[Freesurfer] When/What to edit?
Hello FS experts, I have had a continuing curiosity regarding when/what to edit in FS cortical reconstructions. The wiki does a good job at showing how to deal with large scale problems, (i.e. invalid tal transformation, white matter not being recognized, large portions of the skull included in the surface) however I have yet to come across much that guides edits besides a trained eye. How do we know when a problem is big enough that it needs attention? Are there any tool boxes/ quantitative guidelines that may help someone determine which scans need edits? I know QA tools outputs info on SNR/white matter intensity and I have looked for outliers here. However, I was wondering how else to automate/guide the decision process. Much of the discussion I have seen on this topic in manuscripts is either vague or nonexistent. Does anyone know of any manuscripts that have compared raw FS datasets to selectively edited datasets? What sort of effects do edits make in the grand scheme of a study? One could imagine problems with someone editing the data when they are knowledgable of the study's hypotheses and groups. Any additional info or guidance on this topic would be much appreciated. -Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] using multiple cores
Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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] effect size for conjunction analyses?
Hi! I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and I was wondering whether anyone can make a recommendation how to display effect sizes for this kind of analyses? Would you show the effect size estimate corresponding to the p-value that is chosen, an average, or anything else? Thanks, Caspar ___ 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] MICCAI PC workshop -- May 16 (fwd)
FYI -- Forwarded message -- Date: Fri, 2 May 2014 11:28:11 -0400 From: Polina Golland pol...@csail.mit.edu To: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: MICCAI PC workshop -- May 16 Hi Bruce, Can you please forward this around? Thanks, Polina. MICCAI PC Workshop May 16, 2014, 1-6pm, CSAIL Kiva and Star Conference rooms (32-D463, 32-G449). MICCAI program committee members will present their work in areas of Medical Image Computing and Computer Assisted Interventions. This is a great opportunity to hear about current research of 20 MICCAI groups from all around the world. Open to public; anyone interested in the topics of MICCAI is welcome to attend. Tentative Program can be found here: http://miccai2014.org/pc_workshop.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] Fwd: Optseq2: ntp
Dear Douglas, I would like to use optseq2 to set up my experiment sequence. However it is not clear for me what “number of time points” means. I guessed that it was the number a waveform is sampled, but I saw in some mailing lists that it is the time the event is repeated during the run. In case it is the first meaning, how can I get the information about the number a waveform is sampled? Thanks in advance and kind regards. Conchy ___ 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] using multiple cores
Hi Bruce!I just run: recon-all -s ernie2 -autorecon2 -openmp 4 mri_ca_register uses 100.9% CPU at most ... Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes,LukasHi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes,Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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] using multiple cores
Hi Lukas sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? Does OpenMP have to be enabled somehow? Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi Bruce! I just run: recon-all -s ernie2 -autorecon2 -openmp 4 mri_ca_register uses 100.9% CPU at most ... Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes, Lukas Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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] using multiple cores
If you are compiling with clang openmp might not work. Peace, Matt. On 5/2/14, 2:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lukas sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? Does OpenMP have to be enabled somehow? Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi Bruce! I just run: recon-all -s ernie2 -autorecon2 -openmp 4 mri_ca_register uses 100.9% CPU at most ... Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes, Lukas Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see significant speedups. Try running top in a unix terminal and seeing if the cpu usage of mri_ca_register (during autorecon2, the longest single step) is morethan 100% cheers Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke ___ 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] Fwd: Optseq2: ntp
It is the number of samples in the time series. Eg, if you scan for 10min with a TR=2, then you would have 600/2=300 time points doug On 5/2/14 3:07 PM, Conchy PF wrote: Dear Douglas, I would like to use optseq2 to set up my experiment sequence. However it is not clear for me what number of time points means. I guessed that it was the number a waveform is sampled, but I saw in some mailing lists that it is the time the event is repeated during the run. In case it is the first meaning, how can I get the information about the number a waveform is sampled? Thanks in advance and kind regards. Conchy ___ 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] effect size for conjunction analyses?
Hmmm, I'm not sure an effect size makes sense. I guess I would use the one from the chosen p-value doug On 5/2/14 12:52 PM, Caspar M. Schwiedrzik wrote: Hi! I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and I was wondering whether anyone can make a recommendation how to display effect sizes for this kind of analyses? Would you show the effect size estimate corresponding to the p-value that is chosen, an average, or anything else? Thanks, Caspar ___ 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] FSGD and contrast files for group analysis
Dear Marie,I want to run a group analysis on a set of subjects, correcting for gender(Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus inlh/focus in both h), age and IQ. Should my FSGD file look somewhat like thisbelow:GroupDescriptorFile 2Class NoFocus_MaleClass NoFocus_FemaleClass RhFocus_MaleClass LhFocus_MaleClass BhFocus_MaleClass RhFocus_FemaleClass LhFocus_FemaleClass BhFocus_FemaleVariables age IQIf so, considering that I want to investigate the effect of epilepsy on corticalgyrification, what should my contrast matrix look like?The hypothesis is that the gyrification index is diminished for epilepticpatients, probably more when there is bilateral focus.I know that we need as many number as regressors, so I expect there to be 10numbers, is it so?Thank you so very much for clarifying this point,Kenza ___ 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] FSGD and contrast files for group analysis
The FSGD looks right (you have a 2x4 design, so 8 classes, plus 2 covariates). [1 1 -1 0 0 -1 0 0 0 0 0 0 0 0 0 0] tests for a difference between NoFocus and RhFocus (No-RH) [0 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0] tests for a difference between RhFocus and LhFocus (RH-RH) probably you can figure out the rest from the pattern On 5/2/14 4:40 PM, Kenza Drissi wrote: Dear Marie, I want to run a group analysis on a set of subjects, correcting for gender (Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus in lh/focus in both h), age and IQ. Should my FSGD file look somewhat like this below: GroupDescriptorFile 2 Class NoFocus_Male Class NoFocus_Female Class RhFocus_Male Class LhFocus_Male Class BhFocus_Male Class RhFocus_Female Class LhFocus_Female Class BhFocus_Female Variables age IQ If so, considering that I want to investigate the effect of epilepsy on cortical gyrification, what should my contrast matrix look like? The hypothesis is that the gyrification index is diminished for epileptic patients, probably more when there is bilateral focus. I know that we need as many number as regressors, so I expect there to be 10 numbers, is it so? Thank you so very much for clarifying this point, Kenza ___ 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] brain.finalsurfs.mgz editing
Hi Khadka, Although it is an old mail (sorry), because this topic came up in another thread, I reply here also. You need to edit the brain.finalsurfs.manedit.mgz file. Create this file by copying : cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz then edit the manedit file. Best, Martin On 01/16/2014 01:07 PM, Khadka, Sankalpa wrote: Dear freesurfer community, My question is directed to those who have experience with editing brain.finalsurfs.mgz. According to the tutorials, after making edits on brainmask.finalsurfs.mgz (which is normally done when the pial surface is not accurate), we can run, recon-all -autorecon-pial -subjid subj However, I found an anomaly when I looked at the steps that -autorecon-pial flag goes through. The very first step of autorecon-pial flag is mri_mask command. This takes brain.mgz and brainmask.mgz as inputs and gives brain.finalsurfs.mgz as output. Now, if we have made edits on brain.finalsurfs.mgz, it will be overwritten by the new one and hence our edits won't take an effect. I ran few experiments too. First, I made edits on brain.finalsurfs.mgz and ran recon-all with autorecon-pial flag. I ended up with a new brain.finalsurfs.mgz and my edits did not make any changes. Second, I made edits on brain.finalsurfs.mgz and ran with white, smooth2, inflate2, autorecon3 flag (basically starting from mri_make_surfaces command). On doing so, the edits made desirable changes and brain.finalsurfs.mgz remained intact. Third, I made changes on brainmask.mgz and brain.mgz (inputs for mri_mask). It also works as expected. Finally, I also followed the recommended steps from the tutorial by creating brainmask.finalsurfs.manedit.mgz, however, the edits from manedit were not carried on to brainmask.finalsurfs.mgz Could anyone please shed some light on this? What would be the best strategy to follow? Thank you, Sankalpa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.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] brain.finalsurfs.manedit.mgz file edits longitudinal processing
Hi Doug, so you 1. edited the cross sectionals and surfaces look fine (make sure you edit the brain.finalsurfs.manedit.mgz file, which you create as a copy of the brain.finalsurfs.mgz) 2. checked/edited the base and surfaces look fine too 3. ran the longitudinal from scratch (w/o any edits) and then in the long, the surface looks not good? Edits should automatically be copied from cross-long (if the manedit file exist). Surfaces are taken from the base to initialize longitudinal processing. That is why both step1 and step2 above are important. Step3 is a good idea to make sure that the longs are not polluted by some earlier edits. For example edits from cross are only copied over if the long has no manedit file, else only the edits in the long will be used. (I think this also answers some of the questions in the archive mail 1 you cite below, the archive mail 2 is a question about cross sectional processing, but I think there the problem is that brainmask.finalsurfs.mgz was edited directly, not the manedit file, so edits probably get overwritten). I also have the feeling that we fixed something about the editing in longitudinal processing after 5.1, but cannot find it documented on the wiki (so not sure). You may want to try to run this with 5.3 if it does not work with 5.1 Best, Martin On 05/02/2014 10:45 AM, Douglas Merkitch wrote: Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525). The problem that I am having is that the edits saved in the brain.finalsurfs.manedit.mgz file do not carry over when processing longitudinally. Previous posts have addressed this topic, but have not (to my knowledge) solved the issue. Please see the threads from the Freesurfer archive below for a brief context: 1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html 2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html Please let me know if more information is needed to understand the issue. Any insight/ideas regarding this issue would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 tel:%28312%29%20563-3853 Fax: (312) 563-4660 tel:%28312%29%20563-4660 Email: douglas_merki...@rush.edu mailto:douglas_merki...@rush.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.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.
