[Freesurfer] how to edit the pial surface
Hi FreeSurfer Experts, I had 2 question about the output troubleshooting. 1) when I used the mri_convert command, the format of the input image I choosed was 4D nii format, but not the original dicom format, which would affect the result of reconstruction? 2) When I checked the quality of output using tksurfer, I found the color line representing the surface (pial and white) were not along the folding pattern, and the distance between the two sufaces was rather short. Whether or not it was caused by the bad GM/WM contrast? What is the best way to deal with them? Thanks. Meng Li ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to edit the pial surface
Hi Meng 1. Not positive I understand, but I don't think it should matter. 2. we'll need to see some data to diagnose this. cheers Bruce On Sat, 19 May 2012, ?? wrote: Hi FreeSurfer Experts, I had 2 question about the output troubleshooting. 1) when I used the mri_convert command, the format of the input image I choosed was 4D nii format, but not the original dicom format, which would affect the result of reconstruction? 2) When I checked the quality of output using tksurfer, I found the color line representing the surface (pial and white) were not along the folding pattern, and the distance between the two sufaces was rather short. Whether or not it was caused by the bad GM/WM contrast? What is the best way to deal with them? Thanks. Meng Li ___ 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] 回复: Re: how to edit the pial surface
p.s. looks like an intensity normalization failure. Can you give us details of the acquisition? Sequence name, voxel resolution, etc? If you upload the subject I'll take a look cheers Bruce On Sat, 19 May 2012, limengsecret wrote: Hi Professor, The image blow shows the problems which occur. color lines representing the surfaces (pial and white) were not along the folding pattern, and the distance between the two sufaces was rather short. How to deal with these problems? [IMAGE] Thanks. Meng Li limengsecret From: Bruce Fischl Date: 2012-05-19 22:08 To: ?? CC: freesurfer Subject: Re: [Freesurfer] how to edit the pial surface Hi Meng 1. Not positive I understand, but I don't think it should matter. 2. we'll need to see some data to diagnose this. cheers Bruce On Sat, 19 May 2012, ?? wrote: Hi FreeSurfer Experts, I had 2 question about the output troubleshooting. ? 1)?? when I used the mri_convert command, the format of the input image I choosed was 4D nii format, but not the original dicom format, which would affect the result of reconstruction? 2)?? When I checked the quality of output using tksurfer, I found the color line representing the surface (pial and white) were not along the folding pattern, and the distance between the two sufaces was rather shor t. Whether or not it was caused by the bad GM/WM contrast? What is the best ?? ?way to deal with them? ? Thanks. ? Meng Li The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly 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] ERROR: comparison in expression (FS with SGE)
Rather one unsets it like this: unset POSIXLY_CORRECT Peace, Matt. -Original Message- From: Matt Glasser [mailto:m...@ma-tea.com] Sent: Friday, May 18, 2012 12:47 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE) Another note on this: Apparently, getopt (used in fsl_sub) doesn't work correctly when this flag is not set to 1 (it picks op a lot of options it shouldn't). Thus, instead of commenting out the flag, it is better to set it to zero after the set -- `getopt T:q:a:p:M:j:t:N:n:Fvm:l: $*` Line. Then one gets the best of both worlds. Peace, Matt. -Original Message- From: Matt Glasser [mailto:m...@ma-tea.com] Sent: Thursday, March 22, 2012 5:36 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE) I'm dredging this 2 year old post up for the benefit of Google and anyone else who wonders about the cause of this. It is a non-fatal error (for FreeSurfer, but perhaps not other things) that is caused by having set the variable: POSIXLY_CORRECT=1 It causes bc (on Debian/Ubuntu) systems to fail when making comparisons like: echo '3.5 2.5' | bc -l I am guessing (because this is what I was doing) that the poster was using fsl_sub to launch FreeSurfer jobs in SGE. fsl_sub sets this flag for some reason, but commenting it out seems not to cause any problems. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Xue, Feng Sent: Sunday, March 14, 2010 1:37 PM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: comparison in expression (FS with SGE) Thanks! I would check them later. On Mon, Mar 15, 2010 at 1:24 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: if it was a syntax error then recon-all wouldn't have finished, so I'm not sure what's going on. You should visually inspect the surfaces and segmentations to make sure they are all ok. cheers, Bruce On Mon, 15 Mar 2010, Xue, Feng wrote: Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you post this to the list? There are others better qualified to say what's going on. But if everything finished ok is there really a problem? Maybe this is just a warning? On Sun, 14 Mar 2010, Xue, Feng wrote: Hi Bruce, Thanks for your reply. The recon-all.log said it finished without error. please find the whole scripts root in the attachment. I'm also running a raw testing with one subject and without SGEMaybe I can report the result the day after tomorrow. BTW, I found in my 64bit Debian nodes, I repeated got the error as below (standard_in) 2: Error: comparison in expression but in 32bit, I met both. for the GMail security restriction, I changed recon-all.cmd in the attachment to recon-all.cmds. On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what does the recon-all.log say? Did the recon finish correctly? Does this happen if you just run it on the command line? Bruce On Sat, 13 Mar 2010, Xue, Feng wrote: Dear Bruce FS experts, Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion. ++ We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all: $ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression I also checked the recon-all-status.log file, but not error was found. Has anyone met this problem? Is it critical? Thanks in advance. -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn == Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org ___ 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
[Freesurfer] how to map the anatomical to the diffusion space
Hi FreeSurfer Experts, Using the mri_surfcluster command, I got the labels of the significant regions from qdec comparisons of thickness between two groups. The diffusion data was not processed using the dt_recon, but DTI-studio. So how can I map the significant regions to the individual diffusion space? Thanks a lot. Meng Li ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How to edit the pial surface
Hi professor, The attachment is the subject after running the recon-all command. MR data were obtained on a 1.5T Philips Achieva Nova Dual MR scanner. the sequence name is T1W.3D.FFE.SENSE and the voxel size is 0.90*0.90*1mm. how should I fix the poor quality surface reconstruction? Thanks a lot for your help. Meng Li At 2012-05-19 23:10:31,Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: p.s. looks like an intensity normalization failure. Can you give us details of the acquisition? Sequence name, voxel resolution, etc? If you upload the subject I'll take a look cheers Bruce On Sat, 19 May 2012, limengsecret wrote: Hi Professor, The image blow shows the problems which occur. color lines representing the surfaces (pial and white) were not along the folding pattern, and the distance between the two sufaces was rather short. How to deal with these problems? [IMAGE] Thanks. Meng Li limengsecret From: Bruce Fischl Date: 2012-05-19 22:08 To: ?? CC: freesurfer Subject: Re: [Freesurfer] how to edit the pial surface Hi Meng 1. Not positive I understand, but I don't think it should matter. 2. we'll need to see some data to diagnose this. cheers Bruce On Sat, 19 May 2012, ?? wrote: Hi FreeSurfer Experts, I had 2 question about the output troubleshooting. ? 1)?? when I used the mri_convert command, the format of the input image I choosed was 4D nii format, but not the original dicom format, which would affect the result of reconstruction? 2)?? When I checked the quality of output using tksurfer, I found the color line representing the surface (pial and white) were not along the folding pattern, and the distance between the two sufaces was rather shor t. Whether or not it was caused by the bad GM/WM contrast? What is the best ?? ?way to deal with them? ? Thanks. ? Meng Li The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. 从QQ邮箱发来的超大附件 Sub.rar (262MB, 2012年06月19日 12:40 到期) 进入下载页面：http://mail.qq.com/cgi-bin/ftnExs_download?k=0d636362224297d81b9673551e640018555650550c520a561c5055060a49060409534e5a0f02041a535400500e0051070753545b3863326444014d105916320acode=1ccb8d27t=exs_ftn_download___ 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.
