[Freesurfer] T1 and T2 in one recon-all
Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] T1 and T2 in one recon-all
yes, just the T1. cheers, Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam ___ 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] T1 and T2 in one recon-all
Thank you for the quick reply Bruce. I'm new to freesurfer, do you know if there is any benefit to including T2 in the process workflow somewhere? Cheers, -Sam On 30/11/2009 11:35 PM, Bruce Fischl wrote: yes, just the T1. cheers, Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam ___ 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] T1 and T2 in one recon-all
not for the default workflow, no. There are other things we are working on such as damaged white matter estimation that would benefit, but nothing released. cheers Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Thank you for the quick reply Bruce. I'm new to freesurfer, do you know if there is any benefit to including T2 in the process workflow somewhere? Cheers, -Sam On 30/11/2009 11:35 PM, Bruce Fischl wrote: yes, just the T1. cheers, Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] T1 and T2 in one recon-all
Ok, I would be interested in your damaged white mater tools when it's released (or even if its in a generally usable form now) as I'm working with a large data set of multiple sclerosis subjects. Cheers, -Sam On 30/11/2009 11:54 PM, Bruce Fischl wrote: not for the default workflow, no. There are other things we are working on such as damaged white matter estimation that would benefit, but nothing released. cheers Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Thank you for the quick reply Bruce. I'm new to freesurfer, do you know if there is any benefit to including T2 in the process workflow somewhere? Cheers, -Sam On 30/11/2009 11:35 PM, Bruce Fischl wrote: yes, just the T1. cheers, Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Comments in paradigm files
Hi, Can you add comments to a paradigm file? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TKSURFER error- open GL in Fedora
Hi, I can't seem to run tksurfer in Fedora 7. We are using a Wacom Tablet monitor, and since we installed it, we cannot run tksurfer. We get the following error: surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(fsaverage) Can't create a context! surfer: failed, trying double buffered window Can't create a context! surfer: failed, no suitable display found Does anyone know how to go about this? massih ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Comments in paradigm files
You can append to the end of a line in the 4 column format. Yigal Agam wrote: Hi, Can you add comments to a paradigm file? Thanks, Yigal ___ 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] colin27 skullstrip problem
Hi, I'm trying to get the surfaces for the colin27 brain that is included with the mni packages. Has anyone managed to do this before? I thought I would have an easy time given that this linear average of 27 brains has very good signal to noise and nice contrasts, and even though recon-all completes without errors, the surfaces are way off. The main problem appears to be the skull stripping. My input volume is here: http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz These are the steps I took and where I think the problem might be: 1. gunzip colin27_t1_tal_lin.mnc.gz 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27 3. tkmedit conlin27 orig/001.mgz At this point the image the brightness and contrast levels of the image look very washed out. I am hoping this is only a display issue and that the underlying intensities of the image are still intact and is not a result of something going on in mri_convert, but maybe this is what is causing the downstream skull strip to fail. Can someone take a look? http://opus.bic.mni.mcgill.ca/public/001.mgz 4. recon-all -autorecon1 -subjid colin27 5. tkregister2 --mgz --s colin27 --fstal Results are not perfect but reasonable ie. about the same as many other runs I've had that have passed so I don't think it is the registration. 6. tkmedit colin27 brainmask.mgz -aux T1.mgz It is clear this is where the problem is. http://opus.bic.mni.mcgill.ca/public/brainmask.mgz http://opus.bic.mni.mcgill.ca/public/T1.mgz 7. I have subsequently tried: recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extract the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extracted the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted the brain, but left large chunks of skull) recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted the brain, but left quite a few chunks of skull) I'm concerned that the -wsthresh is so low in order to get a reasonable result, that's why I think the intensities might be off (see step 3). I'm re-running -autorecon2/3 now to see if the surfaces are better, but if someone could take a look at my input file and the converted 001.mgz to see if it isn't a problem there it would be much appreciated. thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] colin27 skullstrip problem
Hi Mishkin, yes, I generates surfaces for the Colin27 dataset. It actually doesn't have great gray/white contrast, probably due to differential B0 distortions in the different sessions. Maybe we should include it as part of our release? In any case, I can send it to you. cheers Bruce On Mon, 30 Nov 2009, Mishkin Derakhshan wrote: Hi, I'm trying to get the surfaces for the colin27 brain that is included with the mni packages. Has anyone managed to do this before? I thought I would have an easy time given that this linear average of 27 brains has very good signal to noise and nice contrasts, and even though recon-all completes without errors, the surfaces are way off. The main problem appears to be the skull stripping. My input volume is here: http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz These are the steps I took and where I think the problem might be: 1. gunzip colin27_t1_tal_lin.mnc.gz 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27 3. tkmedit conlin27 orig/001.mgz At this point the image the brightness and contrast levels of the image look very washed out. I am hoping this is only a display issue and that the underlying intensities of the image are still intact and is not a result of something going on in mri_convert, but maybe this is what is causing the downstream skull strip to fail. Can someone take a look? http://opus.bic.mni.mcgill.ca/public/001.mgz 4. recon-all -autorecon1 -subjid colin27 5. tkregister2 --mgz --s colin27 --fstal Results are not perfect but reasonable ie. about the same as many other runs I've had that have passed so I don't think it is the registration. 6. tkmedit colin27 brainmask.mgz -aux T1.mgz It is clear this is where the problem is. http://opus.bic.mni.mcgill.ca/public/brainmask.mgz http://opus.bic.mni.mcgill.ca/public/T1.mgz 7. I have subsequently tried: recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extract the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extracted the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted the brain, but left large chunks of skull) recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted the brain, but left quite a few chunks of skull) I'm concerned that the -wsthresh is so low in order to get a reasonable result, that's why I think the intensities might be off (see step 3). I'm re-running -autorecon2/3 now to see if the surfaces are better, but if someone could take a look at my input file and the converted 001.mgz to see if it isn't a problem there it would be much appreciated. thanks, mishkin ___ 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] colin27 skullstrip problem
Hi Bruce, A copy of the surfaces would be much appreciated. Just let me know where I can download them from. Ideally if you can tar the whole colin27 directory so I have the aseg and aparc info as well that would be great. I think including this and/or the mni152 and average_305 surfaces would be great, though this might bloat the size of the download. Not sure if you had a chance to look at my files, but do you think the problem I have is just a bad skullstrip, or is it an intensity issue from the conversion? thanks, mishkin On Mon, Nov 30, 2009 at 8:53 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Mishkin, yes, I generates surfaces for the Colin27 dataset. It actually doesn't have great gray/white contrast, probably due to differential B0 distortions in the different sessions. Maybe we should include it as part of our release? In any case, I can send it to you. cheers Bruce On Mon, 30 Nov 2009, Mishkin Derakhshan wrote: Hi, I'm trying to get the surfaces for the colin27 brain that is included with the mni packages. Has anyone managed to do this before? I thought I would have an easy time given that this linear average of 27 brains has very good signal to noise and nice contrasts, and even though recon-all completes without errors, the surfaces are way off. The main problem appears to be the skull stripping. My input volume is here: http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz These are the steps I took and where I think the problem might be: 1. gunzip colin27_t1_tal_lin.mnc.gz 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27 3. tkmedit conlin27 orig/001.mgz At this point the image the brightness and contrast levels of the image look very washed out. I am hoping this is only a display issue and that the underlying intensities of the image are still intact and is not a result of something going on in mri_convert, but maybe this is what is causing the downstream skull strip to fail. Can someone take a look? http://opus.bic.mni.mcgill.ca/public/001.mgz 4. recon-all -autorecon1 -subjid colin27 5. tkregister2 --mgz --s colin27 --fstal Results are not perfect but reasonable ie. about the same as many other runs I've had that have passed so I don't think it is the registration. 6. tkmedit colin27 brainmask.mgz -aux T1.mgz It is clear this is where the problem is. http://opus.bic.mni.mcgill.ca/public/brainmask.mgz http://opus.bic.mni.mcgill.ca/public/T1.mgz 7. I have subsequently tried: recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extract the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extracted the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted the brain, but left large chunks of skull) recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted the brain, but left quite a few chunks of skull) I'm concerned that the -wsthresh is so low in order to get a reasonable result, that's why I think the intensities might be off (see step 3). I'm re-running -autorecon2/3 now to see if the surfaces are better, but if someone could take a look at my input file and the converted 001.mgz to see if it isn't a problem there it would be much appreciated. thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all -qcache question
Hi, there, I have 60 subjects which have been FS analyzed without the flag -qcache. Now, I wan to do group analysis using QDEC. I need run recon-all -s subjectid -qcache for each of my subjects. Just want to know how it will take to finish the recon-all -s subjectid -qcache command for one subject? Will it go through the whole -autorecon1, 2, 3 process again? Thanks a lot! Guang _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -qcache question
Hi Guang, It is much faster as it does not go through the whole autorecon1, 2, 3 process. For us, it take about 45 minutes per subject. Regards Mehul On Mon, Nov 30, 2009 at 8:04 PM, Guang Zeng freesurfer...@hotmail.comwrote: Hi, there, I have 60 subjects which have been FS analyzed without the flag -qcache. Now, I wan to do group analysis using QDEC. I need run recon-all -s subjectid -qcache for each of my subjects. Just want to know how it will take to finish the recon-all -s subjectid -qcache command for one subject? Will it go through the whole -autorecon1, 2, 3 process again? Thanks a lot! Guang -- Hotmail: Trusted email with powerful SPAM protection. Sign up now.http://clk.atdmt.com/GBL/go/177141665/direct/01/ ___ 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] colin27 skullstrip problem
Hello, I am also very interested in having a copy of colin27's FS data! roberto On Tue, Dec 1, 2009 at 2:53 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Mishkin, yes, I generates surfaces for the Colin27 dataset. It actually doesn't have great gray/white contrast, probably due to differential B0 distortions in the different sessions. Maybe we should include it as part of our release? In any case, I can send it to you. cheers Bruce On Mon, 30 Nov 2009, Mishkin Derakhshan wrote: Hi, I'm trying to get the surfaces for the colin27 brain that is included with the mni packages. Has anyone managed to do this before? I thought I would have an easy time given that this linear average of 27 brains has very good signal to noise and nice contrasts, and even though recon-all completes without errors, the surfaces are way off. The main problem appears to be the skull stripping. My input volume is here: http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz These are the steps I took and where I think the problem might be: 1. gunzip colin27_t1_tal_lin.mnc.gz 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27 3. tkmedit conlin27 orig/001.mgz At this point the image the brightness and contrast levels of the image look very washed out. I am hoping this is only a display issue and that the underlying intensities of the image are still intact and is not a result of something going on in mri_convert, but maybe this is what is causing the downstream skull strip to fail. Can someone take a look? http://opus.bic.mni.mcgill.ca/public/001.mgz 4. recon-all -autorecon1 -subjid colin27 5. tkregister2 --mgz --s colin27 --fstal Results are not perfect but reasonable ie. about the same as many other runs I've had that have passed so I don't think it is the registration. 6. tkmedit colin27 brainmask.mgz -aux T1.mgz It is clear this is where the problem is. http://opus.bic.mni.mcgill.ca/public/brainmask.mgz http://opus.bic.mni.mcgill.ca/public/T1.mgz 7. I have subsequently tried: recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extract the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extracted the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted the brain, but left large chunks of skull) recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted the brain, but left quite a few chunks of skull) I'm concerned that the -wsthresh is so low in order to get a reasonable result, that's why I think the intensities might be off (see step 3). I'm re-running -autorecon2/3 now to see if the surfaces are better, but if someone could take a look at my input file and the converted 001.mgz to see if it isn't a problem there it would be much appreciated. thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
