[Freesurfer] aseg2feat for PPI seeds for FSL
Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Thanks. Michelle ___ 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] correction
Dear Freesurfers, could you please give me detailed information about the Bonferroni or clusterwise correction we can do in Freesurfer? How much iterations? Is that cluster- oder voxelwise? Is there anywhere a detailed description about the correction options? Best regards, Viola ___ 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] analysis.cfg not generated by mkanalysis-sess
Dear all, I ran mkanalysis-sess (mkanalysis-sess -analysis junk -TR 2 -paradigm para01.para -event-related -funcstem fmc -nconditions 3 -runlistfile runlist_odd -fsd bold -fir 10 30 -native) but it did't not generate analysis.cfg. The only file I can see after running this is analysis.info. When I ran mkanalysis-sess.new, both analysis-info and analysis.cfg are generated as fine. Could any one know how to solve this problem? ps. I'm running freesurfer5.1.0 on Mac OS X 10.6.8 (the mkanalysis-sess.new is a copy from freesurfer4.5.0). Thanks! Brown ___ 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] Fwd: Talairach transformation
Dear Ms. Kakunoori, sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber - Forwarded Message - From: Maria Felber fel...@cbs.mpg.de To: Avi Snyder a...@npg.wustl.edu Cc: Sita Kakunoori\, fel...@cbs.mpg.de, \Avi Snyder\ a...@npg.wustl.edu, Bruce Fischl s...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation Dear all, indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria - Original Message - From: Avi Snyder a...@npg.wustl.edu To: Sita Kakunoori s...@nmr.mgh.harvard.edu, fel...@cbs.mpg.de, Avi Snyder a...@npg.wustl.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation Hi Sita, Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible. Avi --- On 9/13/11 2:26 PM, Sita Kakunoori s...@nmr.mgh.harvard.edu wrote: I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that. Thanks much, Sita. -- Forwarded message -- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber fel...@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation Hi Bruce, so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria - Original Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Maria Felber fel...@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation Hi Maria you can use tkregister2 to check the accuracy of the talairach.xfm transform (xform for short), and correct it if you want. cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote: Hi Bruce, thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons. Thanks again, Maria - Original Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Maria Felber fel...@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation Hi Maria as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords. cheers Bruce p.s. not sure why it would be smaller On Fri, 9 Sep 2011, Maria Felber wrote: Dear all, sorry, if that question came up before in the mailing list and I simple have been unable to find the thread. Following the wiki
[Freesurfer] Error with mri_glmfit-sim
Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK ___ 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] Folding Index and Gyrification index
Hi Bruce, Nick Doug: How does Folding index differ from Gyrification index? thanks, Alan BIDMC ___ 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] fieldsign-sess: ERROR Surf/src mismatch
Hi Michelle, this almost surely means that the surfaces are out-of-synch. You can try recon-all -s subject -make all -dontrun on one of your subjects. If everything is in synch, then it should print make: Nothing to be done for `all'. If not, it should print out the steps that it would have run (if not for the -dontrun option). doug Michelle Umali wrote: Hi Doug, I get the same MRISripZeros() and MRIScopyMRI Surf/src mismatch error when I use -sphere and not -occip in fieldsign-sess. What else should I try? Thank you. Michelle On Tue, Sep 27, 2011 at 8:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Is the occip patch out of synch with the subject? Does it run if you use -sphere instead of -occip? doug Michelle Umali wrote: Dear Freesurfers, This is related to my retinotopy analysis tksurfer-sess dimension mismatch error message. So another subject had these errors come up during fieldsign-sess selxavg3-sess -a rtopy.self.lh -s sjXX -force (which ran without error) then I ran fieldsign fieldsign-sess -a rtopy.self.lh -occip -s sjXX and got: ERROR: MRISripZeros(): dimension mismatch ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. What may have caused this? Thanks. Michelle ___ 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 -- 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
Re: [Freesurfer] aseg2feat for PPI seeds for FSL
Michelle Umali wrote: Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? don't you need to run it on each feat to get a time course for each run? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Maybe I'm confused, but I thought you had to run it on the time course data (which is not in the GFEAT). doug Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] GM, WM and CSF segmentation for partial volume correction
Hello list, Following this email that I found in the archives: (...) For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X Hope this helps! All the best, Anderson I need to obtain the different % of tissue (GM, WM and CSF) inside one defined voxel. Does FS has a file that can be exported to Matlab to then get these values? Or only FSL/FAST and SPM have this type of info? Thanks! Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] correction
Hi Viola, there's some detailed info if you run mri_glmfit-sim --help mri_glmfit --help mri_glmfit-sim runs mri_glmfit. When you use mri_glmfit-sim with the --cache option, it uses simulations that are based on 10,000 iterations. Here are some slides that give more detail http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt Here's the paper we reference ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hayasaka.2003.ni.1014.clustersize.pdf doug Oertel, Viola wrote: Dear Freesurfers, could you please give me detailed information about the Bonferroni or clusterwise correction we can do in Freesurfer? How much iterations? Is that cluster- oder voxelwise? Is there anywhere a detailed description about the correction options? Best regards, Viola ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] analysis.cfg not generated by mkanalysis-sess
The 5.X version does not produce a cfg anymore, so everything is ok. You cannot use older versions of mkanalysis-sess with 5.X doug Po-Jang (Brown) Hsieh wrote: Dear all, I ran mkanalysis-sess (mkanalysis-sess -analysis junk -TR 2 -paradigm para01.para -event-related -funcstem fmc -nconditions 3 -runlistfile runlist_odd -fsd bold -fir 10 30 -native) but it did't not generate analysis.cfg. The only file I can see after running this is analysis.info http://analysis.info/. When I ran mkanalysis-sess.new, both analysis-info and analysis.cfg are generated as fine. Could any one know how to solve this problem? ps. I'm running freesurfer5.1.0 on Mac OS X 10.6.8 (the mkanalysis-sess.new is a copy from freesurfer4.5.0). Thanks! Brown ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] GM, WM and CSF segmentation for partial volume correction
Hi Andreia you could certainly change our segmentation labels to just these 3 classes easily enough in matlab. Then we have tools for computing partial volume fractions (I think mri_compute_volume_fractions) cheers Bruce On Wed, 28 Sep 2011, _andre...@sapo.pt wrote: Hello list, Following this email that I found in the archives: (...) For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X Hope this helps! All the best, Anderson I need to obtain the different % of tissue (GM, WM and CSF) inside one defined voxel. Does FS has a file that can be exported to Matlab to then get these values? Or only FSL/FAST and SPM have this type of info? Thanks! Andreia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] analysis.cfg not generated by mkanalysis-sess
Dear Doug, Thanks very much! But without analysis.cfg, I cannot run selxave-sess... Am I missing something here? Brown On Wed, Sep 28, 2011 at 11:36 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: The 5.X version does not produce a cfg anymore, so everything is ok. You cannot use older versions of mkanalysis-sess with 5.X doug Po-Jang (Brown) Hsieh wrote: Dear all, I ran mkanalysis-sess (mkanalysis-sess -analysis junk -TR 2 -paradigm para01.para -event-related -funcstem fmc -nconditions 3 -runlistfile runlist_odd -fsd bold -fir 10 30 -native) but it did't not generate analysis.cfg. The only file I can see after running this is analysis.info http://analysis.info/. When I ran mkanalysis-sess.new, both analysis-info and analysis.cfg are generated as fine. Could any one know how to solve this problem? ps. I'm running freesurfer5.1.0 on Mac OS X 10.6.8 (the mkanalysis-sess.new is a copy from freesurfer4.5.0). Thanks! Brown --**--** __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Po-Jang (Brown) Hsieh Neuroscience and Behavioral Disorders Program Duke-NUS Graduate Medical School 8 College Road, Singapore 169857 -- Lab website: Brain Consciousness Labhttps://sites.google.com/site/brainconsciousnesslab/ http://brownhsieh.blogspot.com/ ___ 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] GM, WM and CSF segmentation for partial volume correction
mri_compute_volume_fractions will compute the fractions for each of the tissue types, no need to alter the segmentations. doug Bruce Fischl wrote: Hi Andreia you could certainly change our segmentation labels to just these 3 classes easily enough in matlab. Then we have tools for computing partial volume fractions (I think mri_compute_volume_fractions) cheers Bruce On Wed, 28 Sep 2011, _andre...@sapo.pt wrote: Hello list, Following this email that I found in the archives: (...) For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X Hope this helps! All the best, Anderson I need to obtain the different % of tissue (GM, WM and CSF) inside one defined voxel. Does FS has a file that can be exported to Matlab to then get these values? Or only FSL/FAST and SPM have this type of info? Thanks! Andreia ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] analysis.cfg not generated by mkanalysis-sess
Hi Brown, you should not be mixing versions. There is no selxavg-sess in 5.X. The new version is selxavg3-sess. doug Po-Jang (Brown) Hsieh wrote: Dear Doug, Thanks very much! But without analysis.cfg, I cannot run selxave-sess... Am I missing something here? Brown On Wed, Sep 28, 2011 at 11:36 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The 5.X version does not produce a cfg anymore, so everything is ok. You cannot use older versions of mkanalysis-sess with 5.X doug Po-Jang (Brown) Hsieh wrote: Dear all, I ran mkanalysis-sess (mkanalysis-sess -analysis junk -TR 2 -paradigm para01.para -event-related -funcstem fmc -nconditions 3 -runlistfile runlist_odd -fsd bold -fir 10 30 -native) but it did't not generate analysis.cfg. The only file I can see after running this is analysis.info http://analysis.info http://analysis.info/. When I ran mkanalysis-sess.new, both analysis-info and analysis.cfg are generated as fine. Could any one know how to solve this problem? ps. I'm running freesurfer5.1.0 on Mac OS X 10.6.8 (the mkanalysis-sess.new is a copy from freesurfer4.5.0). Thanks! Brown ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Po-Jang (Brown) Hsieh Neuroscience and Behavioral Disorders Program Duke-NUS Graduate Medical School 8 College Road, Singapore 169857 -- Lab website: Brain Consciousness Lab https://sites.google.com/site/brainconsciousnesslab/ -- 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
Re: [Freesurfer] Folding Index and Gyrification index
have a look at this page: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI folding index is typically a single number summarizing the amount of folding overall on a surface. freesurfer puts these measures in subjid/stats/?h.curv.stats. gyrification index is a new method created by maria schaer to create a surface-based measure of folding (points across a surface describing the local folding measures). n. On Wed, 2011-09-28 at 11:05 -0400, Alan Francis wrote: Hi Bruce, Nick Doug: How does Folding index differ from Gyrification index? thanks, Alan BIDMC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] strange freeview issue
thanks nick. tried with 5.1.0 same issue. here is the output from glxgears. $ glxgears Error: couldn't get an RGB, Double-buffered visual i am beginning to suspect it as a driver issue. cheers, satra On Wed, Sep 28, 2011 at 11:17 AM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: i'm able to replicate what you see on my mac (leopard, w/ XQuartz) connecting via ssh -Y to a linux machine and running fs v5.0.0. however, freeview works in this setup using fs 5.1.0. the change between version is that freeview now uses Qt (instead of Wx). can you switch to v5.1.0? or copy the freeview from 5.1.0 to your 5.0.0 installation? you would need to copy: freesurfer/lib/qt freesurfer/bin/freeview freesurfer/bin/freeview.bin freesurver/bin/qt_setup.csh n. On Tue, 2011-09-27 at 20:40 -0400, Satrajit Ghosh wrote: hi, we are seeing a strange freeview issue at mit and just wanted to check if anybody else has seen this. we are running natty narwhal (ubuntu 11.04). details here: https://github.com/gablab/mindhive/issues/1 cheers, satra ___ 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] strange freeview issue
its a shot in the dark, but you could try updating the mac with XQuartz, which seems to be much better for X stuff than the default X installation. doing so is a necessity for running freesurfer locally on the mac: https://surfer.nmr.mgh.harvard.edu/fswiki/MacTksurfer that page fixes a different issue, but its X related. also, on the linux machine, make sure the /etc/X11/xorg.conf file has Load glx in the Section Module n. On Wed, 2011-09-28 at 11:52 -0400, Satrajit Ghosh wrote: thanks nick. tried with 5.1.0 same issue. here is the output from glxgears. $ glxgears Error: couldn't get an RGB, Double-buffered visual i am beginning to suspect it as a driver issue. cheers, satra On Wed, Sep 28, 2011 at 11:17 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: i'm able to replicate what you see on my mac (leopard, w/ XQuartz) connecting via ssh -Y to a linux machine and running fs v5.0.0. however, freeview works in this setup using fs 5.1.0. the change between version is that freeview now uses Qt (instead of Wx). can you switch to v5.1.0? or copy the freeview from 5.1.0 to your 5.0.0 installation? you would need to copy: freesurfer/lib/qt freesurfer/bin/freeview freesurfer/bin/freeview.bin freesurver/bin/qt_setup.csh n. On Tue, 2011-09-27 at 20:40 -0400, Satrajit Ghosh wrote: hi, we are seeing a strange freeview issue at mit and just wanted to check if anybody else has seen this. we are running natty narwhal (ubuntu 11.04). details here: https://github.com/gablab/mindhive/issues/1 cheers, satra ___ 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 with mri_glmfit-sim
What does FDR have to do with it? FDR should not come into play in this. doug Antonella Kis wrote: Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK -- 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] Error with mri_glmfit-sim
Good afternoon, I tried running the -sim on my QDEC output (as recommended last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK___ 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] GM, WM and CSF segmentation for partial volume correction
Thanks Bruce and Douglas! Andreia Citando Douglas N Greve gr...@nmr.mgh.harvard.edu: mri_compute_volume_fractions will compute the fractions for each of the tissue types, no need to alter the segmentations. doug Bruce Fischl wrote: Hi Andreia you could certainly change our segmentation labels to just these 3 classes easily enough in matlab. Then we have tools for computing partial volume fractions (I think mri_compute_volume_fractions) cheers Bruce On Wed, 28 Sep 2011, _andre...@sapo.pt wrote: Hello list, Following this email that I found in the archives: (...) For the segmentation, FS still works voxelwise, but it's objective is to identify each structure as a whole, whereas SPM and FSL/FAST attempt to classify each voxel as being GM, WM or CSF. A short description of the method in FS is here: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream You may want also to have a look at this paper: http://dx.doi.org/10.1016/S0896-6273(02)00569-X Hope this helps! All the best, Anderson I need to obtain the different % of tissue (GM, WM and CSF) inside one defined voxel. Does FS has a file that can be exported to Matlab to then get these values? Or only FSL/FAST and SPM have this type of info? Thanks! Andreia ___ 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 -- 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
Re: [Freesurfer] Error with mri_glmfit-sim
again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with --cache 2 sign where sign is pos, neg, or abs doug Antonella Kis wrote: Hi Doug, Thanks again for helping. I am trying to use QDEC but there are no clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that I cannot run the -sim if there is no FDR data (stats) so I cannot cache the clusters formed only by thresh 2 in QDEC. Is theer a way to do it? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 12:06 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim What does FDR have to do with it? FDR should not come into play in this. doug Antonella Kis wrote: Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- 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
Re: [Freesurfer] Folding Index and Gyrification index
My understanding is that GI is also a global summary stat across the whole hem, while lGI is *local* GI (vertex-wise). It measures how folded the cortex is at that vertex. GI and lGI are based on area, while the folding index is based on curvature. Truly different measures. Gyrification Index (GI) = Pial surface area / Convex hull surface area (Zilles et al., 1988) Folding Index (FI) = |kmax|(|kmax|-|kmin|) Van Essen and Drury 1997 On Sep 28, 2011, at 10:48 AM, Nick Schmansky wrote: have a look at this page: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI folding index is typically a single number summarizing the amount of folding overall on a surface. freesurfer puts these measures in subjid/stats/?h.curv.stats. gyrification index is a new method created by maria schaer to create a surface-based measure of folding (points across a surface describing the local folding measures). n. On Wed, 2011-09-28 at 11:05 -0400, Alan Francis wrote: Hi Bruce, Nick Doug: How does Folding index differ from Gyrification index? thanks, Alan BIDMC ___ 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
Re: [Freesurfer] Folding Index and Gyrification index
Correction: FI = Sum-over-vertices[ |kmax|(|kmax|-|kmin|)]/SurfaceArea On Sep 28, 2011, at 1:38 PM, Donna Dierker wrote: My understanding is that GI is also a global summary stat across the whole hem, while lGI is *local* GI (vertex-wise). It measures how folded the cortex is at that vertex. GI and lGI are based on area, while the folding index is based on curvature. Truly different measures. Gyrification Index (GI) = Pial surface area / Convex hull surface area (Zilles et al., 1988) Folding Index (FI) = |kmax|(|kmax|-|kmin|) Van Essen and Drury 1997 On Sep 28, 2011, at 10:48 AM, Nick Schmansky wrote: have a look at this page: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI folding index is typically a single number summarizing the amount of folding overall on a surface. freesurfer puts these measures in subjid/stats/?h.curv.stats. gyrification index is a new method created by maria schaer to create a surface-based measure of folding (points across a surface describing the local folding measures). n. On Wed, 2011-09-28 at 11:05 -0400, Alan Francis wrote: Hi Bruce, Nick Doug: How does Folding index differ from Gyrification index? thanks, Alan BIDMC ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] THANKS
*By default, FreeSurfer compputes and uses a two-tailed p-value. When you specify a sign, it lowers the threshold that you give it to reflect a one-tailed test. Probably what happened was that you had two clusters close to each other that merged together with the lower threshold. doug * Antonella Kis wrote: Dear Doug, Finally I've got it. But there is one more problem: when I run the QDEC with Min threshold 2 neg, I am getting 2 clusters, while when I am running the results from QDEC(under Untitled.glmdir) with the -sim: mri_glmfit-sim \ --glmdir Untitled.glmdir \ --cache 2 pos \ --overwrite I am getting only one of the clusters. Can you please advise me what is going on or what should I correct? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 1:33 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with --cache 2 sign where sign is pos, neg, or abs doug Antonella Kis wrote: Hi Doug, Thanks again for helping. I am trying to use QDEC but there are no clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that I cannot run the -sim if there is no FDR data (stats) so I cannot cache the clusters formed only by thresh 2 in QDEC. Is theer a way to do it? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 12:06 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim What does FDR have to do with it? FDR should not come into play in this. doug Antonella Kis wrote: Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto: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 -- 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
Re: [Freesurfer] Error with mri_glmfit-sim
No, unfortunately not. doug jm wrote: Doug: I have processed 20 subjects. By mistake, five of them with LAS orientation and 15 RAS orientation.RAS that's right in my case. I could change name of files in '/surf' folder from left to right in the first ones? or I need do it over? for instance: I could change name of file rh.thickness.fwhm25.fsaverage to lh.thickness.fwhm25.fsaverage? or that have others implications to statistical analysis outcomes thanks On Wed, 2011-09-28 at 13:33 -0400, Douglas N Greve wrote: again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with --cache 2 sign where sign is pos, neg, or abs doug Antonella Kis wrote: Hi Doug, Thanks again for helping. I am trying to use QDEC but there are no clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that I cannot run the -sim if there is no FDR data (stats) so I cannot cache the clusters formed only by thresh 2 in QDEC. Is theer a way to do it? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 12:06 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim What does FDR have to do with it? FDR should not come into play in this. doug Antonella Kis wrote: Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- 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
Re: [Freesurfer] aseg2feat for PPI seeds for FSL
Dear Doug and the Freesurfers, Ok, so is there a special filtered_func.nii generated from reg-feat2anat for each run or can I just use the feat? When one does a cross-subject PPI in FSL and enter each run from each person, isn't everyone in a different space? How do you account for this when doing setting up the PPI feat? Thanks. Michelle Michelle Umali wrote: Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? don't you need to run it on each feat to get a time course for each run? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Maybe I'm confused, but I thought you had to run it on the time course data (which is not in the GFEAT). doug Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] aseg2feat for PPI seeds for FSL
Michelle Umali wrote: Dear Doug and the Freesurfers, Ok, so is there a special filtered_func.nii generated from reg-feat2anat for each run or can I just use the feat? No, just use the FEAT one. When one does a cross-subject PPI in FSL and enter each run from each person, isn't everyone in a different space? How do you account for this when doing setting up the PPI feat? Aren't you just getting a single time course? I have not done PPI analysis before, so I might not know what is required. doug Thanks. Michelle Michelle Umali wrote: Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat on my FEAT data from each of 4 runs. I have 2 questions: 1) Does it matter which run's FEAT I use for aseg2feat --feat featdir --aseg aparc+aseg to generate the binary masks for my seeds? don't you need to run it on each feat to get a time course for each run? 2) Does fslmeants need a special registered filtered_func.nii.gz from a cross-run GFEAT? If so, how do you specify it for this and then for actual PPI analysis in fsl? Maybe I'm confused, but I thought you had to run it on the time course data (which is not in the GFEAT). doug Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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
[Freesurfer] Mcsrch error during recon-all
Hi, Each time I have run recon-all on our subjects, I end up with the same slew of error messages underneath Computing MAP estimate using [x number of] samples and underneath EM alignment process: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES At the very end of the log file I see: Loading source label. Abort Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011 Any help on this would be greatly appreciated. Best, Warren -- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ 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] THANKS
The change in threshold is always 0.3. Eg, to go from a two-tailed threshold of 2.0 to a one-tailed threshold, you would subtract .3 from 2.0 (and so 1.7). Is this what you mean? Antonella Kis wrote: I see. Is there a way that I can get/read both clusters sin other words can I eliminate this inconvenient of two-tailed p-value? Thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 2:59 PM *Subject:* Re: [Freesurfer] THANKS *By default, FreeSurfer compputes and uses a two-tailed p-value. When you specify a sign, it lowers the threshold that you give it to reflect a one-tailed test. Probably what happened was that you had two clusters close to each other that merged together with the lower threshold. doug * Antonella Kis wrote: Dear Doug, Finally I've got it. But there is one more problem: when I run the QDEC with Min threshold 2 neg, I am getting 2 clusters, while when I am running the results from QDEC(under Untitled.glmdir) with the -sim: mri_glmfit-sim \ --glmdir Untitled.glmdir \ --cache 2 pos \ --overwrite I am getting only one of the clusters. Can you please advise me what is going on or what should I correct? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 1:33 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with --cache 2 sign where sign is pos, neg, or abs doug Antonella Kis wrote: Hi Doug, Thanks again for helping. I am trying to use QDEC but there are no clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that I cannot run the -sim if there is no FDR data (stats) so I cannot cache the clusters formed only by thresh 2 in QDEC. Is theer a way to do it? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 12:06 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim What does FDR have to do with it? FDR should not come into play in this. doug Antonella Kis wrote: Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] THANKS
Oh, sorry, I precompute the tables with certain fixed voxel-wise thresholds. But it seems like you may want to use 2.3. Why 1.7? If you want it to match what you see in QDEC at a threshold of 2.0, then you should spec 2.3. Antonella Kis wrote: I am not sure but I tried that and it gives me error: ? --glmdir Untitled.glmdir \ ? --cache 1.7 neg\ ? --overwrite ERROR: thresh = 1.7, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 So how should I fix that? Many thanks! AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 4:07 PM *Subject:* Re: [Freesurfer] THANKS The change in threshold is always 0.3. Eg, to go from a two-tailed threshold of 2.0 to a one-tailed threshold, you would subtract .3 from 2.0 (and so 1.7). Is this what you mean? Antonella Kis wrote: I see. Is there a way that I can get/read both clusters sin other words can I eliminate this inconvenient of two-tailed p-value? Thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 2:59 PM *Subject:* Re: [Freesurfer] THANKS *By default, FreeSurfer compputes and uses a two-tailed p-value. When you specify a sign, it lowers the threshold that you give it to reflect a one-tailed test. Probably what happened was that you had two clusters close to each other that merged together with the lower threshold. doug * Antonella Kis wrote: Dear Doug, Finally I've got it. But there is one more problem: when I run the QDEC with Min threshold 2 neg, I am getting 2 clusters, while when I am running the results from QDEC(under Untitled.glmdir) with the -sim: mri_glmfit-sim \ --glmdir Untitled.glmdir \ --cache 2 pos \ --overwrite I am getting only one of the clusters. Can you please advise me what is going on or what should I correct? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 1:33 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with --cache 2 sign where sign is pos, neg, or abs doug Antonella Kis wrote: Hi Doug, Thanks again for helping. I am trying to use QDEC but there are no clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that I cannot run the -sim if there is no FDR data (stats) so I cannot cache the clusters formed only by thresh 2 in QDEC. Is theer a way to do it? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Mcsrch error during recon-all
the IFLAG messages can be ignored if mri_em_register is not exiting with error. which command is running that is exiting with error? can you send that command line from the recon-all.log file? n. On Wed, 2011-09-28 at 16:02 -0400, Warren Winter wrote: Hi, Each time I have run recon-all on our subjects, I end up with the same slew of error messages underneath Computing MAP estimate using [x number of] samples and underneath EM alignment process: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES At the very end of the log file I see: Loading source label. Abort Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011 Any help on this would be greatly appreciated. Best, Warren -- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: Talairach transformation
Hi Maria have you tried running without the talairach stuff? Try -notalairach and see if it works for you cheers Bruce On Wed, 28 Sep 2011, Maria Felber wrote: Dear Ms. Kakunoori, sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber - Forwarded Message - From: Maria Felber fel...@cbs.mpg.de To: Avi Snyder a...@npg.wustl.edu Cc: Sita Kakunoori\, fel...@cbs.mpg.de, \Avi Snyder\ a...@npg.wustl.edu, Bruce Fischl s...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation Dear all, indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria - Original Message - From: Avi Snyder a...@npg.wustl.edu To: Sita Kakunoori s...@nmr.mgh.harvard.edu, fel...@cbs.mpg.de, Avi Snyder a...@npg.wustl.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation Hi Sita, Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible. Avi --- On 9/13/11 2:26 PM, Sita Kakunoori s...@nmr.mgh.harvard.edu wrote: I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that. Thanks much, Sita. -- Forwarded message -- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber fel...@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation Hi Bruce, so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria - Original Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Maria Felber fel...@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation Hi Maria you can use tkregister2 to check the accuracy of the talairach.xfm transform (xform for short), and correct it if you want. cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote: Hi Bruce, thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons. Thanks again, Maria - Original Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Maria Felber fel...@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation Hi Maria as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords. cheers Bruce p.s. not sure why it would be smaller On Fri, 9 Sep 2011, Maria Felber wrote:
[Freesurfer] fieldsign-sess: ERROR Surf/src mismatch
Hey Doug and Freesurfers, At the bottom is the output showing what steps didn't run. 1) Do you think I did the whole recon-all pipeline wrong? Here's what i did after I originally ran recon-all -all -label_v1: I made edits with talairach registration edits with tkregister2 and ran recon-all -all -label_v1. After that,with tkmedit I made edits to brainmask.mgz and wm-mgz, then recon-all -autorecon2-wm and autorecon 3, -label_v1. 2) Was adding the -label_v1 flag what caused the below steps to not happen and cause the mismatch? Does adding the -label_v1 flag cause recon-all to not run on the rest of the brain? If so, do I just run recon-all -autorecon2 and -autorecon3 without the -label_v1 flag? Thanks. Michelle FreeSurfer:/media/sf_windows/ subjects recon-all -s ld07 -make all -dontrun INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Subject 'ld07': make -n all recon-all -s /media/sf_windows/subjects/ld07 -gcareg recon-all -s /media/sf_windows/subjects/ld07 -canorm recon-all -s /media/sf_windows/subjects/ld07 -careg -careginv recon-all -s /media/sf_windows/subjects/ld07 -rmneck recon-all -s /media/sf_windows/subjects/ld07 -skull-lta recon-all -s /media/sf_windows/subjects/ld07 -calabel recon-all -s /media/sf_windows/subjects/ld07 -normalization2 recon-all -s /media/sf_windows/subjects/ld07 -maskbfs recon-all -s /media/sf_windows/subjects/ld07 -segmentation recon-all -s /media/sf_windows/subjects/ld07 -fill recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -tessellate recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -tessellate recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth1 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth1 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate1 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate1 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -qsphere recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -qsphere recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -fix recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -fix recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -sphere recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -sphere recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -surfreg recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -surfreg recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -jacobian_white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -jacobian_white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -avgcurv recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -avgcurv recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortribbon recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortribbon recon-all -s /media/sf_windows/subjects/ld07 -segstats recon-all -s /media/sf_windows/subjects/ld07 -aparc2aseg recon-all -s /media/sf_windows/subjects/ld07 -wmparc - Hide quoted text - On Wed, Sep 28, 2011 at 11:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Michelle, this almost surely means that the surfaces are out-of-synch. You can try recon-all -s subject -make all -dontrun on one of your subjects. If everything is in synch, then it should print make: Nothing to be done for `all'. If not, it should print out the steps that it would have run (if not for the -dontrun option). doug Michelle Umali wrote: Hi Doug, I
Re: [Freesurfer] Fwd: Talairach transformation
you could also try: -talairach -use-mritotal which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better (not necessary for 3T). you should also probably add: -nuintensitycor-3T to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but will produce better results for 3T data downstream. n. On Wed, 2011-09-28 at 16:38 -0400, Bruce Fischl wrote: Hi Maria have you tried running without the talairach stuff? Try -notalairach and see if it works for you cheers Bruce On Wed, 28 Sep 2011, Maria Felber wrote: Dear Ms. Kakunoori, sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber - Forwarded Message - From: Maria Felber fel...@cbs.mpg.de To: Avi Snyder a...@npg.wustl.edu Cc: Sita Kakunoori\, fel...@cbs.mpg.de, \Avi Snyder\ a...@npg.wustl.edu, Bruce Fischl s...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation Dear all, indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria - Original Message - From: Avi Snyder a...@npg.wustl.edu To: Sita Kakunoori s...@nmr.mgh.harvard.edu, fel...@cbs.mpg.de, Avi Snyder a...@npg.wustl.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation Hi Sita, Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible. Avi --- On 9/13/11 2:26 PM, Sita Kakunoori s...@nmr.mgh.harvard.edu wrote: I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that. Thanks much, Sita. -- Forwarded message -- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber fel...@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation Hi Bruce, so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria - Original Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Maria Felber fel...@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation Hi Maria you can use tkregister2 to check the accuracy of the talairach.xfm transform (xform for short), and correct it if you want. cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote: Hi Bruce, thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the
[Freesurfer] Inclusion of lateral ventricle in pial surface
Dear Experts, I noticed that the inferior horn of the lateral ventricles are not included within the pial surface while the posterior lateral ventricles are and wonder how one should go about when making corrections for the pial surface. This was observed in the subjects that I have worked with and also with the Freesurfer tutorial sample data. For the sample data, it appears that the hippocampus provides a clear delineation of the inferior and posterior lateral ventricles in the sagittal view (see attached image bert) which was not observed with our subjects (see attached images sub). The segmentation of the lateral ventricles, however, looks correct (by using the segmentation label function), so I am unsure if this discrepancy affects the measurements at all. However, it is worth confirming. I look forward to reading your responses. Thank you very much, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: vy_d...@rush.edumailto:vy_d...@rush.edu ___ 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] Inclusion of lateral ventricle in pial surface
Hi Vy, no, it shouldn't. The pial surfaces are not trustworthy near the hippocampus, and we don't use them there. Bruce On Wed, 28 Sep 2011, Vy Dinh wrote: Dear Experts, I noticed that the inferior horn of the lateral ventricles are not included within the pial surface while the posterior lateral ventricles are and wonder how one should go about when making corrections for the pial surface. This was observed in the subjects that I have worked with and also with the Freesurfer tutorial sample data. For the sample data, it appears that the hippocampus provides a clear delineation of the inferior and posterior lateral ventricles in the sagittal view (see attached image bert) which was not observed with our subjects (see attached images sub). The segmentation of the lateral ventricles, however, looks correct (by using the segmentation label function), so I am unsure if this discrepancy affects the measurements at all. However, it is worth confirming. I look forward to reading your responses. Thank you very much, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: vy_d...@rush.edu ___ 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] fieldsign-sess: ERROR Surf/src mismatch
The gcareg step depends on the talairach registration, so if that is changed, it thinks that the gcareg needs to change. If the gcareg needs to change, then the canorm needs to change, and so on. This does not mean that anything really needs to be updated. This is strictly looking at the time stamps and assuming that things have changed and need to be updated. If your results look ok, then there's no need to re-run. Unfortunately, this does not tell us whether the surfaces themselves are up to date. You can do this with: recon-all -vno-check -s subject This looks at the number of vertices in each of the surfaces to make sure they are consistent. doug Michelle Umali wrote: Hey Doug and Freesurfers, At the bottom is the output showing what steps didn't run. 1) Do you think I did the whole recon-all pipeline wrong? Here's what i did after I originally ran recon-all -all -label_v1: I made edits with talairach registration edits with tkregister2 and ran recon-all -all -label_v1. After that,with tkmedit I made edits to brainmask.mgz and wm-mgz, then recon-all -autorecon2-wm and autorecon 3, -label_v1. 2) Was adding the -label_v1 flag what caused the below steps to not happen and cause the mismatch? Does adding the -label_v1 flag cause recon-all to not run on the rest of the brain? If so, do I just run recon-all -autorecon2 and -autorecon3 without the -label_v1 flag? Thanks. Michelle FreeSurfer:/media/sf_windows/ subjects recon-all -s ld07 -make all -dontrun INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Subject 'ld07': make -n all recon-all -s /media/sf_windows/subjects/ld07 -gcareg recon-all -s /media/sf_windows/subjects/ld07 -canorm recon-all -s /media/sf_windows/subjects/ld07 -careg -careginv recon-all -s /media/sf_windows/subjects/ld07 -rmneck recon-all -s /media/sf_windows/subjects/ld07 -skull-lta recon-all -s /media/sf_windows/subjects/ld07 -calabel recon-all -s /media/sf_windows/subjects/ld07 -normalization2 recon-all -s /media/sf_windows/subjects/ld07 -maskbfs recon-all -s /media/sf_windows/subjects/ld07 -segmentation recon-all -s /media/sf_windows/subjects/ld07 -fill recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -tessellate recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -tessellate recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth1 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth1 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate1 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate1 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -qsphere recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -qsphere recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -fix recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -fix recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -sphere recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -sphere recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -surfreg recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -surfreg recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -jacobian_white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -jacobian_white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -avgcurv recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -avgcurv recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats2 recon-all -s
Re: [Freesurfer] fieldsign-sess: ERROR Surf/src mismatch
Hi Doug and Freesurfers, I ran the -vno-check and the number of vertices matches for left and right hemispheres (see below): Since all there are an equal number of vertices, how is the mismatch error occurring in fieldsign-sess and how do I get it to run? Thanks for all your help. Michelle vno_match_check ld07 lh Checking ld07/surf/lh.orig... Checking ld07/surf/lh.white... Checking ld07/surf/lh.pial... Checking ld07/surf/lh.inflated... Checking ld07/surf/lh.smoothwm... Checking ld07/surf/lh.sphere... Checking ld07/surf/lh.curv... Checking ld07/surf/lh.sulc... Checking ld07/surf/lh.area... Checking ld07/surf/lh.thickness... Checking ld07/label/lh.aparc.annot... Checking ld07/label/lh.aparc.a2009s.annot... Pass: all surfaces and surface data for subject ld07 have the same number of vertices. The same is true for the right hemisphere. On Wed, Sep 28, 2011 at 5:21 PM, Douglas N Greve g r...@nmr.mgh.harvard.edu wrote: The gcareg step depends on the talairach registration, so if that is changed, it thinks that the gcareg needs to change. If the gcareg needs to change, then the canorm needs to change, and so on. This does not mean that anything really needs to be updated. This is strictly looking at the time stamps and assuming that things have changed and need to be updated. If your results look ok, then there's no need to re-run. Unfortunately, this does not tell us whether the surfaces themselves are up to date. You can do this with: recon-all -vno-check -s subject This looks at the number of vertices in each of the surfaces to make sure they are consistent. doug Michelle Umali wrote: Hey Doug and Freesurfers, At the bottom is the output showing what steps didn't run. 1) Do you think I did the whole recon-all pipeline wrong? Here's what i did after I originally ran recon-all -all -label_v1: I made edits with talairach registration edits with tkregister2 and ran recon-all -all -label_v1. After that,with tkmedit I made edits to brainmask.mgz and wm-mgz, then recon-all -autorecon2-wm and autorecon 3, -label_v1. 2) Was adding the -label_v1 flag what caused the below steps to not happen and cause the mismatch? Does adding the -label_v1 flag cause recon-all to not run on the rest of the brain? If so, do I just run recon-all -autorecon2 and -autorecon3 without the -label_v1 flag? Thanks. Michelle FreeSurfer:/media/sf_windows/ subjects recon-all -s ld07 -make all -dontrun INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-**stable-pub-v5.1.0 Subject 'ld07': make -n all recon-all -s /media/sf_windows/subjects/**ld07 -gcareg recon-all -s /media/sf_windows/subjects/**ld07 -canorm recon-all -s /media/sf_windows/subjects/**ld07 -careg -careginv recon-all -s /media/sf_windows/subjects/**ld07 -rmneck recon-all -s /media/sf_windows/subjects/**ld07 -skull-lta recon-all -s /media/sf_windows/subjects/**ld07 -calabel recon-all -s /media/sf_windows/subjects/**ld07 -normalization2 recon-all -s /media/sf_windows/subjects/**ld07 -maskbfs recon-all -s /media/sf_windows/subjects/**ld07 -segmentation recon-all -s /media/sf_windows/subjects/**ld07 -fill recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -tessellate recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -tessellate recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -smooth1 recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -smooth1 recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -inflate1 recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -inflate1 recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -qsphere recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -qsphere recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -fix recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -fix recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -smooth2 recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -smooth2 recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -sphere recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -sphere recon-all -s /media/sf_windows/subjects/**ld07 -hemi lh -surfreg recon-all -s /media/sf_windows/subjects/**ld07 -hemi rh -surfreg recon-all -s /media/sf_windows/subjects/**ld07
Re: [Freesurfer] trac-all results
Hi Anastasia, I've tried both options, the choice 1 fixed some of the cases, but not all; and the choice 2 did not work at all. Maybe I've missed something here. Few more questions: 1. Will the initial points have to include the points around start, way, and end points of the tracts need to be segmented? Can I just enter the points in the main stem of tracts? 2. Will EPI distortion correction, like using field map, in the preprocessing steps help co-registration and thus improving the labeling? So far more than 80% (4 out of 5 data sets) of the data have at least one suboptimal tract, either in flt or bbr. (BTW, which flag will call B0 fieldmaps (or phase and magnitude images) for distortion correction? Do the fieldmap images need to be in the same matrix size and resolution as DWI? ) 3. I wonder why these suboptimal segmented tracts are not terribly off the white matter paths but just fewer voxels? Would the probabilistic tractography implemented in FSL be good in working around this problem by lowering the threshold for tract segmentation? Thanks. Ping On Thu, Sep 22, 2011 at 1:18 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - There are 2 possibilities: 1. You can try to fiddle with the initialization points yourself to make sure they're well in the CST. The point coordinates are saved in a text file - look at the --init argument of the dmri_paths command line, which you can find in trac-all.log. 2. You can let trac-all select a different initialization by adding set reinit = 1 to your dmrirc file, then running trac-all -prior again. Once you change the initialization by doing either 1. or 2. above, you need to run trac-all -path to reconstruct this path again. You can change the pathlist in dmrirc to do only the path that failed. We jump through various hoops to make sure this sort of thing doesn't happen but in a few cases it can't be prevented, unfortunately. Let me know if this has helped or if you have any other questions! a.y On Thu, 22 Sep 2011, Ping-Hong Yeh wrote: Hi Anastasia, The both ends were not terribly off of the white matter, though the lower end was a bit off at the level of decussation. any suggestion in fixing this? Thanks. ping On Thu, Sep 22, 2011 at 12:51 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - It looks like the path initialization may have failed. The algorithm needs an initial guess for the path and iterates from there. This initial guess is chosen based on the tracts in the atlas and if your subject is not perfectly aligned with the atlas this initial guess might end up going off the white matter for example. Does the blue line in your snapshot look like it may not coincide well with you subject's CST, going off the white matter close to the end, etc? a.y On Thu, 22 Sep 2011, Ping-Hong Yeh wrote: Hello, The segmented left CST tracts of one of our 3T data was not satisfactory, which has only few voxels with 1000 gray values (see attached snapshot pictures for trac-all and cst_prob). The manually tracking using deterministic tractography seems OK (see cst_stremline). Any suggestions on which step may go wrong in trac-all? Thank you, Ping 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] trac-all results
Hi Ping - You can upload your data if you want me to take a look at it. 1. The initial points ideally should be along the midline of the pathway, starting from one end region of the pathway and going all the way to the other end region. (The default number is 5 control points but you can set ncpts = ... in your dmrirc to change that.) 2. You can look in $FREESURFER_HOME/bin/dmrirc.example for how to specify the field map inputs. They don't need to have the same matrix size and resolution as the DWIs. 3a. If it's the initialization that's failed, the output will just be the initial path and nothing else (which is I think what you mean by fewer voxels). 3b. The diffusion model used here is the same as the ball-and-stick model that FSL uses. If the threshold you're referring to is the minimum volume fraction for the anisotropic compartments of that model, you can set fmin = ... in your dmrirc to choose one. I hope this helps a bit! a.y On Wed, 28 Sep 2011, Ping-Hong Yeh wrote: Hi Anastasia, I've tried both options, the choice 1 fixed some of the cases, but not all; and the choice 2 did not work at all. Maybe I've missed something here. Few more questions: 1. Will the initial points have to include the points around start, way, and end points of the tracts need to be segmented? Can I just enter the points in the main stem of tracts? 2. Will EPI distortion correction, like using field map, in the preprocessing steps help co-registration and thus improving the labeling? So far more than 80% (4 out of 5 data sets) of the data have at least one suboptimal tract, either in flt or bbr. (BTW, which flag will call B0 fieldmaps (or phase and magnitude images) for distortion correction? Do the fieldmap images need to be in the same matrix size and resolution as DWI? ) 3. I wonder why these suboptimal segmented tracts are not terribly off the white matter paths but just fewer voxels? Would the probabilistic tractography implemented in FSL be good in working around this problem by lowering the threshold for tract segmentation? Thanks. Ping On Thu, Sep 22, 2011 at 1:18 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - There are 2 possibilities: 1. You can try to fiddle with the initialization points yourself to make sure they're well in the CST. The point coordinates are saved in a text file - look at the --init argument of the dmri_paths command line, which you can find in trac-all.log. 2. You can let trac-all select a different initialization by adding set reinit = 1 to your dmrirc file, then running trac-all -prior again. Once you change the initialization by doing either 1. or 2. above, you need to run trac-all -path to reconstruct this path again. You can change the pathlist in dmrirc to do only the path that failed. We jump through various hoops to make sure this sort of thing doesn't happen but in a few cases it can't be prevented, unfortunately. Let me know if this has helped or if you have any other questions! a.y On Thu, 22 Sep 2011, Ping-Hong Yeh wrote: Hi Anastasia, The both ends were not terribly off of the white matter, though the lower end was a bit off at the level of decussation. any suggestion in fixing this? Thanks. ping On Thu, Sep 22, 2011 at 12:51 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - It looks like the path initialization may have failed. The algorithm needs an initial guess for the path and iterates from there. This initial guess is chosen based on the tracts in the atlas and if your subject is not perfectly aligned with the atlas this initial guess might end up going off the white matter for example. Does the blue line in your snapshot look like it may not coincide well with you subject's CST, going off the white matter close to the end, etc? a.y On Thu, 22 Sep 2011, Ping-Hong Yeh wrote: Hello, The segmented left CST tracts of one of our 3T data was not satisfactory, which has only few voxels with 1000 gray values (see attached snapshot pictures for trac-all and cst_prob). The manually tracking using deterministic tractography seems OK (see cst_stremline). Any suggestions on which step may go wrong in trac-all? Thank you, Ping 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] Inclusion of lateral ventricle in pial surface
Thank you for the swift response Bruce. Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: vy_d...@rush.edu From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, September 28, 2011 4:16 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.gold...@gmail.com Subject: Re: [Freesurfer] Inclusion of lateral ventricle in pial surface Hi Vy, no, it shouldn't. The pial surfaces are not trustworthy near the hippocampus, and we don't use them there. Bruce On Wed, 28 Sep 2011, Vy Dinh wrote: Dear Experts, I noticed that the inferior horn of the lateral ventricles are not included within the pial surface while the posterior lateral ventricles are and wonder how one should go about when making corrections for the pial surface. This was observed in the subjects that I have worked with and also with the Freesurfer tutorial sample data. For the sample data, it appears that the hippocampus provides a clear delineation of the inferior and posterior lateral ventricles in the sagittal view (see attached image bert) which was not observed with our subjects (see attached images sub). The segmentation of the lateral ventricles, however, looks correct (by using the segmentation label function), so I am unsure if this discrepancy affects the measurements at all. However, it is worth confirming. I look forward to reading your responses. Thank you very much, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: vy_d...@rush.edu 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] Mcsrch error during recon-all
the log does not indicate that mri_em_register exited with an error. it appears that it produced its output correctly and continued through to nearly the end of the stream. the IFLAG messages can be ignored. the log indicates that mri_label2label is exiting with an error when trying to load the label from the fsaverage directory. the fsaverage subject is symlinked to the users SUBJECTS_DIR (to save space), but sometimes this seems to cause problems on some systems. i would try copying it to your subjects dir: cd $SUBJECTS_DIR rm fsaverage cp -r $FREESURFER_HOME/subjects/fsaverage . then you just need to run the last two stages of recon-all: recon-all -s subjid -balabels -label-exvivo-ec or if you dont care about the Brodmann or exvivo EC labels, you dont need to run anything. for reference: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable n. On Wed, 2011-09-28 at 17:36 -0400, Warren Winter wrote: Hi Nick, Thanks for your help. The first set of errors (of the kind I described) follows the command mri_em_register -skull nu.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta The next follows the command mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_2008-03-26.gca transforms/talairach.lta The next follows the command mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /chb/freesurfer/x86_64-Linux/packages/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta I've attached the log if you could use it for reference. Best, Warren On Sep 28, 2011, at 4:18 PM, Nick Schmansky wrote: the IFLAG messages can be ignored if mri_em_register is not exiting with error. which command is running that is exiting with error? can you send that command line from the recon-all.log file? n. On Wed, 2011-09-28 at 16:02 -0400, Warren Winter wrote: Hi, Each time I have run recon-all on our subjects, I end up with the same slew of error messages underneath Computing MAP estimate using [x number of] samples and underneath EM alignment process: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES At the very end of the log file I see: Loading source label. Abort Linux rc-twice 2.6.39.2-mosix #1 SMP Wed Jun 29 11:53:08 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 5 exited with ERRORS at Tue Sep 27 03:23:46 EDT 2011 Any help on this would be greatly appreciated. Best, Warren -- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ 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. -- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA: how to implement DTI repeat sequence?
Hi Anastasia, Thanks so much for your message. You were right about the recon directory, the contents had been accidentally moved elsewhere (sorry!) and once I moved them back and reran the script everything worked like a charm without any errors. However, it looks like I'm now stuck at the next processing stage (fsl's bedpostX). I pasted the output with the error message below. FYI: I'm unfortunately forced to run the bedpostX on a single Linux box (64-bit dual core with 8GB of RAM) which I hope is OK? Thanks so much for all your help, Ansgar == trac-all -bedp -c scripts/dmrirc_single_subject_1only INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA Actual FREESURFER_HOME /usr/local/freesurfer ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 9 slices processed 10 slices processed 11 slices processed 11 slices processed 12 slices processed 12 slices processed 13 slices processed 14 slices processed 14 slices processed 14 slices processed 15 slices processed 15 slices processed 16 slices processed 16 slices processed 16 slices processed 17 slices processed 17 slices processed 17 slices processed 18 slices processed 18 slices processed 18 slices processed 18 slices processed 19 slices processed 19 slices processed 19 slices processed 19 slices processed 20 slices processed 20 slices processed 20 slices processed 20 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 22 slices processed 22 slices processed 22 slices processed 22 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 40 slices processed 40 slices processed 40 slices processed 40 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 42 slices processed 42 slices processed 42 slices processed 42 slices processed 43 slices processed 43 slices processed 43 slices processed 43 slices processed 44 slices processed 44 slices processed 44 slices processed 44 slices processed 45 slices processed 45 slices processed 45 slices processed 46 slices processed 46 slices processed 46 slices processed 46 slices processed 47 slices processed 47 slices processed 47 slices processed 48 slices processed 48 slices processed 49 slices processed 49 slices processed 49 slices processed 50 slices processed 50 slices processed 51 slices processed 51 slices processed 52 slices processed 53 slices
Re: [Freesurfer] TRACULA: how to implement DTI repeat sequence?
Hi Ansgar - Most likely everything is fine. Sometimes the script that's built into bedpost to monitor its progress gives this error but in fact everything has ran fine. You should check that all the outputs are there in the dmri.bedpostX directory. See for list of bedpost output files: http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html a.y On Wed, 28 Sep 2011, Ansgar Furst wrote: Hi Anastasia, Thanks so much for your message. You were right about the recon directory, the contents had been accidentally moved elsewhere (sorry!) and once I moved them back and reran the script everything worked like a charm without any errors. However, it looks like I'm now stuck at the next processing stage (fsl's bedpostX). I pasted the output with the error message below. FYI: I'm unfortunately forced to run the bedpostX on a single Linux box (64-bit dual core with 8GB of RAM) which I hope is OK? Thanks so much for all your help, Ansgar == trac-all -bedp -c scripts/dmrirc_single_subject_1only INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA Actual FREESURFER_HOME /usr/local/freesurfer ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 9 slices processed 10 slices processed 11 slices processed 11 slices processed 12 slices processed 12 slices processed 13 slices processed 14 slices processed 14 slices processed 14 slices processed 15 slices processed 15 slices processed 16 slices processed 16 slices processed 16 slices processed 17 slices processed 17 slices processed 17 slices processed 18 slices processed 18 slices processed 18 slices processed 18 slices processed 19 slices processed 19 slices processed 19 slices processed 19 slices processed 20 slices processed 20 slices processed 20 slices processed 20 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 21 slices processed 22 slices processed 22 slices processed 22 slices processed 22 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 23 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 24 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 25 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 26 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 27 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 28 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 29 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 30 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 31 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 32 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 33 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 34 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 35 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 36 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 37 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 38 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 39 slices processed 40 slices processed 40 slices processed 40 slices processed 40 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 41 slices processed 42 slices processed 42 slices processed 42 slices processed 42 slices
[Freesurfer] aseg2feat and aparc2feat
Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For example, I wanted to use number 433, the Visual_V3d_l. I tried to use aseg2feat -feat featdir --aseg aparc+aseg fslmaths -featdir/reg/freesurfer/aparc+aseg.nii.gz -thr 433v uthr 433 \ featdir/reg/freesurfer/Visual_V3d_l.nii.gz The resulting image was empty. I was able to use aseg2feat for all subcortical regions, so then i used aparc2feat. However, this uses a different color table which is missing many of the regions present in the Freesurfer Color Lookup table that I would like to use. How can I get area 433 (Visual_V3d_l) from the Freesurfer Color Lookup Table so I can later run fslmaths to generate a mask? Thanks. Michelle ___ 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.
