Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

Fwd: Talairach Positioning in Horizontal View
by Peter Boulos 11 Jun '13

11 Jun '13

I am very new to the software and have just begun assessing Talairach outputs for my subjects. I am confused in that I cannot seem to find a balance I am happy with between positioning of the green lines in both the horizontal and sagittal views for multiple subjects. I opened the talairach output with the following command (tkregister2 --mgz --s SUBJID --fstal --surf orig) and everything looked perfectly aligned for all the subjects I have tried in both the coronal and sagittal views but in the horizontal view the green lines went well off the back of the brain. I have attached a screenshot. I tried to translate the brain but that did not seem to solve my issue and I realized I needed to scale the length of the brain. When I did that I was more pleased with the outcome but the corpus callosum did not match up nearly as well after I did that (second attached screenshot) and that was the primary landmark I was using to pass my images in terms of talairach output assessment. Do you have any advice for me? Peter

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Re: [Freesurfer] Problem after installation of the newest security updates for MacOSX
by Jürgen Hänggi 11 Jun '13

11 Jun '13

Hi Zeke As suggested, I deleted the /opt/X11 directory and reinstalled Xquartz and everything works fine again. Thanks a lot Cheers Jürgen On [DATE], "Z K" <[ADDRESS]> wrote: > Jurgen, this is odd. I have never seen an error from X11/XQuartz on Macs > complaining about version numbers... > > Are you saying everything worked fine before the security updates? And > then immediately afterward the updates tkmedit stopped working? If so, > my suggestion would be to delete the /opt/X11 directory and reinstall > XQuartz from this link: > > http://xquartz.macosforge.org/landing/ > > -Zeke > > On 06/11/2013 12:56 PM, Jürgen Hänggi wrote: >> Hi Zeke >> >> Here ls -l in /usr/ >> >> lrwxr-xr-x 1 root wheel 8 Mar 27 10:54 X11 -> /opt/X11 >> lrwxr-xr-x 1 root wheel 8 Mar 27 10:54 X11R6 -> /opt/X11 >> drwxr-xr-x 1091 root wheel 37094 Jun 11 10:59 bin >> drwxr-xr-x 4 root wheel 136 Oct 24 2010 etc >> drwxr-xr-x 271 root wheel 9214 Apr 26 2012 include >> drwxr-xr-x 387 root wheel 13158 Jun 11 10:59 lib >> drwxr-xr-x 111 root wheel 3774 Jun 11 10:59 libexec >> drwxrwxr-x 7 root admin 238 Dec 15 2010 llvm-gcc-4.2 >> drwxr-xr-x 10 root wheel 340 Jan 22 10:28 local >> drwxr-xr-x 237 root wheel 8058 Jun 11 10:59 sbin >> drwxr-xr-x 74 root wheel 2516 Apr 24 09:17 share >> drwxr-xr-x 4 root wheel 136 Dec 14 2009 standalone >> >> >> ls -l in /opt/ >> >> total 0 >> drwxr-xr-x 8 root wheel 272 Sep 28 2012 X11 >> >> Thanks in advance >> Regards >> Jürgen >> >> On [DATE], "Z K" <[ADDRESS]> wrote: >> >>> Hello Jurge, >>> >>> Can you please type "ls -l" in the /usr directory and "ls -l" in the >>> /opt directory and email me the output? >>> >>> -Zeke >>> >>> On 06/11/2013 08:51 AM, Jürgen Hänggi wrote: >>>> Dear FS experts >>>> >>>> After the installation of the newest Mac OS X security updates, the >>>> following error occurred: >>>> >>>> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] >>>> juergenhaenggi% >>>> tksurfer bert lh pial >>>> dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib >>>> Referenced from: /usr/X11/lib/libGL.1.dylib >>>> Reason: Incompatible library version: libGL.1.dylib requires version >>>> 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 >>>> Trace/BPT trap >>>> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] >>>> juergenhaenggi% >>>> >>>> >>>> Any idea to fix it easily is highly appreciated. >>>> >>>> Cheers >>>> Jürgen Hänggi >>>> >>>> --------------------------------------------------------------------------->>>> - >>>> Jürgen Hänggi, Ph.D. >>>> Division Neuropsychology >>>> Institute of Psychology >>>> University of Zurich >>>> Binzmuehlestrasse 14, PO Box 25 >>>> 8050 Zurich, Switzerland >>>> 0041 44 635 73 97 (phone office) >>>> 0041 76 445 86 84 (phone mobile) >>>> 0041 44 635 74 09 (fax office) >>>> BIN 4.D.04 (office room number) >>>> j.haenggi[at]psychologie.uzh.ch (email) >>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>> http://www.juergenhaenggi.ch (private website) >>>> >>>> This e-mail (and any attachment/s) contains confidential and/or privileged >>>> information. If you are not the intended recipient (or have received this >>>> e-mail in error) please notify the sender immediately and destroy this >>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>> material in this e-mail is strictly forbidden. >>>> --------------------------------------------------------------------------->>>> - >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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. >>> >> >> >> ---------------------------------------------------------------------------- >> Jürgen Hänggi, Ph.D. >> Division Neuropsychology >> Institute of Psychology >> University of Zurich >> Binzmuehlestrasse 14, PO Box 25 >> 8050 Zurich, Switzerland >> 0041 44 635 73 97 (phone office) >> 0041 76 445 86 84 (phone mobile) >> 0041 44 635 74 09 (fax office) >> BIN 4.D.04 (office room number) >> j.haenggi[at]psychologie.uzh.ch (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> >> This e-mail (and any attachment/s) contains confidential and/or privileged >> information. If you are not the intended recipient (or have received this >> e-mail in error) please notify the sender immediately and destroy this >> e-mail. Any unauthorised copying, disclosure or distribution of the >> material in this e-mail is strictly forbidden. >> ---------------------------------------------------------------------------- >> >> >> >> >> ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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importing my data
by clelia pellicano 11 Jun '13

11 Jun '13

Dear all, I'm trying to import my data in Freesurfer. I have it on a folder on my desktop. I set my SUBJECTS_DIR variable to my subjects directory (other folder on my desktop). When I run recon-all -i paths_to_myimputfiles -subjid my_sub_name, I got: [cpellica@wmen-ps2208 freesurfer]$ recon-all -i /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm -subjid 001 ERROR: cannot find /home/cpellica/Desktop/MRIs%201-5/001/IM-0003-0001.dcm Linux wmen-ps2208 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed May 15 10:48:38 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Tue Jun 11 17:24:51 BST 2013 I don't understand why it is not finding my data since they are on my desktop. Could you help me? Thanks C.

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Re: [Freesurfer] tkmedit on ssh remote machine error
by Jon Wieser 11 Jun '13

11 Jun '13

hi Zeke, were you able to find a solution to my problem with running tkmedit on a remote machine? thanks Jon ----- Original Message ----- From: "Z K" <zkaufman(a)nmr.mgh.harvard.edu> To: "Jon Wieser" <wieser(a)uwm.edu> Sent: Thursday, May 30, 2013 1:42:41 PM Subject: Re: [Freesurfer] tkmedit on ssh remote machine error Hmm that is a very strange error you are encountering. Im trying to duplicate the issue on my end. I only have one Mac 10.6 and one Mac 10.7 machine but Ill let you know what I find and hopefully I can come up with a solution. -Zeke On 05/30/2013 02:37 PM, Jon Wieser wrote: > both machines have Mac OS X 10.6.8 > > the tkmedit works fine when not logged in remotely > there is no error and the brain image is there > Jon > > ----- Original Message ----- > From: "Z K" <zkaufman(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Thursday, May 30, 2013 12:16:55 PM > Subject: Re: [Freesurfer] tkmedit on ssh remote machine error > > Jon, > > I have not seen or heard of this error before... are both machines Mac > OSX 10.6.8? Also, will the same command will produce a brain image when > not logged in remotely? > > -Zeke > > On 05/30/2013 12:43 PM, Jon Wieser wrote: >> >> hi freesurfer folks >> >> I'm ssh'ing to from one MAc to another >> X11 is on both machines >> MAC OS X 10.6.8 >> >> When I start TKmedit with: (freesurfer files are in the freesurfer directory) >> >> tkmedit freesurfer brainmask.mgz -aux T1.mgz >> >> >> I get the errors: >> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 >> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. >> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d >> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: unknown error code: invalid drawable >> error: xp_attach_gl_context returned: 2 >> >> >> >> tkmedit GUI opens and the image window opens, but the image window is blank (white) , (no image of the brain) >> >> >> >> >> i have set X11forwarding to yes in the /etc/sshd_config file >> so xeyes works ok remotely >> Jon >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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License problem
by Claus Svarer 11 Jun '13

11 Jun '13

Hi We have just updated one of our Linux servers from OpenSuse v. 12.1 to 12.3. After the update we get the following license error message for some of the freesurfer commands: csvarer@hevesy:/usr/local/nru/freesurfer> tkmedit -help -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/nru/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- W have another server still running the older OpenSuse version and there it works without any problems. There hasn't been done any changes to the freesurfer installation directory and it is the same shared NFS mounted directory at both servers. Please help us finding out how to correct this problem so we can use Freesurfer again. Thanks for the help Claus Svarer

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autorecon3 error
by Gabriel Gonzalez Escamilla 11 Jun '13

11 Jun '13

Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name looks different but is exactly the same subject), with the command to fix the ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but now is encountering the following error, this time seems to be something with the seg.mgz. #----------------------------------------- #@# Cortical Parc lh Thu Jun 6 17:01:26 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 qsm1_17 lh ../surf/lh.sphere.reg /root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ f[113526]->v[1] = 539832625 - out of range! reading atlas from /root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17 exited with ERRORS at Thu Jun 6 17:01:33 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas how to fix this? Bests, Gabriel

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Faculty Members and Postdoctoral Fellows in Brainnetome
by Yong Liu 11 Jun '13

11 Jun '13

Dear all, *Faculty Members and Postdoctoral Fellows in Brainnetome* * * Please find the details below: http://www.brainnetome.org/en/job PS. If you also go to attend the OHBM 2013 in Seattle, you can find us at booth 218 at the exhibitor region. Date a meeting time by email to brainnetome(a)gmail.com would be appreciated. *Faculty Members and Postdoctoral Fellows in Brainnetome* Brainnetome Center (www.brainnetome.org) and National Laboratory of Pattern Recognition, Institute of Automation of Chinese Academy of Sciences (CASIA), seeks several postdoctoral fellows and faculty members from assistant to full professor levels in neuroimaging and brainnetome. We specifically seek individuals with expertise in one of the following fields: magnetic resonance imaging, especially diffusion MRI and functional MRI, optical imaging, medical image processing and analysis, pattern recognition. Brainnetome Center at CASIA has established its international reputation in neuroimaging, brain networks, and their applications in brain diseases. It also has established strong collaboration networks with a number of prestigious national and international laboratories and hospitals through Brainnetome consortium (www.brainnetome.org ). The faculty members have chance to work in an Australian partner laboratory on Neuroimaging and Brainnetome at Queensland Brain Institute (www.qbi.uq.edu.au ). * * *Minimum Qualifications:* The position requires a Ph.D. degree in brain imaging, neuroscience, cognitive neuroscience, neuroanatomy, psychiatry and neurology or a related field. Experience in* brain imaging such as MRI/EEG/MEG/fNIRS*, fluent verbal and written communication skills in English are also required, for the candidates with PhD in engineering, strong computer programming skills in Matlab and/or C++ language is a must. *Preferred Qualifications:* Good experience and background knowledge in the research focus areas: brain imaging. [image: *] Ability to work independently and in a team. [image: *] Capability to design and perform experimental plans; knowledge with sensor systems; strong interest to learn, understand statistical analysis procedures and interpret data. [image: *] Sufficient interpersonal skills in dealing with students (graduate and undergraduate), university personnel and other related groups. [image: *] Self-motivation and creativity are highly desirable. *Application Materials:* Applicants should send an e-mail attachment of a cover letter with a brief summary of *research background*, *curriculum vita *, *statement of research goals*, and *contact information of at least three referees* to brainnetome(a)gmail.com. > Best wishes. > -------------------------------------------------------------------- > Liu Yong > Brainnetome Center > National Laboratory of Pattern Recognition (NLPR) > Institute of Automation, Chinese Academy of Sciences (CASIA) > www.brainnetome.org/yongliu > >

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vertices don't match
by Darren Gitelman 11 Jun '13

11 Jun '13

Dear List I am adding to the post on this error from yesterday regarding problems with running qcache. I know this has been posted to the list before, but the suggested fixes and checks don't fix the problem. See the error below (ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file) 1) Running recon-all -s <subjid> -vno-check does not find any problems. It says everything is verified and checks out ok. 2) Running recon-all -s <subjid> -make all returns the message: make: Nothing to be done for `all'. But when I try recon-all -s <subjid> -qcache I get the error on this and several other subjects, but not all subjects. Checking the modification times on some files it looks like the thickness file came after the curv file. [drg@quser03 surf]$ ll *.thickness -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:54 lh.thickness -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:10 rh.thickness [drg@quser03 surf]$ ll *.curv -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:45 lh.curv -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:01 rh.curv Any suggestions for fixing the qcache error would be appreciated. Darren -- --------------------------------------------------- #@# 1/1 3300 Wed Sep 19 13:52:44 CDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.6938/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.volume --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 3300 srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.6938/3300.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg Loading source data Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.volume ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3300 exited with ERRORS at Wed Sep 19 13:52:46 CDT 2012 -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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Problem after installation of the newest security updates for MacOSX
by Jürgen Hänggi 11 Jun '13

11 Jun '13

Dear FS experts After the installation of the newest Mac OS X security updates, the following error occurred: [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% tksurfer bert lh pial dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib Referenced from: /usr/X11/lib/libGL.1.dylib Reason: Incompatible library version: libGL.1.dylib requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 Trace/BPT trap [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% Any idea to fix it easily is highly appreciated. Cheers Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Re: [Freesurfer] Fwd: problem about file format
by huang bs 10 Jun '13

10 Jun '13

Thanks. I now find that, when I copy (or cut) the re-con folder from SUBJECTS_DIR to the shared folder (with XP), it seems that no changes happen - the file format remains the same. But if I restart the Xubuntu, and copy (or cut) this re-con folder from shared folder back to SUBJECTS_DIR, then the file format automatically changes and the re-con results can not be recognized. This is quite odd... I have to move the re-con results to the shared folder because in the Xubuntu FSV5.1.0 virtual hard disk the space is only 10G. So to me now, if I can expand the disk to, say for example, 50G, then at least I don't need to move the re-con results but just save them in SUBJECTS_DIR, and so the file formats will not change. On 7 June 2013 20:38, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > I meant for you to cat them and put them in the text of the email. > Something is badly wrong with them. They should be simple text files with a > 4x3 matrix and a couple of header lines. Not sure what happened but you > will need to delete them and regenerat them > > cheers > Bruce > > On Fri, 7 Jun 2013, huang bs wrote: > > Seems that I can not post the attachements... >> >> ---------- Forwarded message ---------- >> From: huang bs <huangbs(a)gmail.com> >> Date: 5 June 2013 22:51 >> Subject: Re: [Freesurfer] problem about file format >> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> >> >> Dear Bruce, >> >> Yes, sure. I printed the screens and showed you two cases. One can be >> recognized, the other one can not. Please find attached for the six >> figures. I also attached the files talairach.xfm and >> talairach.auto.xfm for the subject linziyi. >> >> One more question: how to extend the hard disk space in Xubuntu, >> especially in the folder /home/virtualuser/freesurfer/**subjects ? If >> possible, I don't want to move the data to the shared folder and then >> face such problem. >> >> Sorry I am quite new to Linux so some questions may be quite stupid. >> >> Thank you very much! >> >> On 05/06/2013, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> > no, I haven't seen that before. Can you cat >> > /home/virtualuser/freesurfer/**subjects/linziyi/mri/** >> transforms/talairach.xfm >> > >> > and send us the contents? >> > >> > Bruce >> > On >> > Wed, 5 Jun 2013, huang bs wrote: >> > >> >> Hi All, >> >> >> >> Sorry to take up your time. >> >> >> >> My freesurfer now can not recognize the re-con files (such as the .mgz >> >> files, or .xfm files, etc). >> >> For example, I run this command to check the talairach transform: >> >> tkregister2 --mgz --s linziyi --fstal --surf orig >> >> The terminal then reports: >> >> ERROR: >> >> >> /home/virtualuser/freesurfer/**subjects/linziyi/mri/** >> transforms/talairach.xfm >> >> does not start as 'MNI Transform File >> >> This file talairach.xfm does exist. But under Xubuntu, this >> >> talairach.auto.xfm file has a different icon and appears as "executable >> >> file". That's quite strange because I did not make such change to it. >> >> >> >> These files did work when I just finished the re-con. But afer the >> re-con, >> >> I >> >> moved them from the freesurfer subjects folder to the shared folder >> >> (shard >> >> with XP), because the freesurfer subjects folder has a limited space. >> >> After >> >> a few days, I moved them back to the subjects folder for doing the >> >> statistical analysis, and then I have such problem. Even under the >> shared >> >> folder, the files can not be read either. >> >> >> >> For the cases I just re-con, since they are not moved to elsewhere, >> >> everything seems OK. >> >> >> >> Have you guys had such problem before and how to fix it? Thanks! >> >> >> >> -- >> >> Best Regards, >> >> >> >> B Huang >> >> >> >> >> >> >> > >> > >> > 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. >> > >> >> >> -- >> Best Regards, >> >> Bingsheng Huang >> Postdoctoral Research Fellow >> Diagnostic Radiology, The University of Hong Kong >> >> >> >> -- >> Best Regards, >> >> Bingsheng Huang >> Postdoctoral Research Fellow >> Diagnostic Radiology, The University of Hong Kong >> >> -- Best Regards, Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong

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