34mm is a lot of smoothing. How much did you apply to the data? doug On 09/27/2012 05:48 AM, Ed Gronenschild wrote: Hi, I want to apply a cluster correction with mri_glmfit-sim with the --cache option: mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs It fails with the error message that it can't find the file: FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/ th1.3/mc- z.csd (FSDir is the directory where FreeSurfer is located, version 5.0.0, Mac OSX10.5) Looking at the content of the fsaverage/lh/cortex directory than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 are present. In the log file from mri_glmfit I can read that the residualFWHM is 34.005014. Since this FWHM is automatically derived by mri_glmfit, does it mean that I can never use the --cache option in this case? Cheers, Ed ___ 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] cluster to annotations
Dear FS: We compared two groups using cluster-wise Montecarlo simulation. Clusters obtained are extended for more than one region of aparc.2009 atlas. How to identify automatically those regions in each cluster?May I get a file with list of aparc.2009 regions and corresponding clusters? best regards attachment: jm.vcf___ 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] cluster to annotations
Dear FS: We compared two groups using cluster-wise Montecarlo simulation. Clusters obtained are extended for more than one region of aparc.2009 atlas. How to identify automatically those regions in each cluster?May I get a file with list of aparc.2009 regions and corresponding clusters? best regards attachment: jm.vcf___ 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] long_mris_slopes command: temporal average calculation
Hi Martin, I am a little confused about these mapped files in the base directories you are referring to. How would I check them? -Shannon K. On Fri, Sep 28, 2012 at 4:08 PM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: I see, Usually people look at thickness maps and volume on an ROI basis. Volume on the surface I think is simply area times thickness. Not sure how meaningful that is as area of a vertex depends on the triangle mesh. Anyway, you look at smoothed maps on fsaverage. The average volume for each vertex should be somewhere in the middle of the individual values across time after they have been resampled to fsaverage. You can find the mapped files in the base directories. Can you double check that the average is in the middle of the time points? Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi Martin, I am running FS version 5.1. This is the command line I ran: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage These are the outputs I get, which are located in the subjects' base template surf folders: lh.long.volume-rate.fwhm10.mgh lh.long.volume-pc1.fwhm10.mgh lh.long.volume-avg.fwhm10.mgh lh.long.volume-spc.fwhm10.mgh I also get the files that end in fsaverage.mgh. I'm a little confused about this volume issue. In a previous post you said that long_mris_slopes works for surface maps (both thickness and volume should work). Therefore I used the long_mris_slopes for the volumes for a VBM analysis. Please let me know if this would not work. Thank you! -Shannon On Fri, Sep 28, 2012 at 4:02 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon, that cannot be. It either indicates a serious bug (which we have not yet encountered in our data) or a problem with your processing. Can you send me: - the version you use - the command line you run - the output you get Also long_mris_slopes is designed for analyzing surface maps (analysis on a vertex by vertex basis). This is usually thickness. So I don't understand what 'volumes' you mean? For an ROI analysis based on stats files you need to use long_stats_slopes. Best, Martin On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote: Hi Martin, Each subject has 3-6 timepoints. They are all about one year apart. Here's an example of the discrepancy: one subject with 5 timepoints had volumes that ranged from 2.2-2.4. However, from the long_mris_slopes command, the temporal average volume was calculated to be 1.67. Thanks for your help! -Shannon K. On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon, long_mris_slopes works for surface maps (both thickness and volume should work). In both cases it should compute the temporal average. I have another scripts that works for stats files (long_stats_slopes) in the same way. How many time points do you have, how far apart (equally spaced?). Best, Martin On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote: Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me
Re: [Freesurfer] CT Method Comparison
Hi Gari, you can use the data from the surf2surf in qdec/mri_glmfit. If you are using qdec, you might want to let qdec generate the file for you to make sure they are consistent. It is just running mris_preproc and should give an identical file, but just to make sure. doug On 09/29/2012 05:17 PM, Garikoitz Lerma-Usabiaga wrote: Hi Doug, you are right, we are very happy with the results, we were just trying to be as conservative as possible and testing different methods and regions before making any decision. We are going to introduce one of the methods in a stream for several studies and we wanted to know if you have any recommendation. As the results are not exactly the same maybe you think one of those is better than the other for any reason. For example, considering that the accuracy between methods is similar, could we use the data in Qdec (with Colin27) with the surf2surf method? I understand that we couldn't do that with the label2label method. Many thanks again for your help! Gari On Fri, Sep 28, 2012 at 4:18 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: hi Gari, looking at this I don't really see a problem. Yes, the t-test is very significant, but I would expect that from a paired t looking across different methods. the size of the effect is very small, about 1.5%. Do you see this as a problem? doug On 09/28/2012 05:14 AM, Garikoitz Lerma-Usabiaga wrote: Hi Doug, I think that the differences are significant enough, but just in case please find attached an excel file with the data and the t-test. Some of the ROI-s are small (Triangularis, Operculum, Orbitalis and then all together in the IFG). I attached images for each of them for reference. If in any case you assume that there are going to be differences, which method would you recommend and why? Thanks! Gari PS after mri_preproc I didn't smooth the surface as in the qdec example, żshould I do that? On Fri, Sep 28, 2012 at 4:24 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: OK, got it (finally). I would not expect the answers to be identical, but I would expect them to be close. How close are they? If the ROI is very small, there might be appreciable differences between the two. doug On 9/27/12 6:26 PM, Garikoitz Lerma-Usabiaga wrote: Hi, You are right, this was one of the methods. The second one is as follows (I copy the repeated steps): For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if it is out. You have a registration between roi.nii and orig.mgz You run mri_vol2surf on roi.nii to get lh.roi.mgh I run mris_preproc for every subject to Colin27: mris_preproc --out /subject/surf/ROI_toColin27.mgh --target Colin27 --hemi lh --meas thickness --s subject mri_segstats --seg /Colin27/surf/lh.roi.mgh --in /subject/surf/ROI_to_Colin127.mgh --sum subject/stats/target_lh.ROI.stats Thanks for your help, Gari Note: You said: You run mri_cor2label (with --surf option) to convert lh.roi.mgh into lh.roi.label Just in case, this is how I run it: * mri_cor2label --i /subjects/Colin27/lh.ROI.mgh --surf Colin27 lh --id 1 --l /subjects/Colin27/lh.ROI.label * mri_label2label --srclabel /subjects/Colin27/lh.ROI.label --srcsubject Colin27 --trgsubject subject --trglabel lh.ROI_Colin27_to_bert --regmethod surface --hemi lh On 26/09/2012, at 23:56, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Sorry, I'm still a little lost. Let me see if I have it right: For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if it is out.
Re: [Freesurfer] random effects analysis with performance values
Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote: Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam -- 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] command to check the regional cortical thicknesses and volumes
Hi Yawu, there is a file in the output called subject/stats/lh.aparc.stats (there is an rh.aparc.stats too as well as ?h.aparc.a2009s.stats files). doug ps. Please send emails to the FreeSurfer list instead of directly to me. Thanks! On 10/01/2012 03:36 AM, Liu Yawu wrote: Hi Douglas, After run recon-all -cw256 -s AA -all, how to check the check the regional cortical thicknesses and volumes? Regards, Yawu -- 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] mri_glmfit-sim with pre-cached fails
wow, that is a big difference. Can you just subtract the y.mgh of the 4.5 version from that of the 5.0 version and see where the differences are? Also, if you take the y.mgh of 4.5 and run it in the mri_glmfit of 5.0, do you see the same FWHM as in the mri_glmfit of 4.5? doug On 10/01/2012 07:38 AM, Ed Gronenschild wrote: Doug, For the PCA residuals we found 37% for the first component. The same analysis has been done for FreeSurfer v4.5.0, and we found a residual FWHM of 15.27 and 30% for the first PCA component. The time courses showed some outliers for both versions, very much dependent on the position on the surface, i.e., each time different subjects were outside the confidence limits. Summarizing: v4.5.0: residualFWHM = 15.27; 1st PCA 30% v5.0.0: residualFWHM = 34.00; 1st PCA 37% (number of subjects is 53). So, it is a puzzle why the residual FWHM is that large for v5.0.0. Ed On 1 Oct 2012, at 9:15, Ed Gronenschild wrote: On 28 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 27 Date: Fri, 28 Sep 2012 10:03:47 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fmri_glmfit-sim with pre-cached fails To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 5065ae43.7060...@nmr.mgh.harvard.edu mailto:5065ae43.7060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hmmm, that's a lot, but I'm very surprised that the final FWHM is over 30. How many subjects do you have? There might be one that is messed up. You can check this by loading the y.mgh as a time course in tksurfer. It will give you a graph with each subject. Finally, you can run mri_glmfit with the --pca option to get a PCA of the residuals. This will create a folder called pca-eres. Look at the stats.dat and see how much variance is explained by the first component (first row, 4th column). doug On 09/28/2012 03:31 AM, Ed Gronenschild wrote: Hi Doug, For mri_glmfit I used a cortical thickness smoothed with a FWHM of 20, resultingfrom using the -qcache option in recon-all. Ed On 27 Sep 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 16 Date: Thu, 27 Sep 2012 11:29:06 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim with pre-cached fails To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 506470c2.5060...@nmr.mgh.harvard.edu mailto:506470c2.5060...@nmr.mgh.harvard.edu mailto:506470c2.5060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking that no one would ever go above it, or maybe should never go above it. I can create tables at higher smoothing levels, but 34mm is a lot of smoothing. How much did you apply to the data? doug On 09/27/2012 05:48 AM, Ed Gronenschild wrote: Hi, I want to apply a cluster correction with mri_glmfit-sim with the --cache option: mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs It fails with the error message that it can't find the file: FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc- z.csd (FSDir is the directory where FreeSurfer is located, version 5.0.0, Mac OSX10.5) Looking at the content of the fsaverage/lh/cortex directory than indeed, only the directories fwhm01, fwhm02, ..., fwhm30 are present. In the log file from mri_glmfit I can read that the residualFWHM is 34.005014. Since this FWHM is automatically derived by mri_glmfit, does it mean that I can never use the --cache option in this case? Cheers, Ed ___ 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] cluster to annotations
I put a new version of mri_glmfit-sim which will do what you want. Use it by adding the --a2009s flag ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim doug On 10/01/2012 12:16 PM, jm wrote: Dear FS: We compared two groups using cluster-wise Montecarlo simulation. Clusters obtained are extended for more than one region of aparc.2009 atlas. How to identify automatically those regions in each cluster?May I get a file with list of aparc.2009 regions and corresponding clusters? best regards ___ 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] random effects analysis with performance values
Hi Doug, The output of the analysis is a volume with performance values in each voxel. the performance ranges between 0 to 1 and I want to see if across subjects there is any region with above chance performance (Chance is 0.5). Maryam On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote: Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. ___ 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] random effects analysis with performance values
So it is only one volume? This won't work with mri_glmfit. glmfit needs to have a value for each subject so that it can compute the variance across subjects (needed to infer whether a difference from 0 is significant). I don't know of any software that will do it. doug On 10/1/12 6:59 PM, Maryam Vaziri Pashkam wrote: Hi Doug, The output of the analysis is a volume with performance values in each voxel. the performance ranges between 0 to 1 and I want to see if across subjects there is any region with above chance performance (Chance is 0.5). Maryam On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote: Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] random effects analysis with performance values
Its one value per voxel per subject. So there is variane across subjects. and I want to see weather that value is different from 0.5 instead of 0. Maryam On Mon, Oct 1, 2012 at 8:54 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: So it is only one volume? This won't work with mri_glmfit. glmfit needs to have a value for each subject so that it can compute the variance across subjects (needed to infer whether a difference from 0 is significant). I don't know of any software that will do it. doug On 10/1/12 6:59 PM, Maryam Vaziri Pashkam wrote: Hi Doug, The output of the analysis is a volume with performance values in each voxel. the performance ranges between 0 to 1 and I want to see if across subjects there is any region with above chance performance (Chance is 0.5). Maryam On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote: Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam -- 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 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] More than two time-points in longitudinal base = Memory allocation error?
Hi Martin, Thanks for your reply. My iMac has 14 GB of RAM. However, the Mac OS version of FreeSurfer is only available as a 32-bit version, and thus any time FreeSurfer requires more than approximately 3.5 GB of memory it will exit with an error. Are there any plans yet for a 64-bit Mac OS version? I have a number of clinical participants with between 3 and 8 scans (timepoints) that I wish to analyse longitudinally. I have already run the cross-sectional reconstructions, performed the necessary pial and white matter edits and inserted control points, and re-run all the cross sectional reconstructions again to take accounts of the edits. If I cannot now create the template reconstructions in Mac OS with all of my timepoints for all of my participants, what are my options? Is it possible to run the 64-bit Linux version of FreeSurfer using VirtualBox on my iMac? Could I then just create the template reconstructions for all my participants using virtualbox linux and return to Mac OS to run the final longitudinal stream on all the participants? I am aware that there are differences in how the 64-bit linux and the 32-bit Mac OS FreeSurfers will approach the analysis, but if I confine my use of the 64-bit Linux to just the creation of the templates for both (clinical and control) groups, then any differences between the systems should not affect the between-group comparisons? I do not have access to an actual Linux system. Best regards, EA Bowman From: mreu...@nmr.mgh.harvard.edu To: ea_bow...@hotmail.com Date: Mon, 30 Jul 2012 18:00:29 -0400 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] More than two time-points in longitudinal base = Memory allocation error? Hi Liz, you need more memory (see the error message: cannot allocate memory). Best, Martin On Mon, 2012-07-23 at 10:21 +1000, Liz Bowman wrote: Hello, I have several patients scans taken over multiple time points (up to nine time points in some patients). I thought I might be able to use these to create a base template for longitudinal processing, however the process fails and exits with errors if I try to create a base with more than two time points from a patient. This is a sample of the error log of the most recent attempt, with three timepoints: Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.876663 Iteration(f): 2 -- diff. to prev. transform: 0.0148738 Iteration(f): 3 -- diff. to prev. transform: 0.00156813 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.263086 Iteration(f): 2mri_robust_template(1035) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 68th slice Cannot allocate memory Darwin 550D-UOM88670.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 recon-all -s KSx3 exited with ERRORS at Mon Jul 23 10:15:13 EST 2012 For more details, see the log file /Applications/freesurfer/subjects/KSx3/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I would be grateful for any advice. Regards, EA Bowman ___ 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.
[Freesurfer] Triangulated surfaces
Dear FreeSurfer Users, I have created a binary mask for the hippocampi and now i want to create the triangulated surfaces of the hippocampi? An one know how to do it? Thanks, Efrat ___ 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] Triangulated surfaces
mri_mc should do the trick Cheers Bruce P.s. it is a marching cubes tessellation algorithm. You could also try mri_tessellate On Oct 1, 2012, at 10:10 PM, Efrat Kliper e.kli...@gmail.com wrote: Dear FreeSurfer Users, I have created a binary mask for the hippocampi and now i want to create the triangulated surfaces of the hippocampi? An one know how to do it? Thanks, Efrat ___ 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] Lesioned brain (surface) registration to fs average
Dear all, I need to mark the cortical extent of a lesion (intersection of the lesion and pial surface, where lesion represent a epilepsy related resection). After the pial labeling of the resection, I need to register the labeled surface to the fsaverage. I completed recon-all routine on the postop T1, and went nicely, corrected pial surface in a few places. Question: what is the best way to mark the pial extent of a resection? Is there a way to accurately register the lesioned pia to the fsaverage, potentially by masking the resection ROI? Thank you for your insight, Octavian. ___ 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] mri_vol2vol
Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html When I run xhemireg I receive the error ERROR: Option --keep-precision unknown I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions? Andrew ___ 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] random effects analysis with performance values
You can subtract .5 from the volume (fscalc vol.mgh sub .5 -o vol-minus.5.mgh), then do a one-sample group mean (--osgm). You should do a permutation test to correct for multiple comparisons because the residuals definitely won't be Gaussian. doug On 10/1/12 9:11 PM, Maryam Vaziri Pashkam wrote: Its one value per voxel per subject. So there is variane across subjects. and I want to see weather that value is different from 0.5 instead of 0. Maryam On Mon, Oct 1, 2012 at 8:54 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: So it is only one volume? This won't work with mri_glmfit. glmfit needs to have a value for each subject so that it can compute the variance across subjects (needed to infer whether a difference from 0 is significant). I don't know of any software that will do it. doug On 10/1/12 6:59 PM, Maryam Vaziri Pashkam wrote: Hi Doug, The output of the analysis is a volume with performance values in each voxel. the performance ranges between 0 to 1 and I want to see if across subjects there is any region with above chance performance (Chance is 0.5). Maryam On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Maryam, I must confess ignorance on search-light analysis. Can you give me more background on what it is, the output data, and what you want mri_glmfit to tell you? doug On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote: Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] mri_vol2vol
I just put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol doug On 10/1/12 10:56 PM, Andrew Bock wrote: Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html When I run xhemireg I receive the error ERROR: Option --keep-precision unknown I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions? Andrew ___ 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] ADC map negative values
Dear FreeSurfers Users, When i am using the dt_recon function to create adc map i get quite a lot negative values, dose anyone encounter this problem? Thanks, Efrat ___ 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 mri_segstats, important
I have download the latest verion of mri_segstats from the release notes. But it does not generate asegstats. 4 x86_64 x86_64 GNU/Linux # #@# ASeg Stats Tue Oct 2 07:36:17 CEST 2012 /home/knutjb/freesurfer/20_ucsd_automatic_version2/004 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 004 ERROR: Option --sum unknown #-- recon-all -s 004 finished without error at Tue Oct 2 07:36:17 CEST 2012 done knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats USAGE: mri_label2vol Possible inputs: --label labelid --label labelid --annot annotfile : surface annotation file --seg segpath : segmentation --aparc+aseg : use aparc+aseg.mgz in subjectdir as seg --temp tempvolid : output template volume --reg regmat : VolXYZ = R*LabelXYZ --regheader volid : label template volume (needed with --label or --annot) for --seg, use the segmentation volume --identity : set R=I --invertmtx : Invert the registration matrix --fillthresh thresh : between 0 and 1 (def 0) --labvoxvol voxvol : volume of each label point (def 1mm3) --proj type start stop delta --subject subjectid : needed with --proj or --annot --hemi hemi : needed with --proj or --annot --surf surface : use surface instead of white --o volid : output volume --hits hitvolid : each frame is nhits for a label --label-stat statvol : map the label stats field into the vol --stat-thresh thresh : only use label point where stat thresh --offset k : add k to segmentation numbers (good when 0 should not be ignored) --native-vox2ras : use native vox2ras xform instead of tkregister-style --version : print version and exit --help $Id: mri_label2vol.c,v 1.39 2012/06/08 17:29:54 greve Exp $ knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats --sum ERROR: Option --sum unknown Knut J ___ 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.
