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: > > 0 0 0 0 0 0 0 0 0 0 0 0 0.5 > 0.5 0.5 0.5 > 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 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/neuraustralia>Follow NeuRA on facebook > <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe 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 -------------- > A non-text attachment was scrubbed... > Name: not available > Type: image/png > Size: 3983 bytes > Desc: not available > Url : > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0007.png > > ------------------------------ > > Message: 2 > Date: Mon, 20 Oct 2014 09:56:41 +0200 > From: Claire Morley <clairemorley2...@u.northwestern.edu > <mailto:clairemorley2...@u.northwestern.edu>> > Subject: [Freesurfer] Bus error when trying to launch tksurfer > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <CACxfM7pPmQNQks_guW+=-u4qj8mp6ddjsshfqjzvjnw+hjs...@mail.gmail.com > <mailto:u4qj8mp6ddjsshfqjzvjnw%2bhjs...@mail.gmail.com>> > Content-Type: text/plain; charset="utf-8" > > Good Morning, > I have now been able to get the testing command: tksurfer bert rh > pial to > run, but it stops midway and issues a bus error. Please see the > following > script: > > DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial > subject is bert > hemi is rh > surface is pial > surfer: current subjects dir: /Applications/freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /Users/dbmuser > checking for nofix files in 'pial' > Reading image info (/Applications/freesurfer/subjects/bert) > Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz > surfer: Reading header info from > /Applications/freesurfer/subjects/bert/mri/orig.mgz > surfer: vertices=133299, faces=266594 > surfer: single buffered window > surfer: tkoInitWindow(bert) > Bus error > > Any idea what might be going wrong? I really need to use tksurfer to > look > at cortical thickness in gyrification in ROIs. (Oh and before I did > this, I > did set the environment as normal). > > Thanks so much for your help! > Claire > > -- > > *We shall not cease from exploration. And the end of all our > exploring will > be to arrive where we started and know the place for the first time- > T.S. > Eliot* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/31619a03/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Mon, 20 Oct 2014 10:13:51 +0200 > From: J?rgen H?nggi <j.haen...@psychologie.uzh.ch > <mailto:j.haen...@psychologie.uzh.ch>> > Subject: Re: [Freesurfer] Bus error when trying to launch tksurfer > To: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <d06a906b.2dc75%j.haen...@psychologie.uzh.ch > <mailto:d06a906b.2dc75%25j.haen...@psychologie.uzh.ch>> > Content-Type: text/plain; charset="iso-8859-1" > > Daer Claire > > The bus error might be related to Xquartz. Installing Xquartz again > solved > the issue on most Intel-based Macs. > > Cheers > J?rgen > > > ---------------------------------------------------------------------------- > J?rgen H?nggi, 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 <http://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. > > ---------------------------------------------------------------------------- > > > Von: Claire Morley <clairemorley2...@u.northwestern.edu > <mailto:clairemorley2...@u.northwestern.edu>> > Antworten an: Freesurfer Mailinglist > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Datum: Montag, 20. Oktober 2014 09:56 > An: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Betreff: [Freesurfer] Bus error when trying to launch tksurfer > > Good Morning, > I have now been able to get the testing command: tksurfer bert rh > pial to > run, but it stops midway and issues a bus error. Please see the > following > script: > > DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial > subject is bert > hemi is rh > surface is pial > surfer: current subjects dir: /Applications/freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /Users/dbmuser > checking for nofix files in 'pial' > Reading image info (/Applications/freesurfer/subjects/bert) > Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz > surfer: Reading header info from > /Applications/freesurfer/subjects/bert/mri/orig.mgz > surfer: vertices=133299, faces=266594 > surfer: single buffered window > surfer: tkoInitWindow(bert) > Bus error > > Any idea what might be going wrong? I really need to use tksurfer to > look at > cortical thickness in gyrification in ROIs. (Oh and before I did > this, I did > set the environment as normal). > > Thanks so much for your help! > Claire > > -- > > We shall not cease from exploration. And the end of all our > exploring will > be to arrive where we started and know the place for the first time- > T.S. > Eliot > > > _______________________________________________ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/8c361fa7/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Mon, 20 Oct 2014 08:21:56 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Bus error when trying to launch tksurfer > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <alpine.lrh.2.03.1410200821380.27...@nmr.mgh.harvard.edu > <mailto:alpine.lrh.2.03.1410200821380.27...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="utf-8" > > Hi Claire > > what version are you using? And what is your hardware and software > environment? RAM, OS version, etc....? > Bruce > On Mon, 20 Oct 2014, Claire Morley > wrote: > > > Good Morning, > > I have now been able to get the testing command: tksurfer bert rh > pial to > > run, but it stops midway and issues a bus error. Please see the > following > > script: > > > > DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial > > subject is bert > > hemi??? is rh > > surface is pial > > surfer: current subjects dir: /Applications/freesurfer/subjects > > surfer: not in "scripts" dir ==> using cwd for session root > > surfer: session root data dir ($session) set to: > > surfer:???? /Users/dbmuser > > checking for nofix files in 'pial' > > Reading image info (/Applications/freesurfer/subjects/bert) > > Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz > > surfer: Reading header info from > > /Applications/freesurfer/subjects/bert/mri/orig.mgz > > surfer: vertices=133299, faces=266594 > > surfer: single buffered window > > surfer: tkoInitWindow(bert) > > Bus error > > > > Any idea what might be going wrong? I really need to use tksurfer > to look at > > cortical thickness in gyrification in ROIs. (Oh and before I did > this, I did > > set the environment as normal). > > > > Thanks so much for your help! > > Claire > > > > -- > > > > We shall not cease from exploration. And the end of all our > exploring will > > be to arrive where we started and know the place for the first > time- T.S. > > Eliot > > > > > > > > > > ------------------------------ > > Message: 5 > Date: Mon, 20 Oct 2014 13:16:31 +0000 > From: "Smaragdi A." <a.smara...@soton.ac.uk > <mailto:a.smara...@soton.ac.uk>> > Subject: [Freesurfer] Do not have 'recon edit' button! Please help! > To: "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <d06ac9be.416a%a.smara...@soton.ac.uk > <mailto:d06ac9be.416a%25a.smara...@soton.ac.uk>> > Content-Type: text/plain; charset="us-ascii" > > Dear mailing list, > > I am really stuck here.. Please can someone tell me why I cannot > find the recon edit button on freeview! > > I am not sure if the version of Freesurfer I have downloaded is old, > or I have > done something wrong, or I am just blind.. But I cannot find the > 'recon edit' > button in freeview (see attached screenshot). What am I not doing right? > > Many thanks, > > Areti > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Screen Shot 2014-10-14 at 13.22.42.png > Type: image/png > Size: 71321 bytes > Desc: Screen Shot 2014-10-14 at 13.22.42.png > Url : > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/4dbc998f/attachment-0001.png > > ------------------------------ > > Message: 6 > Date: Mon, 20 Oct 2014 09:24:42 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Do not have 'recon edit' button! Please > help! > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <alpine.lrh.2.03.1410200924350.27...@nmr.mgh.harvard.edu > <mailto:alpine.lrh.2.03.1410200924350.27...@nmr.mgh.harvard.edu>> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Areti > > what version of freeview are you using? > Bruce > On Mon, 20 Oct 2014, Smaragdi A. > wrote: > > > Dear mailing list, > > > > I am really stuck here.. Please can someone tell me why I cannot > find the recon edit button on freeview! > > > > I am not sure if the version of Freesurfer I have downloaded is > old, or I have > > done something wrong, or I am just blind.. But I cannot find the > 'recon edit' > > button in freeview (see attached screenshot). What am I not doing > right? > > > > Many thanks, > > > > Areti > > > > > > > > > ------------------------------ > > Message: 7 > Date: Mon, 20 Oct 2014 13:30:55 +0000 > From: "Smaragdi A." <a.smara...@soton.ac.uk > <mailto:a.smara...@soton.ac.uk>> > Subject: Re: [Freesurfer] Do not have 'recon edit' button! Please > help! > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <d06acccb.416e%a.smara...@soton.ac.uk > <mailto:d06acccb.416e%25a.smara...@soton.ac.uk>> > Content-Type: text/plain; charset="us-ascii" > > Hi Bruce, > > Thank you for getting back to me! Its the 1.0 version, downloaded > from the > website. > > Thanks, > > Areti > > > > > > On 20/10/2014 14:24, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > >Hi Areti > > > >what version of freeview are you using? > >Bruce > >On Mon, 20 Oct 2014, Smaragdi A. > >wrote: > > > >> Dear mailing list, > >> > >> I am really stuck here.. Please can someone tell me why I cannot > find > >>the recon edit button on freeview! > >> > >> I am not sure if the version of Freesurfer I have downloaded is > old, or > >>I have > >> done something wrong, or I am just blind.. But I cannot find the > 'recon > >>edit' > >> button in freeview (see attached screenshot). What am I not > doing right? > >> > >> Many thanks, > >> > >> Areti > >> > >> > >> > >_______________________________________________ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Screen Shot 2014-10-20 at 14.30.33.png > Type: image/png > Size: 49832 bytes > Desc: Screen Shot 2014-10-20 at 14.30.33.png > Url : > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/bfd7ae42/attachment-0001.png > > ------------------------------ > > Message: 8 > Date: Mon, 20 Oct 2014 14:41:06 +0000 > From: "Alshikho, Mohamad J." <malshi...@mgh.harvard.edu > <mailto:malshi...@mgh.harvard.edu>> > Subject: [Freesurfer] unpacksdcmdir > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > > <e2104e910166894e926b16bcd6dcf00b0f718...@phsx10mb5.partners.org > <mailto:e2104e910166894e926b16bcd6dcf00b0f718...@phsx10mb5.partners.org>> > Content-Type: text/plain; charset="iso-8859-1" > > Hi , > The command <unpacksdcmdir> is only used to unpack Siemens DICOM > files, How can I unpack the non Siemens DICOMs? > > Thanks, > Moahmad > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/3a65f36c/attachment-0001.html > > ------------------------------ > > Message: 9 > Date: Mon, 20 Oct 2014 11:21:36 -0400 (EDT) > From: "Shantanu Ghosh" <shant...@nmr.mgh.harvard.edu > <mailto:shant...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] unpacksdcmdir > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: > > <49253.128.103.186.182.1413818496.squir...@mail.nmr.mgh.harvard.edu > > <mailto:49253.128.103.186.182.1413818496.squir...@mail.nmr.mgh.harvard.edu>> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Mohamad > > You could convert the Dicoms in other s/w to .nii and then read them. > Maybe Bruce and Doug have more elegant solutions > > Hth > Shantanu > > > On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote: > > Hi , > > The command <unpacksdcmdir> is only used to unpack Siemens DICOM > files, > > How can I unpack the non Siemens DICOMs? > > > > Thanks, > > Moahmad > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > -- > Not only is the universe stranger than we think, it is stranger than we > can think. -Werner Heisenberg > > > > ------------------------------ > > Message: 10 > Date: Mon, 20 Oct 2014 11:35:03 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] unpacksdcmdir > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <54452ba7.2050...@nmr.mgh.harvard.edu > <mailto:54452ba7.2050...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > dcmunpack will unpack any dicoms > > On 10/20/2014 11:21 AM, Shantanu Ghosh wrote: > > Hi Mohamad > > > > You could convert the Dicoms in other s/w to .nii and then read them. > > Maybe Bruce and Doug have more elegant solutions > > > > Hth > > Shantanu > > > > > > On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote: > >> Hi , > >> The command <unpacksdcmdir> is only used to unpack Siemens DICOM > files, > >> How can I unpack the non Siemens DICOMs? > >> > >> Thanks, > >> Moahmad > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 11 > Date: Mon, 20 Oct 2014 11:37:09 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] GLM contrast vector for continuous variable > interaction > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <54452c25.9000...@nmr.mgh.harvard.edu > <mailto:54452c25.9000...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > I think this is the contrast you need > > 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 - 0.5 > -0.5 -0.5 -0.5 > > On 10/19/2014 06:33 PM, Bronwyn Overs wrote: > > 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: > > > > 0 0 0 0 0 0 0 0 0 0 0 0 > > 0.5 0.5 0.5 0.5 > > 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 > > 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/neuraustralia>Follow NeuRA on facebook > > <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to > > the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 128, Issue 26 > ******************************************* > > > > > -- > > /We shall not cease from exploration. And the end of all our exploring > will be to arrive where we started and know the place for the first > time- T.S. Eliot/ > > > > > _______________________________________________ > 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
