[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 hemiis 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 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.
Re: [Freesurfer] Bus error when trying to launch tksurfer
Daer Claire The bus error might be related to Xquartz. Installing Xquartz again solved the issue on most Intel-based Macs. Cheers Jürgen 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. Von: Claire Morley clairemorley2...@u.northwestern.edu Antworten an: Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu Datum: Montag, 20. Oktober 2014 09:56 An: Freesurfer Mailinglist 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 hemiis 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 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. ___ Freesurfer mailing list 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.
Re: [Freesurfer] Bus error when trying to launch tksurfer
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 ___ Freesurfer mailing list 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.
[Freesurfer] Do not have 'recon edit' button! Please help!
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 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.
Re: [Freesurfer] Do not have 'recon edit' button! Please help!
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 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.
Re: [Freesurfer] Do not have 'recon edit' button! Please help!
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 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 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. ___ Freesurfer mailing list 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.
[Freesurfer] unpacksdcmdir
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 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.
Re: [Freesurfer] unpacksdcmdir
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 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 ___ Freesurfer mailing list 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.
Re: [Freesurfer] GLM contrast vector for continuous variable interaction
I think this is the contrast you need 00000000 0.50.50.50.5 - 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: 000000000 0 0 0 0.50.50.50.5 000000000.50.50.5 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 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 ___ Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
Re: [Freesurfer] unpacksdcmdir
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
Re: [Freesurfer] adding time points to longitudinal base template
Hi Koushik, no, I cc the list, maybe someone has done tests or seen papers. I read somewhere on atlas construction, that 10 images are fine, but that is cross subject. Here we only have small changes within subject, so from my experience less are fine , BUT - 2 of course are not enough: in 2 the method is actually different (as the median in 2 is simply the average) . Starting with 3 a median intensity even exists for each voxel. - adding 1 new to 5 existing may work without sacrificing too much bias, but adding 10 to 5 is not a good idea. Also if the one that is added is very different from the first 5 (e.g. first 5 within a week, next 3 years later), then that will be problematic also. Best, Martin On 10/20/2014 12:07 PM, Govindarajan, Koushik Athreya wrote: Hi Martin, How are you? We had this below email conversation in March about the longitudinal template and it's stability. You had mentioned that with 5 time points, my template should be stable enough to patch another timepoint. I have another study that has only 2 time points and I was reading through your 2012 Longitudinal analysis paper that had used 2 time points to compare with cross-sectional data. I was wondering if you had any suggested literature for the number of time points needed for stability of a template. Thanks Koushik Govindarajan *From:*Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] *Sent:* Friday, March 14, 2014 9:31 AM *To:* Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] adding time points to longitudinal base template Hi Koushik, there is a way to add time points without recreating the base: recon-all -long tpNsubjid longbasesubjid -addtp -all This is what the recon-all help says about that: If a new timepoint needs to be added to a longitudinal run where a base subject has already been created (from prior timepoints), then the -addtp command can be added to the -long command in order to 'fix-up' the longitudinal stream to accept the new timepoint. Note that the base subject is *not* recomputed using the new timepoint. This potentially introduces a bias, and it is recommended to NOT add a time point this way! Instead recreate the base from all time points and run all longitudinals again. So it's up to you. But given you already have 5 time points in your base and add only 1, you may be fine. The base should be pretty stable with 5 and if the 6th is not too different, it should not matter much. I don't think anyone has ever done a thorough analysis about adding time points. Best, Martin On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote: Dear FS experts, I have a serial study in which I have run cross-sectional and longitudinal analysis on 5 time points. Now, I want to add a 6^th time point to my dataset. Do I have to rerun my base template creation step from scratch or is there a way to just add further time points to an existing template? Thanks Koushik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferk=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0Ar=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0Am=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0As=48648d97d14c3c96469c77ba99084506ab3a9eb1d6046d5937b5a35a037bce5d -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edu mailto:reu...@mit.edu Web :http://reuter.mit.edu https://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.eduk=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0Ar=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0Am=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0As=30e97dd7834b287056c1385ccff33fcd591a190ee3917c4441cadea4d971b918 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. -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of
Re: [Freesurfer] adding time points to longitudinal base template
Thanks for your response Martin. From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 12:56 PM To: Govindarajan, Koushik Athreya Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template Hi Koushik, no, I cc the list, maybe someone has done tests or seen papers. I read somewhere on atlas construction, that 10 images are fine, but that is cross subject. Here we only have small changes within subject, so from my experience less are fine , BUT - 2 of course are not enough: in 2 the method is actually different (as the median in 2 is simply the average) . Starting with 3 a median intensity even exists for each voxel. - adding 1 new to 5 existing may work without sacrificing too much bias, but adding 10 to 5 is not a good idea. Also if the one that is added is very different from the first 5 (e.g. first 5 within a week, next 3 years later), then that will be problematic also. Best, Martin On 10/20/2014 12:07 PM, Govindarajan, Koushik Athreya wrote: Hi Martin, How are you? We had this below email conversation in March about the longitudinal template and it's stability. You had mentioned that with 5 time points, my template should be stable enough to patch another timepoint. I have another study that has only 2 time points and I was reading through your 2012 Longitudinal analysis paper that had used 2 time points to compare with cross-sectional data. I was wondering if you had any suggested literature for the number of time points needed for stability of a template. Thanks Koushik Govindarajan From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] Sent: Friday, March 14, 2014 9:31 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] adding time points to longitudinal base template Hi Koushik, there is a way to add time points without recreating the base: recon-all -long tpNsubjid longbasesubjid -addtp -all This is what the recon-all help says about that: If a new timepoint needs to be added to a longitudinal run where a base subject has already been created (from prior timepoints), then the -addtp command can be added to the -long command in order to 'fix-up' the longitudinal stream to accept the new timepoint. Note that the base subject is *not* recomputed using the new timepoint. This potentially introduces a bias, and it is recommended to NOT add a time point this way! Instead recreate the base from all time points and run all longitudinals again. So it's up to you. But given you already have 5 time points in your base and add only 1, you may be fine. The base should be pretty stable with 5 and if the 6th is not too different, it should not matter much. I don't think anyone has ever done a thorough analysis about adding time points. Best, Martin On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote: Dear FS experts, I have a serial study in which I have run cross-sectional and longitudinal analysis on 5 time points. Now, I want to add a 6th time point to my dataset. Do I have to rerun my base template creation step from scratch or is there a way to just add further time points to an existing template? Thanks Koushik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferk=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0Ar=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0Am=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0As=48648d97d14c3c96469c77ba99084506ab3a9eb1d6046d5937b5a35a037bce5d -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edumailto:reu...@mit.edu Web : http://reuter.mit.eduhttps://urldefense.proofpoint.com/v1/url?u=http://reuter.mit.eduk=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0Ar=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0Am=DVyhlZm48BQ7pEr20iqqosHWjgQ31wzMoC9FDk9YpEo%3D%0As=30e97dd7834b287056c1385ccff33fcd591a190ee3917c4441cadea4d971b918 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
[Freesurfer] Longitudinal prediction
Dear FreeSurfer Experts, How could the longitudinal analysis be performed in order to show whether a parameter at time 1 is predictive of changes in cortical thickness over time ? and can thecorresponding regions be shown in FreeSurfer ? In a statistical analysis, as we see it, we must perform the correlation between the parameter at time 1 and the cortical thickness difference (or ROI)time 2-time1, yet in this case we cannot see it on the cortex. Thank you, Alex ___ Freesurfer mailing list 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.
Re: [Freesurfer] unpacksdcmdir
Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files). when I used this command on a my data set it gives me an error for certain subjects! Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 11:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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 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.
Re: [Freesurfer] unpacksdcmdir
did you try dcmunpack? On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote: Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files). when I used this command on a my data set it gives me an error for certain subjects! Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 11:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
Re: [Freesurfer] unpacksdcmdir
Sorry I did not notice that this is a different command. I will try it now. and I will let you now Thanks a lot From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 3:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir did you try dcmunpack? On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote: Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files). when I used this command on a my data set it gives me an error for certain subjects! Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 11:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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 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.
[Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo
Dear Freesurfer Experts, I have a label file of a number of ROI's I've made based on a mask. I'm trying to get an idea of what cluster are significant within a focused region of the label file. To make the correction a little less sever, I pre-computed some monte-carlo values using mri_mcsim mri_mcsim --o /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain --base mc-z --surface fsaverage rh --nreps 1 --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask mri_mcsim --o $SUBJECTS_DIR/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain --base mc-z --surface fsaverage lh --nreps 1 --label $SUBJECTS_DIR/fsaverage/label/lh.SocialBrainMask Respectively for each surface (the labels are different on each hemisphere). I've run mri_glmfit and have the uncorrected outputs and results (there are actually 6 of these, one for volume, thickness, and surface area for each hemi): mri_glmfit --y rh.diagnosisxagexrightThickslopetest.thickness.10.mgh --fsgd SBM_glmRightthickNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agethickness.glmdir But when I try to do the mri_glmfit-sim, I am having trouble getting it to read in the corrected csd file. I'm wanting to run it at cwp of 0.05 at a threshold of 2 (0.01), with a correction for two hemispheres. However, when I try to run it with --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain , it has trouble understanding the --cwp .05, --2spaces and 2 abs (after cache dir) flags. Additionally, it wants a --sim and --sim-sign value like it wants to compute a monte-carlo from scratch. Could I get an example on how best to direct it to the simulation I've run on it? Thanks much. -Thomas -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpdera...@gmail.com, faus...@uab.edu ___ Freesurfer mailing list 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.
Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo
what do you mean it has trouble understanding? What is your command line and terminal output. Also, are you following these instructions? https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo On 10/20/2014 03:50 PM, Thomas DeRamus wrote: Dear Freesurfer Experts, I have a label file of a number of ROI's I've made based on a mask. I'm trying to get an idea of what cluster are significant within a focused region of the label file. To make the correction a little less sever, I pre-computed some monte-carlo values using mri_mcsim mri_mcsim --o /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain --base mc-z --surface fsaverage rh --nreps 1 --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask mri_mcsim --o $SUBJECTS_DIR/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain --base mc-z --surface fsaverage lh --nreps 1 --label $SUBJECTS_DIR/fsaverage/label/lh.SocialBrainMask Respectively for each surface (the labels are different on each hemisphere). I've run mri_glmfit and have the uncorrected outputs and results (there are actually 6 of these, one for volume, thickness, and surface area for each hemi): mri_glmfit --y rh.diagnosisxagexrightThickslopetest.thickness.10.mgh --fsgd SBM_glmRightthickNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agethickness.glmdir But when I try to do the mri_glmfit-sim, I am having trouble getting it to read in the corrected csd file. I'm wanting to run it at cwp of 0.05 at a threshold of 2 (0.01), with a correction for two hemispheres. However, when I try to run it with --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain , it has trouble understanding the --cwp .05, --2spaces and 2 abs (after cache dir) flags. Additionally, it wants a --sim and --sim-sign value like it wants to compute a monte-carlo from scratch. Could I get an example on how best to direct it to the simulation I've run on it? Thanks much. -Thomas -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 _Phone_: 205-934-0971 tel:205-934-0971 _Email:_ tpdera...@gmail.com mailto:tpdera...@gmail.com, faus...@uab.edu mailto:faus...@uab.edu ___ Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo
I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly. I see on the wiki and in the mailing list you can use a different directory and then spec that folder using mri_glmfit-sim with the --cache-dir flag. When I run it like that, I get this output mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cwp 0.05 --2spaces --sim ERROR: flag --sim requires four arguments When I specify the sim (which I'm not sure I need since I ran the simulation already) and sim-sign abs, and run either of the following, I get these as outputs: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spacescmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir SURFACE: fsaverage rh log file is rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory cd /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory /usr/local/freesurfer/bin/mri_glmfit-sim tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Mon Oct 20 15:06:19 CDT 2014 tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tderamus tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory setenv SUBJECTS_DIR /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory FREESURFER_HOME /usr/local/freesurfer tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Original mri_glmfit command line: tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory DoSim = 1 tee:
Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo
You should not spec --sim. If you do not, does it work? doug On 10/20/2014 04:10 PM, Thomas DeRamus wrote: I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly. I see on the wiki and in the mailing list you can use a different directory and then spec that folder using mri_glmfit-sim with the --cache-dir flag. When I run it like that, I get this output mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cwp 0.05 --2spaces --sim ERROR: flag --sim requires four arguments When I specify the sim (which I'm not sure I need since I ran the simulation already) and sim-sign abs, and run either of the following, I get these as outputs: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spacescmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir SURFACE: fsaverage rh log file is rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory cd /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory /usr/local/freesurfer/bin/mri_glmfit-sim tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Mon Oct 20 15:06:19 CDT 2014 tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tderamus tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory setenv SUBJECTS_DIR /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory FREESURFER_HOME /usr/local/freesurfer tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Original mri_glmfit command line: tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo
It does not I'm afraid. The error I get says the following: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces ERROR: must spec --sim Does the same if I remove the --sim-sign abs as well. On Mon, Oct 20, 2014 at 3:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You should not spec --sim. If you do not, does it work? doug On 10/20/2014 04:10 PM, Thomas DeRamus wrote: I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly. I see on the wiki and in the mailing list you can use a different directory and then spec that folder using mri_glmfit-sim with the --cache-dir flag. When I run it like that, I get this output mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cwp 0.05 --2spaces --sim ERROR: flag --sim requires four arguments When I specify the sim (which I'm not sure I need since I ran the simulation already) and sim-sign abs, and run either of the following, I get these as outputs: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spacescmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir SURFACE: fsaverage rh log file is rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory cd /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory /usr/local/freesurfer/bin/mri_glmfit-sim tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Mon Oct 20 15:06:19 CDT 2014 tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tderamus tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory setenv SUBJECTS_DIR /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory FREESURFER_HOME /usr/local/freesurfer tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Original mri_glmfit command line: tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd
[Freesurfer] (no subject)
Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ? Thank you, Mahmoud ___ Freesurfer mailing list 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.
[Freesurfer] Parenchyma/CSF
Dear all, I used the the 3 steps of longitudinal analysis explained in freesurfer longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each of time points. Is this equivalent to compute the (total gray matter volume + total cortical matter volume)/CSF from aseg.stats file ? Thank you, Mahmoud ___ Freesurfer mailing list 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.
Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo
you need to add --cache threshold sign (and don't use --sim-sign or --sim) On 10/20/2014 05:42 PM, Thomas DeRamus wrote: It does not I'm afraid. The error I get says the following: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces ERROR: must spec --sim Does the same if I remove the --sim-sign abs as well. On Mon, Oct 20, 2014 at 3:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: You should not spec --sim. If you do not, does it work? doug On 10/20/2014 04:10 PM, Thomas DeRamus wrote: I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly. I see on the wiki and in the mailing list you can use a different directory and then spec that folder using mri_glmfit-sim with the --cache-dir flag. When I run it like that, I get this output mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cwp 0.05 --2spaces --sim ERROR: flag --sim requires four arguments When I specify the sim (which I'm not sure I need since I ran the simulation already) and sim-sign abs, and run either of the following, I get these as outputs: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spacescmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir SURFACE: fsaverage rh log file is rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory cd /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory /usr/local/freesurfer/bin/mri_glmfit-sim tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Mon Oct 20 15:06:19 CDT 2014 tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tderamus tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory setenv SUBJECTS_DIR /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory FREESURFER_HOME /usr/local/freesurfer tee:
Re: [Freesurfer] GLM contrast vector for continuous variable interaction
Thanks Douglas. That is exactly what I wanted. 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 On 21/10/2014 2:37 am, Douglas N Greve wrote: I think this is the contrast you need 00000000 0.50.50.50.5 - 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: 000000000 0 0 0 0.50.50.50.5 000000000.50.50.5 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 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 ___ 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 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.
Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo
That one gives the following error: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cache 2 abs cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir SURFACE: fsaverage rh log file is rh.ALESocial__agevolume.glmdir/cache.mri_glmfit-sim.log cd /media/rkbatch/gyrification /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cache 2 abs $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Mon Oct 20 17:39:34 CDT 2014 Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux tderamus setenv SUBJECTS_DIR /media/rkbatch/gyrification FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 14.594354 ERROR: cannot find /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain//fsaverage/rh/cortex/fwhm15/abs/th20/mc-z.csd It looks like its still trying to use the cached monte-carlo from the fsaverage rather than the one for the label. Am I using --cache-dir correctly? On Mon, Oct 20, 2014 at 5:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: you need to add --cache threshold sign (and don't use --sim-sign or --sim) On 10/20/2014 05:42 PM, Thomas DeRamus wrote: It does not I'm afraid. The error I get says the following: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces ERROR: must spec --sim Does the same if I remove the --sim-sign abs as well. On Mon, Oct 20, 2014 at 3:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: You should not spec --sim. If you do not, does it work? doug On 10/20/2014 04:10 PM, Thomas DeRamus wrote: I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly. I see on the wiki and in the mailing list you can use a different directory and then spec that folder using mri_glmfit-sim with the --cache-dir flag. When I run it like that, I get this output mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cwp 0.05 --2spaces --sim ERROR: flag --sim requires four arguments When I specify the sim (which I'm not sure I need since I ran the simulation already) and sim-sign abs, and run either of the following, I get these as outputs: mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 1 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spacescmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir SURFACE: fsaverage rh log file is rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory cd /media/rkbatch/gyrification tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
Re: [Freesurfer] skewed CT viewed in tkregister2
Hi Mia, sorry for the delay. I think the problem is that the geometry info in the CT header is incorrect. The directions are not orgthogonal, and, when made orthogonal, the pixel sizes look wrong. How did you create ct.mgz? doug On 10/12/2014 08:52 PM, Borzello, Mia wrote: Hi, Any insight on this problem I'm having with tkregister2? I haven't been able to resolve this yet. My original posting is below with the output from bugr. Thanks! Mia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, October 06, 2014 11:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] skewed CT viewed in tkregister2 Hi Freesurfers I'm having trouble viewing a CT in tkregister2. Here is the output from bugr: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri 1. BI20 2. tkregister2 --s BI20v2_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3. the coronal/saggital/horizontal views were skewed 4.attached. Thanks a lot, Mia ___ Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
Re: [Freesurfer] unpacksdcmdir
Hi Doug, I ran the following command line dcmunpack -scr dicoms dir path in my script and it gives me a list of the run/series. How can I save this list as a log file. I tried to add the flag -targ and the flag -log but it gives me an error and asked me to specify the series run numbe? Any suggestions please?. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alshikho, Mohamad J. Sent: Monday, October 20, 2014 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] unpacksdcmdir Sorry I did not notice that this is a different command. I will try it now. and I will let you now Thanks a lot From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 3:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir did you try dcmunpack? On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote: Hi Doug, But in freeSurfer wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the following The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files). when I used this command on a my data set it gives me an error for certain subjects! Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 11:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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 ___ Freesurfer mailing list 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.
Re: [Freesurfer] T1 white matter segmentation
In this case if I don't have T1 MPRAGE can I use any other available T1 like sag_T1 or Ax_T1 (the name of run/series after using unpacksdcmdir)? or it is imperative to use T1 MPRAGE for the segmentation. Bests, From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 17, 2014 12:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] T1 white matter segmentation first you have to run recon-all with the T1 On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote: Hi Bruce, The T2 is very good and better than T1 So I will use the T2 image in the following command line recon-all -subjid subjid -T2pial Is this correct? Thanks Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 17, 2014 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] T1 white matter segmentation Hi Mohamad recon-all requires a T1, so use it. If the T2 is good quality you can use it to avoid dura in a subsequent invocation of recon-all with the -T2pial flag cheers Bruce On Fri, 17 Oct 2014, Alshikho, Mohamad J. wrote: Hi FS Experts, The T1 and T2 images in my data set are as the attached images. Kindly do you recommend that I do segmentation for the white matter using recon-all on my T1 or T2 images or to the output of a registration process between T1 and T2 I highly appreciate any recommendation Looking forward to learn from you and thank you Mohamad ___ 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 ___ Freesurfer mailing list 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.
