[Freesurfer] Morphological measures
Dear Freesurfer users after running Freesurfer, I got 11 colums (without structure name) in the recon_all.log file with the different morphological indices: e.g. 208122451 3.056 0.740 0.125 0.0242 0.6 15 0.179 G_cingulate-Isthmus but actually there should be only 9 colums (without structure name). further I am confused because in another subject there are only 10 colums (without structure name) e.g. 188 124 272 2.121 0.641 0.107 0 18 1.966 0.12 G_cingulate-Isthmus and in the second example, the 7th colum (Gaussian curvature) is always zero!!! What happens? Thanks in advance for clarification Best regards Juergen -- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) [EMAIL PROTECTED] (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] automatic processing
Hi, I have to process more than 500 good quality scans (1mm isotropic) for an epidemiological study and have limited time resources. Initial processing of 20 scans seems promising but I am new to freesurfer and therefore I am not quite sure how significant small defects might be in the big picture (where they will be averaged over a large number of subjects). I would be interested to hear the experience of others in using autoreconall for processing most scans and only reprocessing a small portion of scans with obvious substantial defects (mostly on the inflated surface). With good quality scans would most people reprocess most scans? Thanks for sharing your experiences. Nic ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_anatomical_stats error
Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ROI group analysis
Hi Doug, I tried using the registration file in the tal-rfx dir for this group and I received the following error: ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file. Can I use the bhdr file that is in the same directory as the registration file? Cameron There should be a register.dat file in the bold dir of the average subject (or maybe in the bold/analysis/tal dir) doug Cameron Ellis wrote: Hi, I am trying to run mri_volcluster on a group ROI and am having some trouble. I was hoping someone had suggestion. I created individual ROIs and wanted to average them to obtain a group ROI. I ran isxavg-re-sess for each ROI but there is no registration file for mri_volcuster to reference. Have I hit a dead end? Does anyone know another way of creating a group ROI that I can apply the mri_volcluster command to? Thanks, Cameron ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] automatic processing
Hi Nic, in part it depends on where in the brain you are interested. The biggest need for manual intervention in reprocessing is to remove dura. This is mostly a problem near entorhinal cortex where the tentorium is tangent to the pial surface, and extremely difficult to distinguish from gray matter. Most of the brain is pretty accurate though, so if you have limited time you might run them all through automatically and do visual inspection/correction on regions where you find an effect to make sure that the effect is real and not an artifact of the processing. cheers, Bruce On Tue, 31 Oct 2006, Nicolas Cherbuin wrote: Hi, I have to process more than 500 good quality scans (1mm isotropic) for an epidemiological study and have limited time resources. Initial processing of 20 scans seems promising but I am new to freesurfer and therefore I am not quite sure how significant small defects might be in the big picture (where they will be averaged over a large number of subjects). I would be interested to hear the experience of others in using autoreconall for processing most scans and only reprocessing a small portion of scans with obvious substantial defects (mostly on the inflated surface). With good quality scans would most people reprocess most scans? Thanks for sharing your experiences. Nic ___ 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] mri_convert options
Hi, Currently we've been converting from .img to .mgz format using the following syntax: mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz s1501p.img mri/orig/001.mgz It came to my attention today that the values we used for TI, TE, and TR are all actually in ms, and correspond to the Siemen's Vision use of the terms TI and TR for the MRPAGE sequence. This is quite different from how TI and TR are used for the MPRAGE sequence on the Symphony, Sonata, and Trio Siemens platform. Furthermore, we have actually been applying these values to Vision FLASH data as well, for which TI is irrelevant, and the TR and flip were different. Basically, we have just been confused in our use of mri_convert. So, this raises a couple questions: 1) Are the TI, TE, TR and flip parameters important to mri_convert? How are they used? Are they used in any manner in the subsequent Freesurfer processing stream? We wonder if they are not important, since the current documention lists TR as an option, but doesn't mention TI, TE, or flip as options. 2) If these parameters are important in some manner how would the use of such grossly incorrect values affect the results? So basically, we are wondering what parameters, if any, are truly necessary as part of mri_convert? And do we (gasp) need to consider rerunning the stream from stage 1... Thanks! Derin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert options
Hi Derin, we keep the parameters around, but don't use them in the standard recon stream, so it shouldn't matter. cheers, Bruce On Tue, 31 Oct 2006, Derin Cobia wrote: Hi, Currently we've been converting from .img to .mgz format using the following syntax: mri_convert -TI 20 -te 4 -tr 9.7 -flip_angle 0.174532925199433 -ot mgz s1501p.img mri/orig/001.mgz It came to my attention today that the values we used for TI, TE, and TR are all actually in ms, and correspond to the Siemen's Vision use of the terms TI and TR for the MRPAGE sequence. This is quite different from how TI and TR are used for the MPRAGE sequence on the Symphony, Sonata, and Trio Siemens platform. Furthermore, we have actually been applying these values to Vision FLASH data as well, for which TI is irrelevant, and the TR and flip were different. Basically, we have just been confused in our use of mri_convert. So, this raises a couple questions: 1) Are the TI, TE, TR and flip parameters important to mri_convert? How are they used? Are they used in any manner in the subsequent Freesurfer processing stream? We wonder if they are not important, since the current documention lists TR as an option, but doesn't mention TI, TE, or flip as options. 2) If these parameters are important in some manner how would the use of such grossly incorrect values affect the results? So basically, we are wondering what parameters, if any, are truly necessary as part of mri_convert? And do we (gasp) need to consider rerunning the stream from stage 1... Thanks! Derin ___ 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] mris_anatomical_stats error
The problem is that this is being done an the average subject, which does not have a wm.mgz file. Should be easy to fix. Johannes, can you send your cmd line? doug Nick Schmansky wrote: Johannes, wm.mgz is produced in the -autorecon2 stage of recon-all. A handy table to consult is: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable or http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm Nick On Tue, 2006-10-31 at 11:49 +, Johannes Klein wrote: Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all autorecon2 error.
Hello, I ran autorecon1 this step worked fine. The transform obtained from this step looked good. When I run autorecon2, I get a segmentation fault error. Can anybody tell me whats wrong. Thanks a whole bunch. Error: Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux WM removal version #- [EMAIL PROTECTED] EM Registration Tue Oct 31 14:32:46 CST 2006 /usr/pubsw/freesurfer/subjects/sub02/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/pubsw/freesurfer/average/RB_all _2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/pubsw/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 31 14:32:57 CST 2006 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all autorecon2 error.
Mithra, Confirm that your skull-stripped volume (brainmask.mgz) shows just brain w/o skull, and that is has the cerebellum intact. You could also send me the brainmask.mgz and nu.mgz files, and i can have a look. If you want to do that, use the filedrop to upload those files to me: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Tue, 2006-10-31 at 14:47 -0600, Mithra wrote: Hello, I ran autorecon1 this step worked fine. The transform obtained from this step looked good. When I run autorecon2, I get a segmentation fault error. Can anybody tell me whats wrong. Thanks a whole bunch. Error: Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux WM removal version #- [EMAIL PROTECTED] EM Registration Tue Oct 31 14:32:46 CST 2006 /usr/pubsw/freesurfer/subjects/sub02/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/pubsw/freesurfer/average/RB_all _2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/pubsw/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 31 14:32:57 CST 2006 ___ 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
