[Freesurfer] Problem in final analysis
Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-4.4.0 and have been experiencing some problems with the final analysis steps. We are using the qdec. Uploading of the data table has been successful. When we try to use the “Analyze” command (design) in the qdec, we get the following error message: Error in Analyze: Couldn’t open file /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thickness.fwhm10.fsaverage.mgh Obviously, the file was never created during preprocessing. We wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and would be very grateful for your comments. Yours sincerely, Carina $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-4.4.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v4.4.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39- 1 –ql-beowulf i686 $ which surfer - /apps/prod/i486/freesurfer-4.4.0/bin/freesurfer Used command: qdec/design/Analyze Error message: Error in Analyze: Couldn’t open file /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thikness.fwhm10.fsaverage.mgh ___ 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] Major problems with T2-based pial removal
hmmm. That would be strange and would result in complete failure (which I guess is what you have seen). For what it's worth, Matt is right and we haven't tested the code on many datasets, but at least so far it has been independent of contrast (that is, it works on both T2 and FLAIR) cheers Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hmm, Ok. Thanks Matt. I still think it's weird that the T2 didn't seem to ever get registered to the FS volume, but it's not a huge loss if we can't use them. With that said, it might help to clarify the docs on this point a bit, as it sort of sounded like any reasonably-sized T2-weighted image would be useful, and I would have tried to collect a different image if I had known! On Fri, Sep 27, 2013 at 12:58 PM, Matt Glasser m...@ma-tea.com wrote: So the T2-SPACE is a variable flip angle sequence that actually has a fair amount of T1 and MT contrast in it and relatively less T2 contrast. As a result, you can clearly see the difference between grey and white matter, and CSF is not massively brighter than grey and white matter. If you are using a different kind of T2w sequence where the distance between CSF intensity and grey matter intensity is much greater, some of the internal settings to the -T2pial flag will likely not be optimal. I don't know if recon-all allows you to modify those with expert options or not. Bruce, is it possible for the user to modify the –nsigma_above and -nsigma_below flags for mris_make_surfaces when using -T2pial? Peace, Matt. From: Michael Waskom mwas...@stanford.edu Date: Friday, September 27, 2013 2:20 PM To: Matt Glasser m...@ma-tea.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Major problems with T2-based pial removal Hi Matt, It's this sequence: http://cni.stanford.edu/wiki/MR_Protocols#T2_weighted_scans (the 3D T2) You can click the console screenshots for a closer view of the parameters -- let me know if you need me to track down more info. mw On Fri, Sep 27, 2013 at 11:38 AM, Matt Glasser m...@ma-tea.com wrote: Someone sent me a different kind of T2w image and it didn't work so well, so we need to know what kind of image this is. Peace, Matt. On 9/27/13 1:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: nope, pretty much only with T2-space with and without a flair pulse On Fri, 27 Sep 2013, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1 that you overlay on also looks somewhat blurry - what was it? Bruce On Fri, 27 Sep 2013, Michael Waskom wrote: Hi, just to make the problem a bit more transparent, I took a second screenshot of the slices with the pial surface from the -T2pial run in red and the pial surface from the normal run in cyan: https://dl.dropbox.com/s/jv8rcxnq50tdac6/bad_slice_both_pial.png On Fri, Sep 27, 2013 at 10:37 AM, Michael Waskom mwas...@stanford.edu wrote: Hi, I'm using FS 5.3 and trying to use hires T2-weighted scans to refine the pial mesh. However, I've found that using the T2 is causing rather dramatic problems with the pial surface. I processed the same subject's data with and without the -T2pial option. Here are links to a) pial surface image b) slices through the volume and c) the recon-all.log: With -T2pial https://dl.dropbox.com/s/rtjgplajfptr4xb/bad_surf_withT2.png https://dl.dropbox.com/s/d7so5qtujgg8j80/bad_slice_withT2.png https://dl.dropbox.com/s/7o00jy014hihrgu/recon_log_withT2.txt Without -T2pial https://dl.dropbox.com/s/51y15kogecltfbi/bad_surf_noT2.png https://dl.dropbox.com/s/3gps45kp0ngkuli/bad_slice_noT2.png https://dl.dropbox.com/s/6jih6f8fh4nwh0k/recon_log_noT2.txt The release notes for 5.3 claim that the T2 is registered to the T1 before refining the surface, but I actually can't find any evidence of that sequence in the log file. For this subject, the T1 and T2 came from different scan sessions, although I have other data where they were acquired in the same session that have similar, if less dramatic,
Re: [Freesurfer] Problem in final analysis
Hi Carina, run recon-all -s subject -qcache for each subject and this will create the file doug On 9/28/13 5:37 AM, car...@van-vlodrop.de wrote: Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-4.4.0 and have been experiencing some problems with the final analysis steps. We are using the qdec. Uploading of the data table has been successful. When we try to use the Analyze command (design) in the qdec, we get the following error message: Error in Analyze: Couldn't open file /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thickness.fwhm10.fsaverage.mgh Obviously, the file was never created during preprocessing. We wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and would be very grateful for your comments. Yours sincerely, Carina $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-4.4.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v4.4.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39- 1 --ql-beowulf i686 $ which surfer - /apps/prod/i486/freesurfer-4.4.0/bin/freesurfer Used command: qdec/design/Analyze Error message: Error in Analyze: Couldn't open file /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thikness.fwhm10.fsaverage.mgh ___ 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] LGI longitudinal data
Hi, Is it possible to run the LGI on data that has already been longitudinally processed? For example, when I try to run: recon-all -s subject001.long.subject001_base -localGI I get the following error: ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long tpNid templateid \' where tpNid is the time point id (SAME as cross sectional ID) and templateid is the ID created in the -base run. The directory tpNid.long.templateid will be created automatically or used for output, if it already exists. This is using v5.1.0, and no, I'm not trying to re-run a longitudinal time point. Just the LGI. I'd appreciate any suggestions! Thanks so much, Tricia___ 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] Major problems with T2-based pial removal
On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: hmmm. That would be strange and would result in complete failure I agree, but $ grep bbregister recon_log_withT2.txt $ grep fslregister recon_log_withT2.txt both turn up empty ___ 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] Major problems with T2-based pial removal
hmmm, maybe Nick or Doug can investigate, although we are crazy busy at the moment On Sat, 28 Sep 2013, Michael Waskom wrote: On Sat, Sep 28, 2013 at 5:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: hmmm. That would be strange and would result in complete failure I agree, but $ grep bbregister recon_log_withT2.txt $ grep fslregister recon_log_withT2.txt both turn up empty ___ 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.
