[Freesurfer] correlation coefficient
Dear FS experts, I try to look at correlation between thickness and performance. I run mri_glmfit (using performance as covariate) and mri_glmfit-sim. After this I get some significant clusters. I would like to ask if I could get a correlation coefficient for these clusters, or/and a regression plot? Thank you, 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.
Re: [Freesurfer] wm edits
Hi Louis, thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces. Best wishes, Tanja. On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis On Tue, 27 Mar 2012, Tetiana Dadakova wrote: Dear FS list, After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces? Thank you, Tanja. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wm edits
Hello Bruce. Thank you for your reply. I am not sure why the wm is too dark. Our population is very stressed (burnout) people vs controls, scanner GE Discovery MR750 3.0T, coil 8ch, we use BRAVO sequence with 1x1x1mm voxels. Compared to the dataset I worked with before (from 1.5T scanner), here wm is omitted much more often (and often control points do not work), but also sometimes some brighter portions of gm are included as wm. I think the problems can be caused by higher field inhomogeniety with higher static magnetic field, but I am not sure. Tanja. On Wed, Mar 28, 2012 at 3:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja why is the wm too dark? Can you tell us something about your data (population, coil, scanner, etc...)? cheers Bruce On Wed, 28 Mar 2012, Tetiana Dadakova wrote: Hi Louis, thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces. Best wishes, Tanja. On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis On Tue, 27 Mar 2012, Tetiana Dadakova wrote: Dear FS list, After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces? Thank you, Tanja. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wm edits
Do you think 32ch coil would be better? We also have data with the same scanner and same sequence, but 32ch coil. Although, visually, 32ch data is much more inhomogenious, especially in occipital part (it is too bright). We were afraid that wm there would be hard to distinguish from gm and that therefore the thickness would be too underestimated, that is why we decided to use 8ch data. Tanja. On Wed, Mar 28, 2012 at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: it may also be the 8 channel coil, which can make things hard, particularly near the vertex. Dielectric effects are usually still pretty modest at 3T although they are visible. I think control points would be your best bet. cheers Bruce On Wed, 28 Mar 2012, Tetiana Dadakova wrote: Hello Bruce. Thank you for your reply. I am not sure why the wm is too dark. Our population is very stressed (burnout) people vs controls, scanner GE Discovery MR750 3.0T, coil 8ch, we use BRAVO sequence with 1x1x1mm voxels. Compared to the dataset I worked with before (from 1.5T scanner), here wm is omitted much more often (and often control points do not work), but also sometimes some brighter portions of gm are included as wm. I think the problems can be caused by higher field inhomogeniety with higher static magnetic field, but I am not sure. Tanja. On Wed, Mar 28, 2012 at 3:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja why is the wm too dark? Can you tell us something about your data (population, coil, scanner, etc...)? cheers Bruce On Wed, 28 Mar 2012, Tetiana Dadakova wrote: Hi Louis, thank you very much for your reply. The problem with our data is that wm is too dark sometimes to use control points (intensity is too inhomogenious in some parts). That's why we would like to have the opportunity to just draw the wm where needed. But for some reason it doesn't correct the surfaces. Best wishes, Tanja. On Tue, Mar 27, 2012 at 4:23 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Tanja, I would recommend you try using some control points. Place one or two just inside the wm surface near that wm finger which is not being included, and then possibly one or two control points carefully placed along the wm finger on voxels with the highest intensity (in the middle it looks like). Not sure what the other coronal slices look like, but you may want to do something similar on other slices. -Louis On Tue, 27 Mar 2012, Tetiana Dadakova wrote: Dear FS list, After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces? Thank you, Tanja. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS 5.1 control points problem
Thank you, Sita, for your reply. 1. The skull strip was good, the cortex disappeared after we added cp. I removed control points and put new ones that are surely in wm, now re-running. 2. I have one more question: I did previous analysis with FS5.0 on 1.5T data with non-isotropic voxels. Now for FS5.1 we use 3T images with 1x1x1mm voxels. For previous analysis the error, when a part of occipital cortex is excluded, appeared in around 1 per 40 cases. Now with better data and newer version we have this problem in around 1 per 5 cases. The only idea I can think of is increased inhomogeniety in field due to increased static field of scanner. Can it be true? Can you suggest other possible reasons? Thank you, Tanja. On Wed, Mar 7, 2012 at 4:29 PM, Sita Kakunoori s...@nmr.mgh.harvard.edu wrote: Hi Tanja, Sorry if I missed something but was the cortex stripped off even before you made any edits. If so, it's probably skull strip error. Please refer to this wiki for instructions to correct the error. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix But if part of the brain is missing only after you added control points and ran -autorecon2-cp -autorecon3, then please check if any of the control points were placed in GM or really close to GM. Sita. On Wed, 7 Mar 2012, Tetiana Dadakova wrote: Dear FS list, We started using FS 5.1 and encountered a problem with control points. After first recon-all some of the cortex (in occipital part) was missing, so we added control points and re-ran -autorecon2-cp -atorecon3. After that, the part of the brain with control points was removed from brainmask.mgz (Fig1). I never had this problem in 5.0, therefore I assume that something has been changed in 5.1 regarding cp. Could you please suggest what can be the problem and if it is described somewhere? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Number of entries error in trac-all
Hi Fidel, The bvecs/bvals files should have 3/1 columns respectively (as opposed to 3/1 rows that yours have). Could you try if transposing the entries in your files help? Tanja. On Fri, Feb 17, 2012 at 12:29 PM, Fidel falf...@hggm.es wrote: Dear all, I have tried to execute trac-all and I have found this error in the process (From the log): dtifit -k /X/subjects//S1/dmri/dwi.nii.gz -m /X/subjects//S1/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /X/subjects//S1/dmri/bvecs -b /X//S1/dmri/bvals -o /X/subjects//S1/dmri/dtifit Error: data and bvals/bvecs do not contain the same number of entries I have seen in the mailing list that it has happened before, but I have not found the solution. You can find the bvals and bvecs files attached. As far as I can see, they have the same number of rows, so... What is the problem? Thanks and best regards, Fidel. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA bvecs question
Sorry for bothering you again, I have another error now: Error: bvecs and bvals don't have the same number of entries. Visually my bval/bvec files seem ok to me. I can't find the problem. I attach the files, could you please take a look on them? Thank you very much, Tanja. On Tue, Feb 14, 2012 at 7:31 PM, Tetiana Dadakova tetian...@gmail.com wrote: I see, thank you :) On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: PS: The info on what you need to set it here: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 10 On Tue, 14 Feb 2012, Tetiana Dadakova wrote: Dear Priti, Anastasia, Thank you for your help, I created bvec and bval files and it went fine. But now I have another error in preprocessing step. I attach a log file. Could you please take a look at that? Thank you, Tanja. trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs was created at all? It looks like that may not have been created and that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and bvecs information is not encoded in the dicom header, then you can specify it explicitly in the dmrirc file. Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, Priti Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem? Hope this is helpful, Priti Thank you Priti and Anastasia, Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding. I attach my configuration file and the command I use is trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc . I also attach a picture of my file tree and a track-all.log file. Thank you for your time and help, Tanja. On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y On Thu, 2 Feb 2012, Tetiana Dadakova wrote: Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, 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. bval Description: Binary data bvec Description: Binary data ___ 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
Re: [Freesurfer] TRACULA bvecs question
Dear Priti, Anastasia, Thank you for your help, I created bvec and bval files and it went fine. But now I have another error in preprocessing step. I attach a log file. Could you please take a look at that? Thank you, Tanja. trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs was created at all? It looks like that may not have been created and that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and bvecs information is not encoded in the dicom header, then you can specify it explicitly in the dmrirc file. Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, Priti Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem? Hope this is helpful, Priti Thank you Priti and Anastasia, Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding. I attach my configuration file and the command I use is trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc . I also attach a picture of my file tree and a track-all.log file. Thank you for your time and help, Tanja. On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y On Thu, 2 Feb 2012, Tetiana Dadakova wrote: Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, 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. trac-all.log Description: Binary data ___ 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] TRACULA bvecs question
I see, thank you :) On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: PS: The info on what you need to set it here: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 10 On Tue, 14 Feb 2012, Tetiana Dadakova wrote: Dear Priti, Anastasia, Thank you for your help, I created bvec and bval files and it went fine. But now I have another error in preprocessing step. I attach a log file. Could you please take a look at that? Thank you, Tanja. trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs was created at all? It looks like that may not have been created and that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and bvecs information is not encoded in the dicom header, then you can specify it explicitly in the dmrirc file. Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, Priti Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem? Hope this is helpful, Priti Thank you Priti and Anastasia, Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding. I attach my configuration file and the command I use is trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc . I also attach a picture of my file tree and a track-all.log file. Thank you for your time and help, Tanja. On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y On Thu, 2 Feb 2012, Tetiana Dadakova wrote: Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA bvecs question
Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem? Hope this is helpful, Priti Thank you Priti and Anastasia, Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding. I attach my configuration file and the command I use is trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc . I also attach a picture of my file tree and a track-all.log file. Thank you for your time and help, Tanja. On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y On Thu, 2 Feb 2012, Tetiana Dadakova wrote: Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, 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. trac-all.log Description: Binary data ___ 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] problem with visualizing hippo-subfields
Dear FreeSurfer list, I ran recon-all -bert -hippo-subfields, which finished without error. Now I try to open it with freeview using: cd $SUBJECTS_DIR/bert/mri freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt But get the following error: Failed to load posterior_left_CA1.mgz. (posterior_left_CA1.mgz exists in bert/mri) Do you have an idea why it goes wrong? Thank you, 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.
Re: [Freesurfer] running recon-all after editing aseg.mgz
Hi Maria, Yes, you are editing aseg.mgz. After saving the segmentation, you should run recon-all -s subject_name -autorecon2 -autorecon3. If you also added some control points, then you should run recon-all -s subject_name -autorecon2-cp -autorecon3 Best wishes, Tanja. On Fri, Nov 25, 2011 at 10:40 PM, Maria Jalbrzikowski mjalbrzikow...@gmail.com wrote: Hi, I am a relatively new user of Freesurfer and have a couple questions. I have gone through the tutorials and I am now at the point where I check the segmentation. If I open my subject in tkemdit (tkmedit your_subject_name brainmask.mgz -surfs -aseg) and use the edit the segmentation and then press save segmentation, I am editing the aseg.mgz file, correct? After doing that, what parts of recon-all would I need to run again? Thanks, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ 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] control points didn't work
Dear FreeSurfer list, I was trying to edit wm surface by adding control points. After saving them and re-running recon-all -autorecon2-cp -autorecon3, the control points are still there, but wm is not edited (although cp worked in other places for the same brain). The intensity there is around 95-98 depending on slice. Could you please suggest what could go wrong? Thank you, 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.
[Freesurfer] pial area surface - correcting for size of brain
Dear FreeSurfer experts, I have a question regarding pial area analysis. What is commonly used as a nuisance variable to correct for brain size difference between groups (e.g men vs women)? Can you suggest any article where this is discussed or has been done? Thank you, 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.
Re: [Freesurfer] pial area surface - correcting for size of brain
Thank you Michael, I was wondering about a nuisance specific to area analysis. I understand using ICV or brain volume in volumetric analysis, but for area analysis something like overall pial area seems more logical to me. That is why I am curious if there is any literature about area (surface) analysis in particular. Am I at the right track at all? Best wishes, Tanja. On Wed, Nov 2, 2011 at 2:15 PM, Michael Harms mha...@conte.wustl.edu wrote: Typically one uses either a measure of brain volume or an estimate of intracranial volume -- the choice depends on whether or not you want to control for whole brain atrophy when making your interpretations, in which case you would use brain volume rather than ICV. There have been numerous posts to the list on this issue, so try searching the archives. As for articles, you could start with the ones below. cheers, -MH 1: Mathalon DH, Sullivan EV, Rawles JM, Pfefferbaum A. Correction for head size in brain-imaging measurements. Psychiatry Res. 1993 Jun;50(2):121-39. Erratum in: Psychiatry Res 1994 Sep;55(3):179. PubMed PMID: 8378488. 2: Arndt S, Cohen G, Alliger RJ, Swayze VW 2nd, Andreasen NC. Problems with ratio and proportion measures of imaged cerebral structures. Psychiatry Res. 1991 May;40(1):79-89. PubMed PMID: 1946842. 3: O'Brien LM, Ziegler DA, Deutsch CK, Kennedy DN, Goldstein JM, Seidman LJ, Hodge S, Makris N, Caviness V, Frazier JA, Herbert MR. Adjustment for whole brain and cranial size in volumetric brain studies: a review of common adjustment factors and statistical methods. Harv Rev Psychiatry. 2006 May-Jun;14(3):141-51. Review. PubMed PMID: 16787886. 4: O'Brien LM, Ziegler DA, Deutsch CK, Frazier JA, Herbert MR, Locascio JJ. Statistical adjustments for brain size in volumetric neuroimaging studies: some practical implications in methods. Psychiatry Res. 2011 Aug 30;193(2):113-22. PubMed PMID: 21684724. 5: Sanfilipo MP, Benedict RH, Zivadinov R, Bakshi R. Correction for intracranial volume in analysis of whole brain atrophy in multiple sclerosis: the proportion vs. residual method. Neuroimage. 2004 Aug;22(4):1732-43. PubMed PMID: 15275929. On Wed, 2011-11-02 at 12:26 +0100, Tetiana Dadakova wrote: Dear FreeSurfer experts, I have a question regarding pial area analysis. What is commonly used as a nuisance variable to correct for brain size difference between groups (e.g men vs women)? Can you suggest any article where this is discussed or has been done? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] pial area surface - correcting for size of brain
Thank you very much Michael for an extensive answer. I am doing analysis in QDEC, thank you for pointing that, I will check the list. On Wed, Nov 2, 2011 at 2:52 PM, Michael Harms mha...@conte.wustl.edu wrote: Oops -- I missed that aspect of your question. Yes, that would make sense, and is precisely what we did in a 2010 paper in Brit J Psychiatry (196:150-7). Although the measures in that paper were not FS-based, we used appropriate global volume, area, and thickness measures to covary for each respective type of measure (see paper for details). As an aside, are you analyzing the area of parcellated regions, or are you doing a vertex-wise area analysis in QDEC. If the latter, you should be aware that there are issues as to whether the vertex-wise area values are a meaningful, interpretable measure since the area of any given triangle of the mesh is more reflective of the mesh tesselation than an intrinsic property of that subject's brain (see previous posts regarding that as well). cheers, -MH On Wed, 2011-11-02 at 14:39 +0100, Tetiana Dadakova wrote: Thank you Michael, I was wondering about a nuisance specific to area analysis. I understand using ICV or brain volume in volumetric analysis, but for area analysis something like overall pial area seems more logical to me. That is why I am curious if there is any literature about area (surface) analysis in particular. Am I at the right track at all? Best wishes, Tanja. On Wed, Nov 2, 2011 at 2:15 PM, Michael Harms mha...@conte.wustl.edu wrote: Typically one uses either a measure of brain volume or an estimate of intracranial volume -- the choice depends on whether or not you want to control for whole brain atrophy when making your interpretations, in which case you would use brain volume rather than ICV. There have been numerous posts to the list on this issue, so try searching the archives. As for articles, you could start with the ones below. cheers, -MH 1: Mathalon DH, Sullivan EV, Rawles JM, Pfefferbaum A. Correction for head size in brain-imaging measurements. Psychiatry Res. 1993 Jun;50(2):121-39. Erratum in: Psychiatry Res 1994 Sep;55(3):179. PubMed PMID: 8378488. 2: Arndt S, Cohen G, Alliger RJ, Swayze VW 2nd, Andreasen NC. Problems with ratio and proportion measures of imaged cerebral structures. Psychiatry Res. 1991 May;40(1):79-89. PubMed PMID: 1946842. 3: O'Brien LM, Ziegler DA, Deutsch CK, Kennedy DN, Goldstein JM, Seidman LJ, Hodge S, Makris N, Caviness V, Frazier JA, Herbert MR. Adjustment for whole brain and cranial size in volumetric brain studies: a review of common adjustment factors and statistical methods. Harv Rev Psychiatry. 2006 May-Jun;14(3):141-51. Review. PubMed PMID: 16787886. 4: O'Brien LM, Ziegler DA, Deutsch CK, Frazier JA, Herbert MR, Locascio JJ. Statistical adjustments for brain size in volumetric neuroimaging studies: some practical implications in methods. Psychiatry Res. 2011 Aug 30;193(2):113-22. PubMed PMID: 21684724. 5: Sanfilipo MP, Benedict RH, Zivadinov R, Bakshi R. Correction for intracranial volume in analysis of whole brain atrophy in multiple sclerosis: the proportion vs. residual method. Neuroimage. 2004 Aug;22(4):1732-43. PubMed PMID: 15275929. On Wed, 2011-11-02 at 12:26 +0100, Tetiana Dadakova wrote: Dear FreeSurfer experts, I have a question regarding pial area analysis. What is commonly used as a nuisance variable to correct for brain size difference between groups (e.g men vs women)? Can you suggest any article where this is discussed or has been done? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] bug in surface-based area and volume
Dear Doug, Just wanted to ask you when approximately the fix will be ready? I really looking forward to it, to be able to explain some results. Thank you for your time and constant help, Tanja. On Fri, Aug 19, 2011 at 4:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Y'all, I recently found a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. I'm testing a fix now, but you should not use area or volume measures until I've posted the fix and you re-run either mris_preproc or qcache. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. I'll get back soon (next week) with the fix. Sorry for the inconvenience. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mean and stdev group-wise
Dear list, I would like to calculate mean and stdev of thickness group-wise. Could you please give me a hint how to do it? Thank you, 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.
[Freesurfer] two questions: asymmetry and controlling for global thickness abnormality
Dear list, I have two question: 1. Is it possible to do the asymmetry analysis in FS, I mean to compare left and right hemispheres within one group? 2. Is it necessary to somehow control for global abnormality of thickness while looking at regional abnormality, e.g. if one group has thinner brain overall, but also thinner brain in some regions? (Similar to dividing by total brain volume in volumetric analysis) Thank you and best wishes, 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.
Re: [Freesurfer] two questions: asymmetry and controlling for global thickness abnormality
Thank you Michael. I have more questions on this: 1. Is there a method to calculate if I have global difference in thickness between groups? 2. How can I control for global thickness difference vertex-wise using freesurfer? Best wishes, Tanja. On Mon, Sep 5, 2011 at 7:42 PM, Michael Harms mha...@conte.wustl.edu wrote: Regarding #2: Yes, if you a have global difference in thickness between groups, then it is appropriate to control for that in the same manner that one frequently controls for total brain volume in volumetric analyses. cheers, -MH Dear list, I have two question: 1. Is it possible to do the asymmetry analysis in FS, I mean to compare left and right hemispheres within one group? 2. Is it necessary to somehow control for global abnormality of thickness while looking at regional abnormality, e.g. if one group has thinner brain overall, but also thinner brain in some regions? (Similar to dividing by total brain volume in volumetric analysis) Thank you and best wishes, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] what is thalamus-proper and clusters-table related question
Thank you Doug, One more question: what does the column Max mean in the table with clusters' info? Tanja. On Fri, Sep 2, 2011 at 6:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I'm not sure about #1, maybe BF can chime in. Tetiana Dadakova wrote: Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? 1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for multiple comparisons 2. CWPLow - lower 90% confidence limit of CWP based on binomial distribution 3. CWPHi - upper 90% confidence limit of CWP based on binomial distribution Regarding the NVtxs column: is it the number of vertexes in cluster? Yes What kind of information can I get from this value? It is not very informative so don't feel like you have to use it. It is good for assuring that the software is doing the right thing. If two clusters have different areas but the same number of vertexes, does it mean something? It means that the area of the component triangles that make up the vertices is different. doug Thank you very much for your help and for your time, Tanja. ___ 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 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] what is thalamus-proper and clusters-table related question
Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? Regarding the NVtxs column: is it the number of vertexes in cluster? What kind of information can I get from this value? If two clusters have different areas but the same number of vertexes, does it mean something? Thank you very much for your help and for your time, 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.
Re: [Freesurfer] pial and WM missing after reunning skullstrip
Hi Julia, After the skull strip was corrected, you should run: recon-all -autorecon2 -autorecon3 -s Subject_name this will create new surfaces based on new skull strip. Tanja. On Mon, Aug 22, 2011 at 6:47 AM, Julia Hill julia.h...@neura.edu.au wrote: Hi Bruce I am new to freesurfer and im having a few issues with a number of my scans. The cerebellum and sections of the occipital lobe seems to be cut off on a number of subjects, so i went in and altered the skull stripping by increasing the watershed threshold to 35 and using -no-wsgcaatlas. When i review the scans afterwards, the pial and WM surfaces haven't included the original missing sections of the scans. How do i go back and include these missing sections? I have attached a screenshots. Thank you kindly Julia Julia Hill Research Assistant School of Psychiatry University of New South Wales Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au http://neura.edu.au/ Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia *T *+61 2 9399 1268 ___ 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] DOSS or DODS
Hello Douglas, I did as you suggested and I got the results, but I still have difficulty understanding how exactly the choice of Design Matrix Type influences the analysis, so I have several questions: 1. When I look at thickness difference between two groups and choose age as nuisance parameter, doesn't it mean that calculation take into account the difference in slopes already (as I correct for age)? So therefore, when I also choose DODS or DOSS I do kind of double correction (matrix type + nuisance), don't I? 2. When I choose e.g. DODS and do the analysis, can I see the slopes (or the values of slopes) for two groups somehow? In which file this output is? 3. Can you recommend me anything to read regarding mathematics of how the analysis is done with either matrix type? 4. Just in case you know: how is this step implemented in SPM? It also uses glm, but it doesn't ask for the DODS vs DOSS choice. Thank you, I appreciate you time and help, Tanja. On Wed, Aug 17, 2011 at 6:19 PM, Tetiana Dadakova tetian...@gmail.com wrote: Thank you, Douglas. On Wed, Aug 17, 2011 at 5:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Tanja, you should use DODS and test for a difference between the age slopes of the groups (ie, an interaction between group and age). If there are no significant interactions, you should then use DOSS to test for the difference between thicknesses. doug Tetiana Dadakova wrote: Dear all, I have two groups of subjects, and I want to see a difference in thickness between them controlling for age. I couldn't find any information in the literature on how the subject's brains in my groups develop with age. Therefore I can't tell whether thickness as a function of age for both groups has the same slope or different. My question is if in this case I should use DODS? Thank you, Tanja. ___ 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 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] qdec: Measure: area vs area.pial
Dear list, In qdec in Measure option I can choose either area or area.pial. What is the difference between them? Thank you, 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.
Re: [Freesurfer] Error while loading qdec project file
Dear Nick, dear all, I am still having problem with loading the Project FIle. When I save the Project File, one of the lines I get in the terminal window is: cp: /Applications/freesurfer/subjects/qdec/*.levels: No such file or directory I have several folders in /qdec, and a separate *.levels file in each folder. Can it cause the problem? Thank you, Tanja. On Wed, Jul 20, 2011 at 1:30 PM, Tetiana Dadakova tetian...@gmail.com wrote: Hi Nick, Unfortunately doesn't help. When I remove the folder qdec_project_archive from /tmp, and then try to Load Project File, a new qdec_project_archive is created, but it only contains those four folders/files that I mentioned in previous email. No qdec.table.dat. Is it the same qdec.table.dat that I use as Data Table just after starting qdec? Thank you, Tanja. On Tue, Jul 12, 2011 at 11:00 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: try deleting the directory qdec_project_archive: cd /tmp rm -Rf qdec_project_archive then run the Load Project command in Qdec. n. On Tue, 2011-07-12 at 19:10 +0200, Tetiana Dadakova wrote: When the Load Project is run, nothing is created in /tmp/qdec_project_archive, and then the error appears in terminal window. The only files/folders I have in /tmp/qdec_project_archive are: fsaverage, QdecProjectMetadata.txt, Untitled (this is the folder named as my project), Version.txt. Thank you, Tanja. On Mon, Jul 11, 2011 at 8:15 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what happens when the Load Project selection is run? when it is being saved, i expect it to exist in the tmp dir while it is being created, then it is deleted. when it is loaded, it should extract it to that directory. n. On Thu, 2011-07-07 at 09:59 +0200, Tetiana Dadakova wrote: Hi Nick, I have Mac OS X 10.6.7. Now I found the tmp folder, and can explain in more details what happens: As I save the Project File, the qdec_project_archive/qdec.table.dat is created, but it exists in /tmp only for several seconds and then disappears. Have you heard about something like this before? Do you know what the problem can be? Thank you, Tanja. On Wed, Jul 6, 2011 at 10:03 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what is your operating system? linux and mac typically have a /tmp dir, unless you're running on a cluster? n. On Wed, 2011-07-06 at 15:46 +0200, Tetiana Dadakova wrote: Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] DOSS or DODS
Dear all, I have two groups of subjects, and I want to see a difference in thickness between them controlling for age. I couldn't find any information in the literature on how the subject's brains in my groups develop with age. Therefore I can't tell whether thickness as a function of age for both groups has the same slope or different. My question is if in this case I should use DODS? Thank you, 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.
[Freesurfer] literature about multiple comparison correction
Dear list, Could you please recommend the literature about multiple comparisons correction, especially about Monte-Carlo simulation. Thank you, 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.
Re: [Freesurfer] Error while loading qdec project file
Hi Nick, Unfortunately doesn't help. When I remove the folder qdec_project_archive from /tmp, and then try to Load Project File, a new qdec_project_archive is created, but it only contains those four folders/files that I mentioned in previous email. No qdec.table.dat. Is it the same qdec.table.dat that I use as Data Table just after starting qdec? Thank you, Tanja. On Tue, Jul 12, 2011 at 11:00 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: try deleting the directory qdec_project_archive: cd /tmp rm -Rf qdec_project_archive then run the Load Project command in Qdec. n. On Tue, 2011-07-12 at 19:10 +0200, Tetiana Dadakova wrote: When the Load Project is run, nothing is created in /tmp/qdec_project_archive, and then the error appears in terminal window. The only files/folders I have in /tmp/qdec_project_archive are: fsaverage, QdecProjectMetadata.txt, Untitled (this is the folder named as my project), Version.txt. Thank you, Tanja. On Mon, Jul 11, 2011 at 8:15 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what happens when the Load Project selection is run? when it is being saved, i expect it to exist in the tmp dir while it is being created, then it is deleted. when it is loaded, it should extract it to that directory. n. On Thu, 2011-07-07 at 09:59 +0200, Tetiana Dadakova wrote: Hi Nick, I have Mac OS X 10.6.7. Now I found the tmp folder, and can explain in more details what happens: As I save the Project File, the qdec_project_archive/qdec.table.dat is created, but it exists in /tmp only for several seconds and then disappears. Have you heard about something like this before? Do you know what the problem can be? Thank you, Tanja. On Wed, Jul 6, 2011 at 10:03 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what is your operating system? linux and mac typically have a /tmp dir, unless you're running on a cluster? n. On Wed, 2011-07-06 at 15:46 +0200, Tetiana Dadakova wrote: Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how can do ''mri_convert''quickly when there are too many subjects
Hi Wang, You can try foreach s (subj1 subj2 etc) mri_convert $s.nii $s.nii.gz end Hope it works, Tanja. 2011/7/15 汪贵宏 wgh0...@126.com: Hi Bruce, In our research,if there are 100 subjects,how can I process these data easily.For example，when I want to compare their thickness's difference，at first，I should do mri_convert bert.nii bert.nii.gz,but when there are too many subjects,is there a way to do all of these 100 subjects at the same time? Many thanks, Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error while loading qdec project file
When the Load Project is run, nothing is created in /tmp/qdec_project_archive, and then the error appears in terminal window. The only files/folders I have in /tmp/qdec_project_archive are: fsaverage, QdecProjectMetadata.txt, Untitled (this is the folder named as my project), Version.txt. Thank you, Tanja. On Mon, Jul 11, 2011 at 8:15 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what happens when the Load Project selection is run? when it is being saved, i expect it to exist in the tmp dir while it is being created, then it is deleted. when it is loaded, it should extract it to that directory. n. On Thu, 2011-07-07 at 09:59 +0200, Tetiana Dadakova wrote: Hi Nick, I have Mac OS X 10.6.7. Now I found the tmp folder, and can explain in more details what happens: As I save the Project File, the qdec_project_archive/qdec.table.dat is created, but it exists in /tmp only for several seconds and then disappears. Have you heard about something like this before? Do you know what the problem can be? Thank you, Tanja. On Wed, Jul 6, 2011 at 10:03 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what is your operating system? linux and mac typically have a /tmp dir, unless you're running on a cluster? n. On Wed, 2011-07-06 at 15:46 +0200, Tetiana Dadakova wrote: Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error while loading qdec project file
Hi Nick, I have Mac OS X 10.6.7. Now I found the tmp folder, and can explain in more details what happens: As I save the Project File, the qdec_project_archive/qdec.table.dat is created, but it exists in /tmp only for several seconds and then disappears. Have you heard about something like this before? Do you know what the problem can be? Thank you, Tanja. On Wed, Jul 6, 2011 at 10:03 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what is your operating system? linux and mac typically have a /tmp dir, unless you're running on a cluster? n. On Wed, 2011-07-06 at 15:46 +0200, Tetiana Dadakova wrote: Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] having two freesurfer versions at one computer
Dear list, I would like to install both 5.0 and 5.1 versions on my computer. But I am not sure how exactly I should proceed after downloading the 5.1 (5.0 is already installed). For example, how should I set FREESURFER_HOME, can it be the same for both versions? Also, can I have my 5.0 in /Applications/freesurfer and 5.1 in /Applications/freesurfer5.1/freesurfer ? Thank you, 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.
[Freesurfer] Error while loading qdec project file
Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, 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.
Re: [Freesurfer] loading qdec.table.dat error
Thank you Nick, Now I have another error: Loading data table /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... Number of columns: 384 fsid column:1 Number of factors: 383 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. Although there are just 3 columns and 126 subjects.Maybe I do something wrong when creating the file, therefore here are my steps: 1. Create table it in MS Excel, save it as tab-delimited qdec.table.txt 2. Open qdec.table.txt and end one carriage return in the end to prevent problem described above 3. change .txt into .dat Am I doing something wrong? Thanks, Tanja. On Sat, May 21, 2011 at 6:09 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: I think you might need to add an extra carriage return at the end of the last line. in other words, your cursor should go an empty line at the bottom of the file. n. On Sat, 2011-05-21 at 14:34 +0200, Tetiana Dadakova wrote: Dear list, I am trying to load qdec.table.dat file using qdec, and get the following error: Loading data table /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 3 fsid column: 1 Number of factors: 2 Number of subjects: 126 ERROR: QdecDataTable::Load: problem parsing file /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat This line did not appear to end with a newline: PAT_ViOl 25 pat Error loading the data table. This is the last line in the file and therefore there is no new line after it. What can cause this error? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] loading qdec.table.dat error
Ok, now everything works. I just opened the file in terminal using pico and saved it. On Mon, May 23, 2011 at 9:43 AM, Tetiana Dadakova tetian...@gmail.com wrote: Thank you Nick, Now I have another error: Loading data table /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... Number of columns: 384 fsid column: 1 Number of factors: 383 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. Although there are just 3 columns and 126 subjects.Maybe I do something wrong when creating the file, therefore here are my steps: 1. Create table it in MS Excel, save it as tab-delimited qdec.table.txt 2. Open qdec.table.txt and end one carriage return in the end to prevent problem described above 3. change .txt into .dat Am I doing something wrong? Thanks, Tanja. On Sat, May 21, 2011 at 6:09 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: I think you might need to add an extra carriage return at the end of the last line. in other words, your cursor should go an empty line at the bottom of the file. n. On Sat, 2011-05-21 at 14:34 +0200, Tetiana Dadakova wrote: Dear list, I am trying to load qdec.table.dat file using qdec, and get the following error: Loading data table /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 3 fsid column: 1 Number of factors: 2 Number of subjects: 126 ERROR: QdecDataTable::Load: problem parsing file /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat This line did not appear to end with a newline: PAT_ViOl 25 pat Error loading the data table. This is the last line in the file and therefore there is no new line after it. What can cause this error? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] loading qdec.table.dat error
Dear list, I am trying to load qdec.table.dat file using qdec, and get the following error: Loading data table /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 3 fsid column:1 Number of factors: 2 Number of subjects: 126 ERROR: QdecDataTable::Load: problem parsing file /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat This line did not appear to end with a newline: PAT_ViOl25 pat Error loading the data table. This is the last line in the file and therefore there is no new line after it. What can cause this error? Thank you, 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.
Re: [Freesurfer] How to proceed after manual edit of segmentation
Thank you Bruce, So if I want to edit both cortex and subcortical structures, should the steps be the following: 1. edit wm.mgz 2. recon-all -autorecon2-wm -subjid 3. edit subcortical structures 4. recon-all -autorecon2 -autorecon3 -subjid ? Best wishes, Tanja. On Thu, May 5, 2011 at 2:40 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja yes, there is really no visible extreme capsule white matter, I guess because it is so thin. If you are trying to fix the surfaces you will want to edit the wm.mgz though, not the aseg.mgz. cheers Bruce On Thu, 5 May 2011, Tetiana Dadakova wrote: Dear Bruce, For some of my subjects the segmentation of putamen sticks to the cortex (please look at attached image before.jpg). Therefore, I do some manual corrections that affect the cortex (please look at attached image after.jpg). How should I proceed after this kind of manual correction? Thank you, Tanja. On Wed, Mar 30, 2011 at 3:31 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja unless the editing would change the cortex, you don't need to worry about it Bruce On Wed, 30 Mar 2011, Tetiana Dadakova wrote: Dear FreeSurfer list, I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] inflated surface
Dear Bruce, Allison, Thank you for your answer. In tkmedit the surfaces look good. Can this concavity mean that sulci are deeper in this region as compared to neighboring regions? I am not sure I understand how to interpret the inflated surface, therefore I cannot control if it is correct. Best wishes, Tanja. On Fri, Apr 29, 2011 at 8:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I agree, sometimes this happens in the inflated surface and I don't think it's cause for concern Bruce On Fri, 29 Apr 2011, Allison Stevens wrote: When you look at the case in tkmedit, in that same area, do you see an error? Looking at your snapshot, it looks like it could be normal. On Apr 26, 2011, at 8:45 AM, Tetiana Dadakova tetian...@gmail.com wrote: Dear FreeSurfer list, When I look at inflated surface of my subjects (healthy males and females), almost all of them have a concavity in the posterior part of the brain (the arrow in attached image). It doesn't look correct to me. What can cause this problem? Thank you, Tanja. tksurfer.tiff ___ 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
[Freesurfer] Non-linear Volumetric Registration
Dear list, Could you please recommend me the literature on non-linear volumetric registration used in FS? Also, is there a possibility to view talairach.m3z file? Thank you, 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.
[Freesurfer] ?h.aparc.stats file question
Dear list, I was trying to find the values of volumes for different cortical regions. What I found is the 4th column (called GrayVol) in ?h.aparc.stats file. Although, the values don't really seem to be what I look for, as values are too small (e.g. 0.5 mm^3 for cuneus). Could you please guide me where I should look for these values, or probably how should I interpret the values in ?h.aparc.stats file. Thank you, 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.
Re: [Freesurfer] ?h.aparc.stats file question
Thank you Doug, I was looking at the wrong column. Best wishes, Tanja. On Thu, Apr 14, 2011 at 5:18 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Tanja, the GrayVol is the number that you should be looking at. Are you sure you're looking at the right column? It should be the 4th col (including the structure name). Eg: cuneus 1722 1127 2145 1.835 0.411 0.160 0.072 45 5.1 this one has: NumVert 1722 SurfArea 1127 GrayVol 2145 ThickAvg 1.835 doug Tetiana Dadakova wrote: Dear list, I was trying to find the values of volumes for different cortical regions. What I found is the 4th column (called GrayVol) in ?h.aparc.stats file. Although, the values don't really seem to be what I look for, as values are too small (e.g. 0.5 mm^3 for cuneus). Could you please guide me where I should look for these values, or probably how should I interpret the values in ?h.aparc.stats file. Thank you, Tanja. ___ 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 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] N3 for improving cerebellum segmentation
Dear list, I have a question regarding intensity non-uniformity correction using N3 (as in Boyes et al, 2008). Does anyone have experience of using it for improving cerebellum segmentation, specifically distinguishing between white and grey matter in cerebellum? If yes, what are the best values for the options: -distance and -iterations? Cerebellum is very important for our study, therefore I am looking for ways of how to make the segmentation as good as possible. 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.
[Freesurfer] How to proceed after manual edit of segmentation
Dear FreeSurfer list, I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options? Thank you, 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.
[Freesurfer] open .gca file
Dear FreeSurfer list, I try to open RB_all_2008-03-26.gca by typing mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz and get an error: mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from RB_all_2008-03-26.gca... reading frame 0 of gca TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to means.mgz... mghWrite(means.mgz, -1): could not open file ERROR: failure writing means.mgz Could you please tell me what can be wrong? Thank you, 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.
Re: [Freesurfer] fixing hippocampus segmentation
Dear Bruce, The problem is that the volumes I get for hippocampus are much larger than they should be (like 5000 mm^3 for healthy female). Same is for some other structures. Best wishes, Tanja. On Wed, Feb 23, 2011 at 3:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tetiana, I think what you're seeing are just the consequences of a voxel-based segmentation. The borders have to be voxelated. Note that much of this will be corrected in the volume calculation that performs a partial-volume correction. cheers Bruce On Wed, 23 Feb 2011, Tetiana Dadakova wrote: Dear Bruce, dear all, I attach several images to show where I would like to manually interfere into segmentation process. img1: Hippocampus' volume covers part of amygdala and parahippocampal area. The intensity in these non-hippocampal regions are between 75-95. img2: Segmentation of brain stem (problem point are shown by arrows). This problem repeats more or less for every subject. img3: Edges of thalamus are too pixelated. I mean, shouldn't the line be smoother? Can this cause overestimation of thalamus' volume? Manual correction (drawing) of all the mis-segmented parts would take a lot of time, so I would like to find out other way of controlling the segmentation process. (Something like putting control points would be perfect). Thank you, Tanja. On Mon, Feb 21, 2011 at 2:56 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja, Can you send us an image? Is parahippocampal white matter significantly darker than 110? Bruce On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova tetian...@gmail.com wrote: Dear Freesurfer users, For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there any way to fix the segmentation of hippocampus by e.g. adding some control points (like for white matter here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volume of CSF for hemispheres
Hello Bruce, Could you please give me a link to this coordinate tutorial. I don't think I can find it. Thank you, Tanja. On Wed, Feb 16, 2011 at 5:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think Doug just put up a coordinate tutorial. For each voxel in the aseg label you are interested, compute it's tal coords and if the x is negative assign it to one pool and if it is positive assign it to the other cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: Thank you, Bruce. Could you recommend me any tutorial on this? Or probably can you just mention some steps or commands, where I should insert coordinates? Tanja. On Wed, Feb 16, 2011 at 3:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja we don't do this by default, but I guess you could use the Talairach x coordinate to try to differentiate. cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: Dear list, I would like to calculate CSF volume separately for left and right hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th ventricles as a whole. Is there any possibility to get volume values for right/left parts of 3rd, 4th and 5th ventricles? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fixing hippocampus segmentation
Dear Freesurfer users, For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there any way to fix the segmentation of hippocampus by e.g. adding some control points (like for white matter here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? Thank you, 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.
[Freesurfer] volume of CSF for hemispheres
Dear list, I would like to calculate CSF volume separately for left and right hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th ventricles as a whole. Is there any possibility to get volume values for right/left parts of 3rd, 4th and 5th ventricles? Thank you, 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.
Re: [Freesurfer] volume of CSF for hemispheres
Thank you, Bruce. Could you recommend me any tutorial on this? Or probably can you just mention some steps or commands, where I should insert coordinates? Tanja. On Wed, Feb 16, 2011 at 3:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja we don't do this by default, but I guess you could use the Talairach x coordinate to try to differentiate. cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: Dear list, I would like to calculate CSF volume separately for left and right hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th ventricles as a whole. Is there any possibility to get volume values for right/left parts of 3rd, 4th and 5th ventricles? Thank you, 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Three starting questions
Dear FreeSurfer community, You were very helpful for my last question, thank you. Now I have three basic questions. 1. I would like to check the segmentation by loading T1.mgz and aseg.mgz as an -aux volume, so that I can switch between them. How can I do this? (tkmedit subject T1.mgz -aux aseg.mgz gives some king of black and white segmentation instead of colorful one). 2. When I press View - View configuration, I have three options there (Single view, Multiple orientations, and Mosaic). How can I view just 3 orientations or 2 (e.g. sagittal and transverse)? 3. Do MacOS users have problems with mouse? When I try to edit segmentation or surfaces with Edit Tools, my mouse doesn't seem to work. I mean, when I click on the pixel with any of three buttons, nothing changes. I saw similar problem on the mailing list, but there was no answer. Thank you for your time, 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.
Re: [Freesurfer] Segmentation problems
Dear Bruce and all, I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question: 1. Regarding mri_gcut: should I use the default intensity of 110 for white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36? 2. Regarding manual removing of some voxels: the 'Edit Voxels' tool doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong? Thank you, Tetiana. On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tetiana, do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut. cheers Bruce On Mon, 31 Jan 2011, Tetiana Dadakova wrote: Dear FreeSurfer users, I run a recon-all -all for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction? Thank you, Tetiana. 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] Testing installation, recon-all problem
Dear Freesurfer users, I installed Freesurfer and now I am trying to test the installation. When I type recon-all -s bert -all, I get an error ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert But actually I do have write permission to this folder. Do you have any idea what can be wrong? Or what else should I check regarding installation to understand where this problem comes from? Thank you for your time, Tetiana. ___ 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.
