Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

How to set the -retinotopy number in mkanalysis-sess due to different cycle time in the eccen and polar
by yufeng huang 18 Apr '13

18 Apr '13

Dear Doug, I want you could give me some guidances with my retinotopic analysis. Eccen run: TR 2 Ncycles 6, 64 sec per cycle, all scan 384 sec. Polar run: TR 2, then follow Ncycles 10, 32 sec per cycle, all scan 320 sec. I write the rtopy.par: stimtype polar diretion neg ncycles 10 and stimtype eccen diretion pos ncycles 6 My question is: How to set the value of -retinotopy in the mkanalysis as the eccen value should be -retinotopic 64 while the polar value should be -retinotopic 32 in the mkanalysis-sess Thanks a lot! Yours Yufeng

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error while performing recon-all for multiple datasets
by Anupa AV 18 Apr '13

18 Apr '13

Dear All, I want to run recon-all for multiple subjects. I named my sbjects as SZ01.nii, SZ02.nii etc. After setting the cd and environmanet variable, I ran using following for loop: >for x in * > do >recon-all -i SZ*.nii -s $x -all >done I got the following error: WHAT MIGHT BE THE REASON FOR THE ERROR??? WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ01.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ02.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ03.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ04.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Thank you
by Valtina Pouegue 18 Apr '13

18 Apr '13

Hi everyone, I would just say you thank you for the help you give to Freesurfer users. I use Freesurfer for my school project and I ended yesterday. I didn't know anything about Linux before and before segmentation software of cortical surface. I don't think I would did an so great job without your help. Again, Thank you! And Good Luck !!! VP

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Autoreg-sess and mri_surf2vol
by Lucille Deroche 18 Apr '13

18 Apr '13

Hi, My name is Lucille and I'm really new with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum. For converting a surface in volume. I would like to use mri_surf2vol but for that I need a volume registration file . For creating that file, I would use autoreg-sess. In documentation, it is said that : 'The volume registration file contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume' My question is : what here, represent the anatomical reference ? The functionnal volume ? Secondly, for autoreg-sess, the arguments are the subject name and the subject directory. I think the registration I need to create must be between my 2 volumes, so should I use the subject name and subject directory for my 2 subjects ? Sorry,I am really messed... Cheers Lucille

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mri_segstats SNR calculation
by Jordi Delgado 18 Apr '13

18 Apr '13

Dear Freesurfers, After running the first tests of freesurfer 5.2, I found a file named $hemi.w-g.pct.stats on the stats folder. The last column of the file is a SNR calculation, i found on the help manual, that is required to add --snr to perform this calculation. I'm interested to know how this SNR is calculated. Is there any method or paper related? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

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Problems with Saving Segmentation
by iripp＠smail.uni-koeln.de 18 Apr '13

18 Apr '13

Hello, I have troubles with saving my files, after I did some segmentation changes. I think this could be related to a problem, which I have, when I load the brainmask: libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details. This is shown, but it would still be loading and open the brainmask (aseg). Can anyone help me with this problem? Thanks a lot, Isabelle Ripp

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recon-all -autorecon2 bug?
by Jitesh Joshi 18 Apr '13

18 Apr '13

Hi, I too am facing the same problem as mentioned by Miklos Argyelan: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html Jitesh

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Hippo-subfields
by Marcos Martins da Silva 17 Apr '13

17 Apr '13

Hi, all After running recon-all with -hippo-subfield several .mgz files are created. I could add each of those files as volumes in freeview , toggle " show as isosurface in 3D view" and select a different color for each kind of subfield and got the attached screenshots. They are very interesting but now I have some doubts. 1- How do I save the combined 3D view I got as a surface? 2-I know the hippo-subifields .mgz files are probability maps and if I guess right kvlQuantifyPosteriorProbabilityImages read these files to count how many voxels you have in each subfield. I also guess it count only the voxels with reasonable high probability to be part of each subfield. If so, what is the minimum value between 1 and 255 the program use to decide if a particular voxel is valid? 3- Is it possible to merge hippo-subfield .mgz files data and to generate a different segmentation like anterior (anterior quarter), body (the2 intermediate quarters) and posterior (posterior quarter). TY in advance

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hippo-subfields
by Marcos Martins da Silva 17 Apr '13

17 Apr '13

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Crash reports on several situations.
by Nate Lee 17 Apr '13

17 Apr '13

Hello everyone, I'm using Freesurfer from Texas Medical Center. I'm using an iMac, and am experiencing regular crashes during these several occasions: 1. Opening more than two volumes at once 2. When one volume and one surface is open and: a. switching back and forth between different exposé desktops b. opening up Internet or other files such as Excel c. right after I press "save" (the work is saved, thankfully) Is anyone else experiencing this as well? I make sure that none of the other programs or files are open when using freesurfer. Do you have any suggestions to avoid such crashes? Best regards, Nate

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