[Freesurfer] Bus error still when trying to launch tksurfer
Hello again Bruce, Thanks so much for your reply. I tried uninstalling XQuartz completely and reinstalling it, and I`m still getting the bus error. I have XQuartz`s newest version (2.7.7) that was launched in August of this year installed and it works with Macs 10.6 and newer. My Mac environment is such: Mac OS X Snow Leopard 10.6.8 Memory: 4GB 1067 MHz DDR3 Model Name:iMac Model Identifier:iMac10,1 Processor Name:Intel Core 2 Duo Processor Speed:3.06 GHz Number Of Processors:1 Total Number Of Cores:2 L2 Cache:3 MB Memory:4 GB Bus Speed:1.07 GHz Boot ROM Version:IM101.00CC.B00 Any further ideas what might be going on? Do I need a newer version of OS X in order to use Freesurfer optimally? Thank you so much again for your time! All the best, Claire On Mon, Oct 20, 2014 at 6:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. GLM contrast vector for continuous variable interaction (Bronwyn Overs) 2. Bus error when trying to launch tksurfer (Claire Morley) 3. Re: Bus error when trying to launch tksurfer (J?rgen H?nggi) 4. Re: Bus error when trying to launch tksurfer (Bruce Fischl) 5. Do not have 'recon edit' button! Please help! (Smaragdi A.) 6. Re: Do not have 'recon edit' button! Please help! (Bruce Fischl) 7. Re: Do not have 'recon edit' button! Please help! (Smaragdi A.) 8. unpacksdcmdir (Alshikho, Mohamad J.) 9. Re: unpacksdcmdir (Shantanu Ghosh) 10. Re: unpacksdcmdir (Douglas N Greve) 11. Re: GLM contrast vector for continuous variable interaction (Douglas N Greve) -- Message: 1 Date: Mon, 20 Oct 2014 09:33:13 +1100 From: Bronwyn Overs b.ov...@neura.edu.au Subject: [Freesurfer] GLM contrast vector for continuous variable interaction To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 54443c29.9000...@neura.edu.au Content-Type: text/plain; charset=iso-8859-1 Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three continuous variables (age, prs, sles). My fsgd file looks like this: GroupDescriptorFile 1 Title GLM_sles-group-gender-age Class genderMale-groupControl Class genderFemale-groupControl Class genderMale-groupAtRisk Class genderFemale-groupAtRisk Variables age prs sles Input ID_001 genderFemale-groupAtRisk 20 21 96 Input ID_002 genderFemale-groupControl 21 13 79 ... I want to test for an interaction between prs and sles, while controlling for age, gender, and group. Can you tell me if the following contrast vector will correctly test for this interaction: 000000000 0 0 0 0.5 0.50.50.5 000000000.50.50.50.5 0 0 0 0 -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0001.html -- next part -- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 13292 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0004.png -- next part -- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 1233 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0005.png -- next part -- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 834 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0006.png -- next part
Re: [Freesurfer] Bus error still when trying to launch tksurfer
Hello Claire, Sorry this has been such a pain. There has been some reports that the newer versions of XQuartz may have broken some of the freesurfer GUIs. Could you please try deleting XQuartz again an resinstalling XQuartz version 2.7.5. You can download it from this page: http://xquartz.macosforge.org/trac/wiki/Releases Then try again. Let me know how it goes. And please send me an exact copy of any error that may be produced. Thanks. -Zeke On 10/23/2014 06:21 AM, Claire Morley wrote: Hello again Bruce, Thanks so much for your reply. I tried uninstalling XQuartz completely and reinstalling it, and I`m still getting the bus error. I have XQuartz`s newest version (2.7.7) that was launched in August of this year installed and it works with Macs 10.6 and newer. My Mac environment is such: Mac OS X Snow Leopard 10.6.8 Memory: 4GB 1067 MHz DDR3 Model Name:iMac Model Identifier:iMac10,1 Processor Name:Intel Core 2 Duo Processor Speed:3.06 GHz Number Of Processors:1 Total Number Of Cores:2 L2 Cache:3 MB Memory:4 GB Bus Speed:1.07 GHz Boot ROM Version:IM101.00CC.B00 Any further ideas what might be going on? Do I need a newer version of OS X in order to use Freesurfer optimally? Thank you so much again for your time! All the best, Claire On Mon, Oct 20, 2014 at 6:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu mailto:freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. GLM contrast vector for continuous variable interaction (Bronwyn Overs) 2. Bus error when trying to launch tksurfer (Claire Morley) 3. Re: Bus error when trying to launch tksurfer (J?rgen H?nggi) 4. Re: Bus error when trying to launch tksurfer (Bruce Fischl) 5. Do not have 'recon edit' button! Please help! (Smaragdi A.) 6. Re: Do not have 'recon edit' button! Please help! (Bruce Fischl) 7. Re: Do not have 'recon edit' button! Please help! (Smaragdi A.) 8. unpacksdcmdir (Alshikho, Mohamad J.) 9. Re: unpacksdcmdir (Shantanu Ghosh) 10. Re: unpacksdcmdir (Douglas N Greve) 11. Re: GLM contrast vector for continuous variable interaction (Douglas N Greve) -- Message: 1 Date: Mon, 20 Oct 2014 09:33:13 +1100 From: Bronwyn Overs b.ov...@neura.edu.au mailto:b.ov...@neura.edu.au Subject: [Freesurfer] GLM contrast vector for continuous variable interaction To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 54443c29.9000...@neura.edu.au mailto:54443c29.9000...@neura.edu.au Content-Type: text/plain; charset=iso-8859-1 Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three continuous variables (age, prs, sles). My fsgd file looks like this: GroupDescriptorFile 1 Title GLM_sles-group-gender-age Class genderMale-groupControl Class genderFemale-groupControl Class genderMale-groupAtRisk Class genderFemale-groupAtRisk Variables age prs sles Input ID_001 genderFemale-groupAtRisk 20 21 96 Input ID_002 genderFemale-groupControl 21 13 79 ... I want to test for an interaction between prs and sles, while controlling for age, gender, and group. Can you tell me if the following contrast vector will correctly test for this interaction: 000000000 0 0 0 0.5 0.50.50.5 000000000.50.50.50.5 0 0 0 0 -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook
