Re: [Freesurfer] tracula executables for snow leopard now online
Yes, there are no more malloc issues, thanks for the update. However I still have a question, related to the merged_avg33_mni file. It still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ? David Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki: Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that! I've now updated the snow leopard tar file, so if you download it again you should not get this error any more. As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz Let me know how it goes, a.y On Tue, 23 Aug 2011, David Coynel wrote: Hi Anastasia, Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg). David Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki: Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks! a.y On Tue, 23 Aug 2011, David Coynel wrote: Dear Anastasia, Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path : Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid. Dr. David Coynel Division of Cognitive Neuroscience University of Basel Birmannsgasse 8 4055 Basel - Switzerland david.coy...@unibas.ch tel: +41(0)612.670.240 Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki: Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out. Let us know if there are any problems, a.y ___ 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 ___ 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 ___ 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
[Freesurfer] Brain volume in FreeSurfer analysis
Hello, I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)? Thank you for reply. ___ 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] .curv
Hi, I need a sulcal map and I saw that freesurfer can generate .curv and .sulc files that have this information. It is possibile to convert these formats into a vtk one, or to join the information of a .curv file format whit a volumetric one, having a volumetric file with the infomations of a .curv file? -- Antonella ___ 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] GLM analysis - covariates
I'm examining differences in cortical thickness in a sample of drug users and non-users. From the literature, it appears that the 2 covariates I should use for the GLM analysis will be gender and age. Other researchers have examined other possible covariates (like age of first use, # past year uses, IQ, etc.) using correlations between those variables and significant clusters that differed between groups. Is this the best way to go about translating a typical regression model into the Freesurfer statistical package (especially if I'm interested in dose-dependent relationships)? Also, how do you suggest controlling for total brain volume? Other researchers have performed univariate analyses between groups on TBV controlling for age and gender, then examined mean cortical thickness, but I'm not quite sure what the steps are for this. Could someone help me identify the best way to control for TBV (i.e., is there a way to control from the first GLM analysis, or is this a possible covariate to enter in to the analysis)? Thanks! -- Jenessa S. Price, M.A. Graduate Student, Clinical Psychology and Neuropsychology University of Cincinnati Campus Representative, American Psychological Association of Graduate Students (APAGS) ___ 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] .curv
Hi Antonella you can use mri_surf2vol to sample either one into the volume and go from there. cheers Bruce On Wed, 24 Aug 2011, Antonella Cappelletti wrote: Hi, I need a sulcal map and I saw that freesurfer can generate .curv and .sulc files that have this information. It is possibile to convert these formats into a vtk one, or to join the information of a .curv file format whit a volumetric one, having a volumetric file with the infomations of a .curv file? -- Antonella ___ 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] correction for multiple comparisons
Good morning Doug, Thank you for your help. I followed your advise and unfortunately I do not understand why after adding the threshold 2 cwpvalthresh .025 in order to do the correction across lh and rh I still get in my clusters summary and clusters with cwp.01 as well as cwp .025. This is what I was running: mri_glmfit-sim \ --glmdir rh.age.glmdir \ --cache 2 neg \ --cwpvalthresh .025 \ --overwrite And this is my output: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -6.24 104279 2004.41 6.4 -83.6 34.4 0.0001 0 0 3539 cuneus 2 -5.71 56656 2923.03 24.4 25.4 37.1 0.0001 0 0 5020 superiorfrontal 3 -4.89 156133 1826.82 5.1 -29.7 38.6 0.0001 0 0 4324 posteriorcingulate 4 -4.57 117278 1917.42 43.2 43.4 -8.2 0.0001 0 0 3393 parsorbitalis 5 -4.32 134603 910.13 10.5 45.7 -9.2 0.0009 0 0 1597 medialorbitofrontal 6 -4.01 47845 1018.06 38.9 -73.9 34.6 0.0003 0 0 1802 inferiorparietal 7 -3.97 12268 580.81 14.2 -51 63.3 0.0132 0.01 0.01 1415 superiorparietal 8 -3.78 54798 871.02 53 -39.7 -5.1 0.0010 0 0 1969 bankssts 9 -3.78 21941 555.51 45.8 -28.2 6.4 0.0175 0.02 0.02 1369 superiortemporal 10 -2.91 86118 884.25 10.1 -98.9 11.7 0.0010 0 0 1089 lateraloccipital 11 -2.86 13271 674.26 21.5 -65.4 -6.1 0.0056 0 0.01 722 lingual Is this right? Please advise. Thank you. Antonella From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 23, 2011 4:33 PM Subject: Re: [Freesurfer] correction for multiple comparisons Yes, that is correct, you should use .025 if you are correcting for both hemispheres. doug Antonella Kis wrote: Hi Doug, I would like to run the correction for multiple comparisons. I know glmfit-sim corrects for multiple comparisons. My question is: the corrections for multiple comparisons will be done while running mri_glmfit-sim \ --glmdir rh.age.glmdir \ --cache 2 neg \ --overwrite or I need to add --cwpvalthresh .025 before --overwrite. I found on-line that setting a treshold = 2 means p 0.05 but adding --cwpvalthresh .025 will do the correction across 2 spaces: lh and rh: .025 = .05/2 Bonferroni Correction and will show only the clusters with p.025. Is this right? So to run for multiple corrections in fact I will need to run: mri_glmfit-sim \ --glmdir rh.age.glmdir \ --cache 2 neg \ --cwpvalthresh .025 --overwrite Please advise me. Thank you for your time and help. Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, August 22, 2011 2:28 PM *Subject:* Re: [Freesurfer] GLM or Qdec ? Antonella Kis wrote: Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get more clusters than the number of clusters obtained from mri_glmfit-sim? When you look at it in tksurfer, you are looking at uncorrected data. glmfit-sim corrects for multiple comparisons. Some of the clusters don't survive. 2). What sig.mgh represents? -log10(p) 3) What's the real significance of a cluster (how a cluster is formed)? It is based on the likelihood of getting a cluster of that size by chance given the search space (cortical surface area), smoothness (FWHM), and cluster-forming threshold (eg, p.05). 4). Why my thickness value in clusters (eg cluster no. 1 which coresponds to the posteriorcingulate) for subject no.1 is different that the thickness value obtained for the same region in the lh.aparc.stats while running recon-all? 5). After running the GLM should I use visualizing and plotting method to further analyse my data and load FSGD file lh.gender_age.glmdir/y.fsgd? 6). Should my ROI's be defined or be the same with my clusters? I don't know what you mean by that. 7). What is the difference between GLM and Qdec? What method is the best to analyse the relation between age and cortical thickness for my patients versus control group? They are the same statistically. They are just different ways to provide information about your design and contrasts. QDEC is graphical (point and click). mri_glmfit you create FSGD files and run it from the command-line. QDEC actually creates FSGD files and contrast files and runs mri_glmfit. 8). Why when analysing with Qdec I get more
Re: [Freesurfer] tracula executables for snow leopard now online
Yes, it should be a concatenation of all existing pathway reconstructions under dpath/... If you open it with trackvis --tv, you should be able to see a 3d view of all the pathways. Sometimes the default threshold might be too high for some pathways and you might need to adjust it individually in freeview to be able to see them. Does the output of dmri_mergepaths show you that it's found multiple pathways or just ccg? Yes, there are no more malloc issues, thanks for the update. However I still have aays question, related to the merged_avg33_mni file. It still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ? David Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki: Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that! I've now updated the snow leopard tar file, so if you download it again you should not get this error any more. As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz Let me know how it goes, a.y On Tue, 23 Aug 2011, David Coynel wrote: Hi Anastasia, Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg). David Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki: Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks! a.y On Tue, 23 Aug 2011, David Coynel wrote: Dear Anastasia, Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path : Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid. Dr. David Coynel Division of Cognitive Neuroscience University of Basel Birmannsgasse 8 4055 Basel - Switzerland david.coy...@unibas.ch tel: +41(0)612.670.240 Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki: Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out. Let us know if there are any problems, a.y ___ 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 ___ 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 ___ Freesurfer mailing list
Re: [Freesurfer] tracula executables for snow leopard now online
Everything looks to be running fine. Wether I look at the merged file with freeview or fslview, I still have only one tract. Here's an extract of the outputs : Input files: lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz lh.unc_AS_avg33_mni_flt/path.pd.nii.gz rh.ccg_PP_avg33_mni_flt/path.pd.nii.gz rh.unc_AS_avg33_mni_flt/path.pd.nii.gz Lower threshold for display: 0.15 Merging volume 1 of 4... Threshold: 111 Name: Left Cingulum - Cingulate Gyrus Merging volume 2 of 4... Threshold: 74.85 Name: Left Uncinate Fasciculus Merging volume 3 of 4... Threshold: 87.9 Name: Right Cingulum - Cingulate Gyrus Merging volume 4 of 4... Threshold: 57.6 Name: Right Uncinate Fasciculus Done in 0.621 sec. dmri_mergepaths done It remains the same if I take a very low threshold (0.001). David Am 24.08.2011 um 16:49 schrieb ayend...@nmr.mgh.harvard.edu: Yes, it should be a concatenation of all existing pathway reconstructions under dpath/... If you open it with trackvis --tv, you should be able to see a 3d view of all the pathways. Sometimes the default threshold might be too high for some pathways and you might need to adjust it individually in freeview to be able to see them. Does the output of dmri_mergepaths show you that it's found multiple pathways or just ccg? Yes, there are no more malloc issues, thanks for the update. However I still have aays question, related to the merged_avg33_mni file. It still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ? David Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki: Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that! I've now updated the snow leopard tar file, so if you download it again you should not get this error any more. As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz Let me know how it goes, a.y On Tue, 23 Aug 2011, David Coynel wrote: Hi Anastasia, Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg). David Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki: Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks! a.y On Tue, 23 Aug 2011, David Coynel wrote: Dear Anastasia, Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path : Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid. Dr. David Coynel Division of Cognitive Neuroscience University of Basel Birmannsgasse 8 4055 Basel - Switzerland david.coy...@unibas.ch tel: +41(0)612.670.240 Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki: Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out. Let us know if there are any problems, a.y ___ 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
Re: [Freesurfer] tracula executables for snow leopard now online
Hi David, Can you visualize these tracts individually? type in freeview -v lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz and to visualize the merged you could try freeview -tv merged_avg33_mni_flt.nii.gz If both of these do not work you can try running dmri_mergepaths seperately using the following command and see if that works for you: dmri_mergepaths --indir main input dir --in path to all the path.pd.nii.gz files --out path to outputdir/merged_avg32_mni_flt.mgz --ctab /usr/local/freesurfer/dev/FreeSurferColorLUT.txt --thresh .15 You should have a copy of this command in your log file you can copy paste that on to the terminal as well. Can you try these things to see if it solves your problem? -Priti Everything looks to be running fine. Wether I look at the merged file with freeview or fslview, I still have only one tract. Here's an extract of the outputs : Input files: lh.ccg_PP_avg33_mni_flt/path.pd.nii.gz lh.unc_AS_avg33_mni_flt/path.pd.nii.gz rh.ccg_PP_avg33_mni_flt/path.pd.nii.gz rh.unc_AS_avg33_mni_flt/path.pd.nii.gz Lower threshold for display: 0.15 Merging volume 1 of 4... Threshold: 111 Name: Left Cingulum - Cingulate Gyrus Merging volume 2 of 4... Threshold: 74.85 Name: Left Uncinate Fasciculus Merging volume 3 of 4... Threshold: 87.9 Name: Right Cingulum - Cingulate Gyrus Merging volume 4 of 4... Threshold: 57.6 Name: Right Uncinate Fasciculus Done in 0.621 sec. dmri_mergepaths done It remains the same if I take a very low threshold (0.001). David Am 24.08.2011 um 16:49 schrieb ayend...@nmr.mgh.harvard.edu: Yes, it should be a concatenation of all existing pathway reconstructions under dpath/... If you open it with trackvis --tv, you should be able to see a 3d view of all the pathways. Sometimes the default threshold might be too high for some pathways and you might need to adjust it individually in freeview to be able to see them. Does the output of dmri_mergepaths show you that it's found multiple pathways or just ccg? Yes, there are no more malloc issues, thanks for the update. However I still have aays question, related to the merged_avg33_mni file. It still only contains the first path that was passed as an input to dmri_mergepaths. If I understand correctly I should see all generated paths, thresholded and merged into this file ? David Am 23.08.2011 um 21:28 schrieb Anastasia Yendiki: Hi David - Thanks for catching this. There was something wrong with the new snow leopard build of dmri_mergepaths. (The original from the 5.1 distribution didn't have this problem). Sorry about that! I've now updated the snow leopard tar file, so if you download it again you should not get this error any more. As before it's here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz Let me know how it goes, a.y On Tue, 23 Aug 2011, David Coynel wrote: Hi Anastasia, Thanks for your answer. Unfortunately I overwrote the executables (I could still retrieve them from the website distribution ?). Interestingly this message does not show up when selecting only a subset of the pathways, as for example ( lh.ccg rh.ccg lh.unc rh.unc ), however the merged_avg33_mni file only appears to contain the first pathway (lh.ccg). David Am 23.08.2011 um 17:06 schrieb Anastasia Yendiki: Hi David - Glad to hear things are working! I can look into dmri_mergepaths and see if something is wrong with the snow leopard build. Have you by any chance kept the original leopard build of it? If you haven't overwritten it, it'd be useful to run the same thing with that version and see if it works. Thanks! a.y On Tue, 23 Aug 2011, David Coynel wrote: Dear Anastasia, Thanks a lot for the upload. The procedure now runs perfectly, except for that last message at the end of trac-all -path : Merging volume 18 of 18... Threshold: 68.1 Name: Right Uncinate Fasciculus dmri_mergepaths(26008) malloc: *** mmap(size=18446744073709543424) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Done in 2.433 sec. dmri_mergepaths done #- trac-paths finished without error at Do 18 Aug 2011 11:39:42 CEST This however does not seem to affect the pipeline, as all the expected outputs seem to be present and valid. Dr. David Coynel Division of Cognitive Neuroscience University of Basel Birmannsgasse 8 4055 Basel - Switzerland david.coy...@unibas.ch tel: +41(0)612.670.240 Am 17.08.2011 um 23:44 schrieb Anastasia Yendiki: Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into
Re: [Freesurfer] Brain volume in FreeSurfer analysis
A side note: If you are using FS 4.5.0 or earlier, there is also BrainSegVolNotVent, which discount ventricles. If you want to capture effects of aging or atrophy, perhaps this could be more sensitive than BrainSegVol. On 24/08/11 12:32, Anderson Winkler wrote: Hi Zuzana, Yes, you can use BrainSegVol as a measurement of brain volume (I'd assume you are using FS =4.5.0). Note that there is another measurement that you might be interested in, the IntraCranialVol. These measurements tell different things and not necessarily correlate well one with another depending on the sample. BSV considers the voxels labelled as GM and WM, including subcortical structures and cerebellum and so, it correlates better with amount of GM and WM and tends to be more sensitive to pathology, atrophy and aging. ICV is more robust to these effects. You may want to choose the one that is more appropriate to your study. Also, if you are considering brain volume as a covariate for cortical thickness, it's not necessary. Thickness correlates poorly with brain volume, and these two things are not correlated genetically. Hope this helps! All the best, Anderson On 24/08/11 05:39, zuzana nedelska wrote: Hello, I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)? Thank you for reply. ___ 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 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] Brain volume in FreeSurfer analysis
Hi Anderson: Your explanation is very well put. I have a question. Suppose one is looking at High Risk datasets (for example Schizophrenia) where the brain morphological alterations are subtle but spread across the brain, which covariate would you use? thanks, Alan [Beth Israel Deaconess Medical Center] On Wed, Aug 24, 2011 at 12:43 PM, Anderson Winkler andersonwink...@hotmail.com wrote: ** A side note: If you are using FS 4.5.0 or earlier, there is also BrainSegVolNotVent, which discount ventricles. If you want to capture effects of aging or atrophy, perhaps this could be more sensitive than BrainSegVol. On 24/08/11 12:32, Anderson Winkler wrote: Hi Zuzana, Yes, you can use BrainSegVol as a measurement of brain volume (I'd assume you are using FS =4.5.0). Note that there is another measurement that you might be interested in, the IntraCranialVol. These measurements tell different things and not necessarily correlate well one with another depending on the sample. BSV considers the voxels labelled as GM and WM, including subcortical structures and cerebellum and so, it correlates better with amount of GM and WM and tends to be more sensitive to pathology, atrophy and aging. ICV is more robust to these effects. You may want to choose the one that is more appropriate to your study. Also, if you are considering brain volume as a covariate for cortical thickness, it's not necessary. Thickness correlates poorly with brain volume, and these two things are not correlated genetically. Hope this helps! All the best, Anderson On 24/08/11 05:39, zuzana nedelska wrote: Hello, I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)? Thank you for reply. ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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 listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Brain volume in FreeSurfer analysis
Hi Alan, I'd say it depends on what the study is about, but in principle, I'd think that the covariates should remove what would have potential to be confounding more what the main effect would be. In the example of schizophrenia, I'd choose BrainSegVolNotVent, and run both models, with and without it, and interpret the results combined. Also, unless if the samples are too small or unless one wants to explicitly test the effect of ICV and/or BV, I don't see any problem in including both ICV and BV in the model, even considering they are well correlated to some extent. The shared variance between them interferes on the beta-estimates for them, but not on the betas for the other regressors that you would be testing, and the part of the variance that is not shared between them will absorb the effects for which they were chosen to be covaryied out. This is my opinion. Others may think differently. All the best! Anderson On 24/08/11 12:51, Alan Francis wrote: Hi Anderson: Your explanation is very well put. I have a question. Suppose one is looking at High Risk datasets (for example Schizophrenia) where the brain morphological alterations are subtle but spread across the brain, which covariate would you use? thanks, Alan [Beth Israel Deaconess Medical Center] On Wed, Aug 24, 2011 at 12:43 PM, Anderson Winkler andersonwink...@hotmail.com mailto:andersonwink...@hotmail.com wrote: A side note: If you are using FS 4.5.0 or earlier, there is also BrainSegVolNotVent, which discount ventricles. If you want to capture effects of aging or atrophy, perhaps this could be more sensitive than BrainSegVol. On 24/08/11 12:32, Anderson Winkler wrote: Hi Zuzana, Yes, you can use BrainSegVol as a measurement of brain volume (I'd assume you are using FS =4.5.0). Note that there is another measurement that you might be interested in, the IntraCranialVol. These measurements tell different things and not necessarily correlate well one with another depending on the sample. BSV considers the voxels labelled as GM and WM, including subcortical structures and cerebellum and so, it correlates better with amount of GM and WM and tends to be more sensitive to pathology, atrophy and aging. ICV is more robust to these effects. You may want to choose the one that is more appropriate to your study. Also, if you are considering brain volume as a covariate for cortical thickness, it's not necessary. Thickness correlates poorly with brain volume, and these two things are not correlated genetically. Hope this helps! All the best, Anderson On 24/08/11 05:39, zuzana nedelska wrote: Hello, I have a question about calculating brain volume (in mm3) when performing recon-all. Do I take brainseg volume in the analysis stream line as subject's brain volume (in mm3)? Thank you for reply. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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] .curv
Hi Antonella, .sulc and .curv are not surfaces, they are scalar fields over the surface stored in what we informally call curvature format. Try --surval and --fillribbon and see if that gives you what you want. cheers Bruce On Wed, 24 Aug 2011, Antonella Cappelletti wrote: Thank you Bruce.I have some other questions. I tried to look at the mri_surf2vol --help to undersand how to use it. I tried with this command: mri_surf2vol --surf curv --hemi lh --template orig.mgz --outvol curv-orig.mgz but there is something wrong with it. I'm using the bert folder as example. I don't understand how I have to set the input ( lh.curv) and the output ( volume file .mgz) Antonella 2011/8/24 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Antonella you can use mri_surf2vol to sample either one into the volume and go from there. cheers Bruce On Wed, 24 Aug 2011, Antonella Cappelletti wrote: Hi, I need a sulcal map and I saw that freesurfer can generate .curv and .sulc files that have this information. It is possibile to convert these formats into a vtk one, or to join the information of a .curv file format whit a volumetric one, having a volumetric file with the infomations of a .curv file? -- Antonella 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. -- Antonella ___ 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] Procedure to get amygdalar sub-regions and brainstem Brainstem consituents volumes
Hi Wil sorry, we don't have anything for that yet, although we are actively working on it. cheers Bruce On Wed, 24 Aug 2011, Irwin, William wrote: Hello- In the FreeSurferColorLUT.txt,v 1.70.2.1 2011/05/02 file, there are labels for sub-regions of interest. For example amygdala and brainstem. How does one go about extracting the volumes for these regions? Thank you in advance, Wil #No. Label Name: R G B A 7001 Lateral-nucleus 72 132 181 0 7002 Basolateral-nucleus 243 243 243 0 7003 Basal-nucleus 207 63 79 0 7004 Centromedial-nucleus 121 20 135 0 7005 Central-nucleus 197 60 248 0 7006 Medial-nucleus 2 149 2 0 7007 Cortical-nucleus 221 249 166 0 7008 Accessory-Basal-nucleus 232 146 35 0 7009 Corticoamygdaloid-transitio 20 60 120 0 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 7011 Fusion-amygdala-HP-FAH 122 187 222 0 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 7013 Endopiriform-nucleus 10 49 255 0 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 7015 Paralaminar-nucleus 45 205 165 0 7016 Intercalated-nucleus 117 160 175 0 7017 Prepiriform-cortex 221 217 21 0 7018 Periamygdaloid-cortex 20 60 120 0 7019 Envelope-Amygdala 141 21 100 0 7020 Extranuclear-Amydala 225 140 141 0 # Label names and colors for Brainstem consituents # No. Label Name: R G B A 170 brainstem 119 159 176 0 171 DCG 119 0 176 0 172 Vermis 119 100 176 0 173 Midbrain 119 200 176 0 174 Pons 119 159 100 0 175 Medulla 119 159 200 0 ___ 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] Procedure to get amygdalar sub-regions and brainstem Brainstem consituents volumes
Thanks, Bruce. That was my assumption, but I thought it was worthwhile asking. Related, for the hippocampal subfield segmentation, I understand the voxel values are the probabilities of belonging to a given subfield. Is there way to extract a list of voxels with their values for each region? I realize this would generate a very long stream of data. But then one could post-hoc adjust the number of voxels per region by setting some criteria (e.g., the probability of belonging to the fornix has to be 95%). Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Wednesday, August 24, 2011 12:28 PM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] Procedure to get amygdalar sub-regions and |brainstem Brainstem consituents volumes | |Hi Wil | |sorry, we don't have anything for that yet, although we are actively working |on it. | |cheers |Bruce |On Wed, 24 Aug 2011, Irwin, William wrote: | | | Hello- | | | | In the FreeSurferColorLUT.txt,v 1.70.2.1 2011/05/02 file, there are labels for |sub-regions of interest. For example amygdala and brainstem. | | | | How does one go about extracting the volumes for these regions? | | | | Thank you in advance, | | Wil | | | | | | #No. Label Name: R G B A | | 7001 Lateral-nucleus 72 132 181 0 | | 7002 Basolateral-nucleus 243 243 243 0 | | 7003 Basal-nucleus 207 63 79 0 | | 7004 Centromedial-nucleus 121 20 135 0 | | 7005 Central-nucleus 197 60 248 0 | | 7006 Medial-nucleus 2 149 2 0 | | 7007 Cortical-nucleus 221 249 166 0 | | 7008 Accessory-Basal-nucleus 232 146 35 0 | | 7009 Corticoamygdaloid-transitio 20 60 120 0 | | 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 | | 7011 Fusion-amygdala-HP-FAH 122 187 222 0 | | 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 | | 7013 Endopiriform-nucleus 10 49 255 0 | | 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 | | 7015 Paralaminar-nucleus 45 205 165 0 | | 7016 Intercalated-nucleus 117 160 175 0 | | 7017 Prepiriform-cortex 221 217 21 0 | | 7018 Periamygdaloid-cortex 20 60 120 0 | | 7019 Envelope-Amygdala 141 21 100 0 | | 7020 Extranuclear-Amydala 225 140 141 0 | | | | | | # Label names and colors for Brainstem consituents | | # No. Label Name: R G B A | | 170 brainstem 119 159 176 0 | | 171 DCG 119 0 176 0 | | 172 Vermis 119 100 176 0 | | 173 Midbrain 119 200 176 0 | | 174 Pons 119 159 100 0 | | 175 Medulla 119 159 200 0 | | | | | |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] pial surfaces totally off
Hello, I've tried a number of ways to generate pial surfaces for a monkey brain that has, to my eyes, very clear contrast. The white matter is segmented without too much pain and is mostly correct, but the pial surface never completely covers the gray matter. Instead, it either attaches to the white matter surface or meets the pial surface half way. I've tried more non-uniformity correction, and even painting in the gray matter more uniformly so that it could not possibly miss it, yet it does. Are there some secret parameters (i.e., low, hi gray values, etc. ) that one can play with it? Any guidance would be much appreciated. Cheers, Reza ___ 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] Cortical Flattening
Dear Doug, Tank you for your response. The freesurfer wikipage I was following: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch Do I have to do some additional steps? Thank you in advance, Regards, Chantal ___ 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] Cortical Flattening
Hi Chantal, what went wrong? Sorry, I've lost this thread. cheers Bruce On Wed, 24 Aug 2011, Tax, C.M.W. wrote: Dear Doug, Tank you for your response. The freesurfer wikipage I was following: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch Do I have to do some additional steps? Thank you in advance, Regards, Chantal ___ 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] Cortical Flattening
Louis just pointed out to me what the thread was about. What operating system are you running on? This seems to be a problem in the depths of openGL on ubuntu. We haven't seen it on CentOS or red hat. Bruce On Wed, 24 Aug 2011, Bruce Fischl wrote: Hi Chantal, what went wrong? Sorry, I've lost this thread. cheers Bruce On Wed, 24 Aug 2011, Tax, C.M.W. wrote: Dear Doug, Tank you for your response. The freesurfer wikipage I was following: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch Do I have to do some additional steps? Thank you in advance, Regards, Chantal ___ 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 ___ 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] Procedure to get amygdalar sub-regions and brainstem Brainstem consituents volumes
Hi Wil Koen will have to answer that one for you Bruce On Wed, 24 Aug 2011, Irwin, William wrote: Thanks, Bruce. That was my assumption, but I thought it was worthwhile asking. Related, for the hippocampal subfield segmentation, I understand the voxel values are the probabilities of belonging to a given subfield. Is there way to extract a list of voxels with their values for each region? I realize this would generate a very long stream of data. But then one could post-hoc adjust the number of voxels per region by setting some criteria (e.g., the probability of belonging to the fornix has to be 95%). Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Wednesday, August 24, 2011 12:28 PM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] Procedure to get amygdalar sub-regions and |brainstem Brainstem consituents volumes | |Hi Wil | |sorry, we don't have anything for that yet, although we are actively working |on it. | |cheers |Bruce |On Wed, 24 Aug 2011, Irwin, William wrote: | | | Hello- | | | | In the FreeSurferColorLUT.txt,v 1.70.2.1 2011/05/02 file, there are labels for |sub-regions of interest. For example amygdala and brainstem. | | | | How does one go about extracting the volumes for these regions? | | | | Thank you in advance, | | Wil | | | | | | #No. Label Name: R G B A | | 7001 Lateral-nucleus 72 132 181 0 | | 7002 Basolateral-nucleus 243 243 243 0 | | 7003 Basal-nucleus 207 63 79 0 | | 7004 Centromedial-nucleus 121 20 135 0 | | 7005 Central-nucleus 197 60 248 0 | | 7006 Medial-nucleus 2 149 2 0 | | 7007 Cortical-nucleus 221 249 166 0 | | 7008 Accessory-Basal-nucleus 232 146 35 0 | | 7009 Corticoamygdaloid-transitio 20 60 120 0 | | 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 | | 7011 Fusion-amygdala-HP-FAH 122 187 222 0 | | 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 | | 7013 Endopiriform-nucleus 10 49 255 0 | | 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 | | 7015 Paralaminar-nucleus 45 205 165 0 | | 7016 Intercalated-nucleus 117 160 175 0 | | 7017 Prepiriform-cortex 221 217 21 0 | | 7018 Periamygdaloid-cortex 20 60 120 0 | | 7019 Envelope-Amygdala 141 21 100 0 | | 7020 Extranuclear-Amydala 225 140 141 0 | | | | | | # Label names and colors for Brainstem consituents | | # No. Label Name: R G B A | | 170 brainstem 119 159 176 0 | | 171 DCG 119 0 176 0 | | 172 Vermis 119 100 176 0 | | 173 Midbrain 119 200 176 0 | | 174 Pons 119 159 100 0 | | 175 Medulla 119 159 200 0 | | | | | |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] two questions regarding qdec and conjunction analysis is FS
See inline responses.On Wed, Aug 24, 2011 at 7:35 AM, Tetiana Dadakova tetian...@gmail.com wrote: Dear FS experts, I have two questions: 1. In qdec.table.dat file I am specifying several continuous factors, e.g factor1 and factor2. For some subjects factor2 is missing, therefore I leave empty space in those cells. When I load a qdec.table.dat into qdec, the whole line of the subject with missing factor2 is omitted. I was wondering if I can make some input into the empty cell, so that qdec recognizes that for this subject the value is missing only for factor2, and the value for factor1 is present. I'm not sure about Freesurfer, but in all my work with neuroimaging data across platforms, missing data in X requires that the subject to be excluded. The reason is the Y=X1*B+X2*B. Since you don't know X2, you can't find predicted Y and thus you can't find the error associated with that subject. Programs that all allow you to keep the subject often impute the value of the missing data to get the full X matrix or do not use the General Linear Model to find the solution. The GLM approach inverts the X matrix and you can't invert a matrix with an empty cell, as far as I know. 2. Is it possible to do conjunction analysis in FreeSurfer, I mean looking at common differences in two groups as compared to the third group? When I do conjunctions, I use a logical AND. There are other ways, but there are statistical issues. The logical AND will show where group A group C and where group B group C. To do this, I load the thresholded surfaces into matlab, make them both binary, multiply one of them by 2, then add the two datasets together. Then write the data back out to the surface. The new values will be 0 for no difference in either group, 1 or 2 for a difference in one of the group comparison, 3 where both groups are different from the third. Thank you for your time and help, Tanja. ___ 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. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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] Intensity normalization parameters to fix dura included in pial surface
Hello freesurfers, Dura is being included in the pial surface of the superior section of the brain in about 80% of the subjects (about 200) that I'm processing in fs version 5.1 on Mac OS X 10.6.8. The T1s were acquired on a GE 3T scanner. It takes too much time to manually edit the dura and I would not like to do so much manual intervention on the other 2 time points. Adjusting the watershed parameters and the -gcut flag did not help. Would I be able to adjust nu_correct or mri_normalize (the intensity normalization steps prior to skull stripping)? I'm also thinking of using another intensity correction software (i.e. unicorr) to put back into the freesurfer pipeline but I would prefer a flag or parameter I can adjust within fs. Any suggestions would be appreciated! Best, Martina ___ 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] Intensity normalization parameters to fix dura included in pial surface
Hi Martina Can you send us one example dataset? Bruce On Aug 24, 2011, at 10:52 PM, Martina Ly ly.mart...@gmail.com wrote: Hello freesurfers, Dura is being included in the pial surface of the superior section of the brain in about 80% of the subjects (about 200) that I'm processing in fs version 5.1 on Mac OS X 10.6.8. The T1s were acquired on a GE 3T scanner. It takes too much time to manually edit the dura and I would not like to do so much manual intervention on the other 2 time points. Adjusting the watershed parameters and the -gcut flag did not help. Would I be able to adjust nu_correct or mri_normalize (the intensity normalization steps prior to skull stripping)? I'm also thinking of using another intensity correction software (i.e. unicorr) to put back into the freesurfer pipeline but I would prefer a flag or parameter I can adjust within fs. Any suggestions would be appreciated! Best, Martina ___ 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.
