Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

statical question recon-all -qcache -s (subject) ?
by Knut J Bjuland 14 Sep '11

14 Sep '11

Hi Can I use a different version of Freesurfer to run recon-all -qcache -s (subject) than the version used for recon-all -all -s (subject)? Knut J

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.img extension read as analyze even though hdr says nifti1
by Satrajit Ghosh 14 Sep '11

14 Sep '11

hi all, when a .img extension file is passed to freesurfer routines, it is read in as analyze even if the header says it's a nifti image. we have observed that this causes a left-right flip in some cases. since a .img cannot exist without a header to be meaningful, shouldn't the appropriate type be detected from the header? also it would be good to know if this behavior is consistent across all of freesurfer or restricted to certain binaries. see below for mri_info output cheers, satra $ mri_info con_0001.img Volume information for con_0001.img type: analyze4d dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 78.0000 0.0000 2.0000 0.0000 -112.0000 0.0000 0.0000 2.0000 -50.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 0.0000 0.0000 39.0000 -0.0000 0.5000 -0.0000 56.0000 -0.0000 -0.0000 0.5000 25.0000 0.0000 0.0000 0.0000 1.0000 $ mri_info con_0001.hdr Volume information for con_0001.hdr type: nifti1 dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 78.0000 0.0000 2.0000 0.0000 -112.0000 0.0000 0.0000 2.0000 -50.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 0.0000 0.0000 39.0000 -0.0000 0.5000 -0.0000 56.0000 -0.0000 -0.0000 0.5000 25.0000 0.0000 0.0000 0.0000 1.0000

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flipped orientation in tksurfer and tkmedit
by Ilana Hairston 14 Sep '11

14 Sep '11

Hi there, We recently had a problem that tksurfer and tkmedit were flipped relative to each other. Basically, when saving a point in the left hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit. Any ideas how this could have happened? Thanks ilana -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

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mean and stdev group-wise
by Tetiana Dadakova 14 Sep '11

14 Sep '11

Dear list, I would like to calculate mean and stdev of thickness group-wise. Could you please give me a hint how to do it? Thank you, Tanja.

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tksurfer sliver problem
by Michael Harms 14 Sep '11

14 Sep '11

Hi guys, So, the infamous tksurfer "sliver" display problem has reared its ugly head on some of the systems that I'm accessing, but in a manner that I can't make any sense of across the systems. Machine 1: CentOS 5.5, 64 bit, FS versions 4.5.0 and 5.0.0 installed Sliver problem is present for v4.5.0, but not 5.0.0 Machine 2: RHEL Server 5.7, 64 bit, FS versions 4.5.0, 5.0.0, and 5.1.0 installed. Sliver problem is present for all 3 FS versions. For both machines, I'm viewing the results in a VNC server, and 'glxgears' works fine in each. The results of 'glxinfo' in a terminal within the VNC Server on each machine indicates that the same rendering is being used on each. i.e,. direct rendering: No OpenGL renderer string: Mesa GLX Indirect OpenGL version string: 1.2 (1.5 Mesa 6.5.1) What I find particularly puzzling is that tksurfer works fine on FS v5.0.0 on Machine 1, but not FS 4.5.0 on the same machine. Yet the sliver problem is present for v5.0.0 on Machine 2, indicating that it isn't simply an FS version issue either. I was wondering if the above behavior makes sense to someone, so that I can have something more concrete to take to the admins of each system. thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Re: [Freesurfer] Reference
by Louis Nicholas Vinke 14 Sep '11

14 Sep '11

Hi, On the pages below there are some links to articles describing how the FS cortical and sub-cortical atlases were created. https://surfer.nmr.mgh.harvard.edu/fswiki/SubcorticalSegmentation https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation -Louis On Wed, 14 Sep 2011, Anne Bailey wrote: > Hi, > > > I am a PhD student currently using Freesurfer for analyses and I was > wondering if you could provide me with the reference for the original brains > that were used as the basis for the automatic parcellation of cortical and > subcortical structures. > > If I have contacted the wrong person, could you please forward my inquiry to > someone who can point me to this information? > > Thank you! > > Anne Bailey > >

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Segmentation fault during -autorecon1
by Palzes, Vanessa 14 Sep '11

14 Sep '11

Hello, I am continuously getting a "Segmentation fault" error during -autorecon1 when it's running mri_binarize. I have been running Freesurfer on a Mac, but now I am trying to implement it using Linux. I am running this version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on Linux 2.6.9-89.0.20.ELsmp x86_64. I this a memory issue, or can there be another explanation? I've tried multiple times and with different subjects. Here is my log output: home/harshad/data5/Freesurfer/PATHD/process/P2608/mri/] [2011-09-13 16:08:43] running: /usr/local/freesurfer//mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.31037/nu1.mnc ./tmp.mri_nu_correct.mni.31037/1//template.mnc Transforming slices:................................................................. .....................Done Transforming slices:................................................................. .....................Done mri_binarize --i ./tmp.mri_nu_correct.mni.31037/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31037/ones.mgz Segmentation fault Linux vhasfcapp21 2.6.9-89.0.20.ELsmp #1 SMP Mon Jan 18 12:19:33 EST 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s P2608 exited with ERRORS at Tue Sep 13 16:10:11 PDT 2011 Any help would be greatly appreciated. Thanks, Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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Re: [Freesurfer] Recon-all Error: _FindFacePath
by Daniel Ferreira Padilla 14 Sep '11

14 Sep '11

Hi Fatima, I used the Martinos Center File drop ( <https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html) Daniel 2011/9/14 Ahmed, F, Me <fahmed(a)sun.ac.za> <fahmed(a)sun.ac.za> Hi Daniel, How did you send your scans to Bruce? Thanks, Fatima From: <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto: <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu]On Behalf Of Daniel Ferreira Padilla Sent: 14 September 2011 09:19 To: 'Khoa Nguyen' Cc: <mailto:freesurfer@nmr.mgh.harvard.edu> freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all Error: _FindFacePath Hello Khoa, Thank you very much for your suggestion. I checked both brainmask.mgz and wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope something can be done. Cheers! Daniel Ferreira - Ocultar texto citado - 2011/9/13 Khoa Nguyen < <mailto:khoa@nmr.mgh.harvard.edu> khoa(a)nmr.mgh.harvard.edu> Hi Daniel, Usually when I get the FindFacePath error, the wm.mgz is very bad. You can try placing control points on the wm and rerun -autorecon2 and -autorecon3. That worked for me. -Khoa On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote: Dear Bruce and experts, I would really appreciate if you can help me with my scans. I have successfully processed all my sample but got this same FindFacePath error with 2 subjects. I checked the brainmask and wm files and for me they look ok. So I do not know how can I fix this error. Thank you very much in advance ERROR: _FindFacePath: could not find path! Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC 2011 x86_64 GNU/Linux recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011 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> 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.

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Re: [Freesurfer] Recon-all Error: _FindFacePath
by Daniel Ferreira Padilla 14 Sep '11

14 Sep '11

Hello Khoa, Thank you very much for your suggestion. I checked both brainmask.mgz and wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope something can be done. Cheers! Daniel Ferreira 2011/9/13 Khoa Nguyen <khoa(a)nmr.mgh.harvard.edu> Hi Daniel, Usually when I get the FindFacePath error, the wm.mgz is very bad. You can try placing control points on the wm and rerun -autorecon2 and -autorecon3. That worked for me. -Khoa On Sat, 10 Sep 2011, Daniel Ferreira Padilla wrote: Dear Bruce and experts, I would really appreciate if you can help me with my scans. I have successfully processed all my sample but got this same FindFacePath error with 2 subjects. I checked the brainmask and wm files and for me they look ok. So I do not know how can I fix this error. Thank you very much in advance ERROR: _FindFacePath: could not find path! Linux neuroimagen 2.6.35-30-generic #54-Ubuntu SMP Tue Jun 7 18:41:54 UTC 2011 x86_64 GNU/Linux recon-all -s GJ169_3D exited with ERRORS at Sat Aug 20 07:53:56 WEST 2011 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> 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.

2 1

Longitudinal 5.0 with data from earlier version
by Erica Griffith 13 Sep '11

13 Sep '11

Hi all, Does anyone have experience running a longitudinal analysis in version 5.0, using .mgz files generated from the last version of freesurfer? My understanding is that the only major differences between the previous and current versions were in the longitudinal stream. Any input would be appreciated! Thanks.

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