[Freesurfer] qdec control variable limitation
Dear all, I am using qdec to do a shape analysis with 16 control variables. I was wondering if there is a limit on how many covariates can be used in qdec? Because it seems that I cannot select all my covariates in nuisance factors. Thanks and regards, Jiyang ___ 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] mri_cvs_register std:: bad_alloc
Dear FreeSurfers, I'm trying to use mri_cvs_register, however the process can't complete and I get the following error: [...] loading transform id string = data size = 18728074 uilen = 6 loading transform id string = data size = 19845421 uilen = 6 loading transform id string = data size = 19120776 uilen = 6 loading transform id string = data size = 71 uilen = 7 loading transform id string = saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 16 saveTransform code writing transform size = 21339696 saveTransform code writing transform size = 21092930 saveTransform code writing transform size = 20795616 saveTransform code writing transform size = 20591898 saveTransform code requested buffer size = 436643894 Exception caught while saving morph ZlibStringCompressor::setBufferSize - Caught std::bad_alloc My command line was: mri_cvs_register --mov subject01 --mni --openmp 8 --m3d At the time of crash all RAM is consumed by createMorph process (10 GB). Is this crash related to the ammount of RAM on my machine (12 GB)? If so, how much RAM is needed to complete mri_cvs_register? Best regards, Marcel ___ 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] custom fill function for matlab
Dear freesurfer admin, I'm writing a piece of code in matlab based on freesurfer reconstructed brains generating series of labels to an annotation file. However, I wanted to include a process similar to the existing in tksurfer options in the 'custom fill' where you can fill in all vertices up to a label border/up to included paths. I have searched on the web for a piece of matlab code that would process this, but I coulnt seem to find it. Is there any quick way to do this? The basic idea is that I have a group of non-labeled vertices enclosed within a label, and I just want to 'fill them with the same label as the label that surrounds it. Thank you very much in advance. I really do hope this can be possible! Cheers! Catarina Rua ___ 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] Artefactual skull stripping for some subjects
Thanks for clarifying this Doug! Please let me know if anyone has suggestions about my other questions below, re skull stripping. Cheers! T On 8 July 2013 18:01, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: 001.mgz - raw.mgz - orig.mgz - nu.mgz - T1.mgz If you only have one run, then 001 and raw are the same orig.mgz is the first conformed volume doug On 07/08/2013 12:38 PM, Tudor Popescu wrote: Thanks Bruce. I have looked at that part of the wiki but I was wondering whether the screenshots at all suggest that all artefacts are likely to be the result of the same problem, and that e.g. re-running recon for all subjects with a watershed25 and with the -no-wsgcaatlas flag might be the thing to do in this case, rather than manually editing slices in tkmedit. So after making these corrections to all affected subjects, before proceeding to analyses, is a visual inspection in freeview of the brain.mgz of all subjects enough? It seems like some of these skull-stripping errors are quite subtle and can be easily missed (as I have, in fact, when I checked the output after my first recon-all). the T1.mgz is intensity corrected and conformed (the orig.mgz is just conformed). So are both derived from 001.mgz? Otherwise, what is the difference between 001.mgz and orig.mgz? Thanks! Tudor ___ 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. ___ 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] custom fill function for matlab
Hi Cararina, sorry, I don't think we have anything to do this in matlab. You could write a tcl script to do it automatically in tksurfer and call that from inside matlab I guess. cheers Bruce On Tue, 9 Jul 2013, Catarina Rua wrote: Dear freesurfer admin, I'm writing a piece of code in matlab based on freesurfer reconstructed brains generating series of labels to an annotation file. However, I wanted to include a process similar to the existing in tksurfer options in the 'custom fill' where you can fill in all vertices up to a label border/up to included paths. I have searched on the web for a piece of matlab code that would process this, but I coulnt seem to find it. Is there any quick way to do this? The basic idea is that I have a group of non-labeled vertices enclosed within a label, and I just want to 'fill them with the same label as the label that surrounds it. Thank you very much in advance. I really do hope this can be possible! Cheers! Catarina Rua ___ 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] qdec categories for discrete variables
Dear Freesurfer experts, is it already possible to define more than two possible factors for discrete variables in the latest qdec version or is that option still limited to 2 possible variables? Thanks for your help! Best regards Peter ___ 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] average/RB_all_2008-03-26.gca not found error
Hi Salil what is FREESURFER_HOME set to? Is it /usr/local/freesurfer? Does /usr/local/freesurfer/average/RB_all_2008-03-26.gca exist? cheers Bruce On Mon, 8 Jul 2013, Salil Soman wrote: Hi, Am running this command: $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -use-cuda -all And am get this out put / error: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 5.50 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: GeForce GTX 660 === NUMBER OF OPENMP THREADS = 50 === stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 319.32 Wed Jun 19 15:51:20 PDT 2013 ERROR: cannot find /usr/local/freesurfer/average/RB_all_2008-03-26.gca Any suggestions what I am doing incorrectly? Thank you, Sal ___ 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] how to use mris_register?
Dear Mr, When I execute mris_register to register one subject to a template., I have this message of error: mris_register -1 s000/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif sphere_reg treating target as a single subject's surface... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file s000/surf/lh.sphere No such file or directory note that the file exist in the specifeid SUBJECT_DIR Thank you for your help Fatma ___ 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] how to use mris_register?
Hi Fatma don't use the -1 flag if you are regtering to a template, only if you are registering individual surfaces to each other. You probably want the output to be named lh.sphere_reg and go in the s000/surf dir. cheers Bruce On Tue, 9 Jul 2013, fatma zribi wrote: Dear Mr, When I execute mris_register to register one subject to a template., I have this message of error: mris_register -1 s000/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif sphere_reg treating target as a single subject's surface... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file s000/surf/lh.sphere No such file or directory note that the file exist in the specifeid SUBJECT_DIR Thank you for your help Fatma ___ 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] Tracula problem in pre-processing
Helo all, I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file. ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 I have also attached the trac-all log. trac-all.log Description: trac-all.log ___ 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] Is this an example of pial surface extending into cerebellum?
Ye, Since no one's replied, I'll say it does look like the cb is infringing on the pial surface. It's easier to tell the boundary toward the center of the brain than it is toward the lower portion. It's easier to tell, in my opinion, in the coronal view. Toggling the surface off may help as well. jon On Mon, Jul 8, 2013 at 4:04 PM, ye tian tianye...@gmail.com wrote: Dear Freesurfers, My first attempt of this message didn't get through. Sorry for those who are receiving it for the second time. Basically, I think that the pial surface in the blue circle is extending into cerebellum. I need a second vote on my decision to manual edit. Thank you very much! Sincerely, Ye On Mon, Jul 8, 2013 at 11:33 AM, ye tian tianye...@gmail.com wrote: Dear Freesurfers, Is the attached file an example of pial surface extending into cerebellum? Thank you very much! Sincerely, Ye ___ 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] qdec categories for discrete variables
Hi Peter, no it is not. You will have to use mri_glmfit. doug On 7/9/13 9:29 AM, Peter Bohn wrote: Dear Freesurfer experts, is it already possible to define more than two possible factors for discrete variables in the latest qdec version or is that option still limited to 2 possible variables? Thanks for your help! Best regards Peter ___ 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] mri_cvs_register std:: bad_alloc
Hi Marcel, You would ned at least twice as much. Also, is there a specific reason for you to use the --m3d flag? That will result in writing out uncompressed morph files which will take up a lot of space. Lilla On Tue, 9 Jul 2013, Marcel Falkiewicz wrote: Dear FreeSurfers, I'm trying to use mri_cvs_register, however the process can't complete and I get the following error: [...] loading transform id string = data size = 18728074 uilen = 6 loading transform id string = data size = 19845421 uilen = 6 loading transform id string = data size = 19120776 uilen = 6 loading transform id string = data size = 71 uilen = 7 loading transform id string = saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 16 saveTransform code writing transform size = 21339696 saveTransform code writing transform size = 21092930 saveTransform code writing transform size = 20795616 saveTransform code writing transform size = 20591898 saveTransform code requested buffer size = 436643894 Exception caught while saving morph ZlibStringCompressor::setBufferSize - Caught std::bad_alloc My command line was: mri_cvs_register --mov subject01 --mni --openmp 8 --m3d At the time of crash all RAM is consumed by createMorph process (10 GB). Is this crash related to the ammount of RAM on my machine (12 GB)? If so, how much RAM is needed to complete mri_cvs_register? Best regards, Marcel ___ 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] mri_cvs_register std:: bad_alloc
Hi Lilla, thanks for the advice, I'll just upgrade my RAM to 24 GB (maybe it will help FSFAST too ;-)). I used the --m3d flag as a blind guess about the possible cause of the aforementioned error, thank you for clearing that up, I'll skip it next time. Best regards, Marcel 2013/7/9 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Marcel, You would ned at least twice as much. Also, is there a specific reason for you to use the --m3d flag? That will result in writing out uncompressed morph files which will take up a lot of space. Lilla On Tue, 9 Jul 2013, Marcel Falkiewicz wrote: Dear FreeSurfers, I'm trying to use mri_cvs_register, however the process can't complete and I get the following error: [...] loading transform id string = data size = 18728074 uilen = 6 loading transform id string = data size = 19845421 uilen = 6 loading transform id string = data size = 19120776 uilen = 6 loading transform id string = data size = 71 uilen = 7 loading transform id string = saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 16 saveTransform code writing transform size = 21339696 saveTransform code writing transform size = 21092930 saveTransform code writing transform size = 20795616 saveTransform code writing transform size = 20591898 saveTransform code requested buffer size = 436643894 Exception caught while saving morph ZlibStringCompressor::**setBufferSize - Caught std::bad_alloc My command line was: mri_cvs_register --mov subject01 --mni --openmp 8 --m3d At the time of crash all RAM is consumed by createMorph process (10 GB). Is this crash related to the ammount of RAM on my machine (12 GB)? If so, how much RAM is needed to complete mri_cvs_register? Best regards, Marcel 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/**compliancelinehttp://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] average/RB_all_2008-03-26.gca not found error
Thank you for your email. Yes that v is what freesurfer home is set to. Somehow that GCA file (SMS numerous others) were missing from the averages folder. I manually chopped them from a different 5.3 install, but am not sure v why they are missing (I am the only person using this machine and did not delete anything from the averages folder). Now that I copied the files over the command I listed runs but crashes with the error mpr2mni305 failed. I get this error on a dataset I have already processed using freesurfer 5.3 centos 6 version without the use-cuda option. Any suggestions would be greatly appreciated. Best wishes, Sal Hi Salil what is FREESURFER_HOME set to? Is it /usr/local/freesurfer? Does /usr/local/freesurfer/average/**RB_all_2008-03-26.gca exist? cheers Bruce On Mon, 8 Jul 2013, Salil Soman wrote: Hi, Am running this command: $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -use-cuda -all And am get this out put / error: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 5.50 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: GeForce GTX 660 === NUMBER OF OPENMP THREADS = 50 === stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 319.32 Wed Jun 19 15:51:20 PDT 2013 ERROR: cannot find /usr/local/freesurfer/average/**RB_all_2008-03-26.gca Any suggestions what I am doing incorrectly? Thank you, Sal 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/**compliancelinehttp://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] qdec control variable limitation
you can have two discrete variables (two levels each) and two continuous variables. If you want more than that, you will need to run mri_glmfit instead. doug On 07/09/2013 02:30 AM, Jiang Jiyang wrote: Dear all, I am using qdec to do a shape analysis with 16 control variables. I was wondering if there is a limit on how many covariates can be used in qdec? Because it seems that I cannot select all my covariates in nuisance factors. Thanks and regards, Jiyang ___ 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] Is this an example of pial surface extending into cerebellum?
Ye, personally I edit once I see an issue in any view, and I continue to look for problems in all 3 views. In those images it seems like the issue with the cb is less drastic this time around. Is it the same area? In any case I would make minor edits in the images you provided, very minor. The images are a bit small so I may be seeing incorrectly... Really it's up to you, just edit consistently. jon On Tue, Jul 9, 2013 at 11:16 AM, ye tian tianye...@gmail.com wrote: Dear Jonathan, Thank you very much for your response. This actually brings me to my second question. What is the criteria for manual editing? Do you only edit when the problem appears in all three views? Or do you start editing when there seems to be a problem in only one view? Would you personally edit in my case (where the horizontal and sagittal views look okay)? Thank you very much! PS: I didn't see my first message in the mailing archive, so I thought it didn't go through. It seems that an email with images will only show in the archive until it solicits a response. Sorry to bother you guys. Sincerely, Ye On Tue, Jul 9, 2013 at 9:22 AM, Jonathan Holt whats...@umich.edu wrote: Ye, Since no one's replied, I'll say it does look like the cb is infringing on the pial surface. It's easier to tell the boundary toward the center of the brain than it is toward the lower portion. It's easier to tell, in my opinion, in the coronal view. Toggling the surface off may help as well. jon On Mon, Jul 8, 2013 at 4:04 PM, ye tian tianye...@gmail.com wrote: Dear Freesurfers, My first attempt of this message didn't get through. Sorry for those who are receiving it for the second time. Basically, I think that the pial surface in the blue circle is extending into cerebellum. I need a second vote on my decision to manual edit. Thank you very much! Sincerely, Ye On Mon, Jul 8, 2013 at 11:33 AM, ye tian tianye...@gmail.com wrote: Dear Freesurfers, Is the attached file an example of pial surface extending into cerebellum? Thank you very much! Sincerely, Ye ___ 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] Is this an example of pial surface extending into cerebellum?
Dear Jon, Thank you very much! Yes, it is the same area. I set the cursor in one place and clicked the C, H and C buttons in tkmedit tools. Sincerely, Ye On Tue, Jul 9, 2013 at 10:20 AM, Jonathan Holt whats...@umich.edu wrote: Ye, personally I edit once I see an issue in any view, and I continue to look for problems in all 3 views. In those images it seems like the issue with the cb is less drastic this time around. Is it the same area? In any case I would make minor edits in the images you provided, very minor. The images are a bit small so I may be seeing incorrectly... Really it's up to you, just edit consistently. jon On Tue, Jul 9, 2013 at 11:16 AM, ye tian tianye...@gmail.com wrote: Dear Jonathan, Thank you very much for your response. This actually brings me to my second question. What is the criteria for manual editing? Do you only edit when the problem appears in all three views? Or do you start editing when there seems to be a problem in only one view? Would you personally edit in my case (where the horizontal and sagittal views look okay)? Thank you very much! PS: I didn't see my first message in the mailing archive, so I thought it didn't go through. It seems that an email with images will only show in the archive until it solicits a response. Sorry to bother you guys. Sincerely, Ye On Tue, Jul 9, 2013 at 9:22 AM, Jonathan Holt whats...@umich.edu wrote: Ye, Since no one's replied, I'll say it does look like the cb is infringing on the pial surface. It's easier to tell the boundary toward the center of the brain than it is toward the lower portion. It's easier to tell, in my opinion, in the coronal view. Toggling the surface off may help as well. jon On Mon, Jul 8, 2013 at 4:04 PM, ye tian tianye...@gmail.com wrote: Dear Freesurfers, My first attempt of this message didn't get through. Sorry for those who are receiving it for the second time. Basically, I think that the pial surface in the blue circle is extending into cerebellum. I need a second vote on my decision to manual edit. Thank you very much! Sincerely, Ye On Mon, Jul 8, 2013 at 11:33 AM, ye tian tianye...@gmail.com wrote: Dear Freesurfers, Is the attached file an example of pial surface extending into cerebellum? Thank you very much! Sincerely, Ye ___ 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] Editing the endpoint ROIs, and re-running trac-all -path
Hi Anastasia, For one of my subjects, I am noticing that the right uncinate fasciculus is very diffuse and more importantly, erroneously crosses from the frontal to the temporal lobe. I looked at the original endpoint ROI generated by trac-all -prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the dilated endpoint ROI in the temporal lobe (rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz) and noticed that the endpoints appeared to cross over into the frontal lobe. Attached is a snapshot for your perusal. On the left side is a display of the subject/dmri/dtifit_FA.nii with the subject/dpath/rh.unc_AS_avg33_mni_bbr/path.pd.nii.gz tract superimposed over. As you can see, the right unc tract crosses from the frontal to the temporal lobe. On the right side is a display of the subject/dmri/brain_anat_mni.nii.gz with the endpoints subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2.nii.gz in green and subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1.nii.gz in blue (the red dots are control points). As you can see, the blue endpoints bleed over from the temporal to the frontal lobe. I tried to eliminate these blue points with fslview and then writing over rh.unc_AS_avg33_mni_bbr_end1.nii.gz. I performed a similar function manually editing rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz to better reflect the boundaries . I subsequently tried to re-run trac-all -path, and unfortunately, all my tracts looked much worse. Do you know if incorrectly placed endpoints impair the path reconstruction? Do you think you can help me? Any advice you can give would be much appreciated. -- Susie Kuo NIH Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* attachment: incorrect_endpoint_roi.png___ 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] Subcortical volume stream
Hello, I would like to verify something regarding subcortical volume estimation in Freesurfer before we move forward with our analyses. From what I've read on the wiki and listserv, it seems the subcortical and cortical processing streams are largely independent. If one were only interested in subcortical volumes (e.g. hippocampus, striatum) is it sufficient to run recon-all -all on the participants, verify/correct any issues with the registration, verify that the segmentations look correct, and then move forward with statistical analyses on the subcortical volumes using aseg.stats, or will refinements in the surfaces (e.g. manually removing dura mater from the pial surface) have an effect on subcortical volume and thus it is necessary to check the surfaces as well, make the corrections, rerun autorecon 2 and 3, the and then perform stats on the subcortical volumes? Thank you in advance for your time. Sincerely, Jim Monti -- Jim Monti PhD Candidate 2012-2013 Beckman Institute Graduate Fellow Memory Systems Laboratory (http://msl.beckman.illinois.edu/) Psychology-Cognitive Neuroscience University of Illinois at Urbana-Champaign ___ 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] longitudinal processing versioning
Hi guys, We have some longitudinal scans in which the time1 (T1) scans were processed with FS 5.1, and the T2/T3 scans haven't been processed yet. I'm trying to assess whether the differences between FS 5.1 and 5.3 warrant us re-running the T1 scans under FS 5.3. I see two possible options: 1) Process all cross-sectional runs under FS 5.1. i.e., we already have T1 under FS 5.1, so do the cross-runs of T2/T3 under 5.1 as well. (I'm assuming that it wouldn't be desirable to have a mix of versions at the cross-sectional stage). Then switch to using FS 5.3 for creating the template (-base) and longitudinal (-long) data. 2) Re-process the cross-sectional scans for T1 using FS 5.3, and do everything with FS 5.3. Do you have any reason to expect relevant differences in the final -long output between these two approaches? And, if approach (2) is necessary, do we need to re-run the T1 through FS 5.3 with the -clean flag? i.e,. if we were to re-run the cross-sectional version of the T1 scan using FS 5.3, but keeping previous edits, would that potentially bias the T1 scan in some fashion, since the T2/T3 scans will be run fresh in FS 5.3 without any prior manual edits? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] Group Analysis
Dear Freesurfer group I am interested to do group analysis on my data. If I want to do inter-individual group analysis, what is the minimum number of subjects I need to have? Also if I want to do intra-individual analysis, what is the best way in FS? I appreciate your time and your help. Thanks a lot, Nooshin ___ 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] (no subject)
Dear Freesurfer Users, I am trying to regress out the activity associated with button presses in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)? Thanks you, Nick ___ 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] FSFAST mkcontrast-sess with spmhrf 2 question
On 07/09/2013 04:11 PM, Joseph Dien wrote: Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a derivative boost amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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] (no subject)
Why not include it as a condition in your paradigm file? doug On 07/09/2013 03:47 PM, Nicholas Paul Denisuk wrote: Dear Freesurfer Users, I am trying to regress out the activity associated with button presses in my GLM analysis. How do I generate a nuisance regressor file analogous to a white matter regressor generated in functional connectivity (a one column time course file)? Thanks you, Nick ___ 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.
[Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question
Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a derivative boost amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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] Longitudinal processing
Hi Jon, I am also confused about this whole discussion. It seems from what you said earlier that at some point you have been able to run freesurfer on your images. You did not use the -i flag back then, but somehow managed to get from the original dicom (via nifti, via some mri_convert command) to some image that free surfer was able to use. Just do the same thing here and then once that is done, run the base and long stream on top of it. Best, Martin On Jul 8, 2013, at 2:45 PM, Jonathan Holt whats...@umich.edu wrote: I potentially have access to dicoms. My PI was confused as we're using GE 2D dcm images with 126 images per timepoint, he wasn't sure how to have them organized for a test run. On Jul 8, 2013, at 2:20 PM, Allison Stevens Player wrote: I see now. If the orientation information is incorrect, this will continue to be a problem. It sounds like you have access to the dicoms? If so, it's better to wait and use those. Allison On Mon, 8 Jul 2013, Jonathan Holt wrote: Allison I'm running the following recon-all -all -s subjID -i path/to/nifti attatched is the error recon log I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and these mgz's are generated before the recon-all process exits with errors. On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote: In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running? On Mon, 8 Jul 2013, Jonathan Holt wrote: As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s subjID for the second and third steps of the workflow. jon ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter 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 reu...@mit.edu Web : http://reuter.mit.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] FSFAST mkcontrast-sess with spmhrf 2 question
Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable sum(X(1:207,4).*X(1:207,5)) but not hugely non-zero so maybe just rounding errors? On Jul 9, 2013, at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 07/09/2013 04:11 PM, Joseph Dien wrote: Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a derivative boost amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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. Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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] Is it true that wm.mgz should lie inside the boundary of the white matter?
Dear Freesurfers, I have carefully gone through the tutorial data good_output, and find that wm.mgz lies inside the boundary of the white matter almost all the time, with fewer than 10 slices of exception. Whenever there is an exception, the affected area is relatively small. Therefore, I am wondering 1) Should wm.mgz always lie inside the boundary of the white matter? 2) If I have subjects whose wm.mgz lies outside the boundary of the white matter (which I do), should I add control points until the two nearly match? Thank you very much! Sincerely, Ye ___ 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] longitudinal processing versioning
Hi Michael, I think you should be fine with option 1. Just make sure that all cross are run with the same version (5.1). It is a little more complicated to keep track of things, but there should be no bias. That way you don't have to worry about edits. If you only have very few edits, I would do the clean thing an re-run all data from scratch with 5.3 manually transferring edits only where needed. Best, Martin On Jul 9, 2013, at 3:01 PM, Harms, Michael mha...@wustl.edu wrote: Hi guys, We have some longitudinal scans in which the time1 (T1) scans were processed with FS 5.1, and the T2/T3 scans haven't been processed yet. I'm trying to assess whether the differences between FS 5.1 and 5.3 warrant us re-running the T1 scans under FS 5.3. I see two possible options: 1) Process all cross-sectional runs under FS 5.1. i.e., we already have T1 under FS 5.1, so do the cross-runs of T2/T3 under 5.1 as well. (I'm assuming that it wouldn't be desirable to have a mix of versions at the cross-sectional stage). Then switch to using FS 5.3 for creating the template (-base) and longitudinal (-long) data. 2) Re-process the cross-sectional scans for T1 using FS 5.3, and do everything with FS 5.3. Do you have any reason to expect relevant differences in the final -long output between these two approaches? And, if approach (2) is necessary, do we need to re-run the T1 through FS 5.3 with the -clean flag? i.e,. if we were to re-run the cross-sectional version of the T1 scan using FS 5.3, but keeping previous edits, would that potentially bias the T1 scan in some fashion, since the T2/T3 scans will be run fresh in FS 5.3 without any prior manual edits? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter 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 reu...@mit.edu Web : http://reuter.mit.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] Is it true that wm.mgz should lie inside the boundary of the white matter?
No, the wm.mgz is just a means to initialize the surface deformation, and the final white surface can be inside or outside of it. cheers Bruce On Tue, 9 Jul 2013, ye tian wrote: Dear Freesurfers, I have carefully gone through the tutorial data good_output, and find that wm.mgz lies inside the boundary of the white matter almost all the time, with fewer than 10 slices of exception. Whenever there is an exception, the affected area is relatively small. Therefore, I am wondering 1) Should wm.mgz always lie inside the boundary of the white matter? 2) If I have subjects whose wm.mgz lies outside the boundary of the white matter (which I do), should I add control points until the two nearly match? Thank you very much! Sincerely, Ye ___ 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] Is it true that wm.mgz should lie inside the boundary of the white matter?
Dear Bruce, Thank you very much! Sincerely, Ye On Tue, Jul 9, 2013 at 3:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: No, the wm.mgz is just a means to initialize the surface deformation, and the final white surface can be inside or outside of it. cheers Bruce On Tue, 9 Jul 2013, ye tian wrote: Dear Freesurfers, I have carefully gone through the tutorial data good_output, and find that wm.mgz lies inside the boundary of the white matter almost all the time, with fewer than 10 slices of exception. Whenever there is an exception, the affected area is relatively small. Therefore, I am wondering 1) Should wm.mgz always lie inside the boundary of the white matter? 2) If I have subjects whose wm.mgz lies outside the boundary of the white matter (which I do), should I add control points until the two nearly match? Thank you very much! Sincerely, Ye 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/**compliancelinehttp://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] FSFAST mkcontrast-sess with spmhrf 2 question
I tried correlations and the 2nd derivative is definitely not orthogonal. corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) ans = 1. -0. -0.5427 -0.1. -0.0298 -0.5427 -0.02981. I looked at the regressors that SPM generates for the same data: ans = 1.0.04360.1740 0.04361. -0.0226 0.1740 -0.02261. The first derivative is not as orthogonal but the second derivative was much more orthogonal. Does this have to do with what you noted below about how the second derivative is being calculated? So does this mean I should avoid the spmhrf 2 option entirely to avoid loss of statistical power? Thanks for the help! Joe On Jul 9, 2013, at 4:34 PM, Joseph Dien jdie...@mac.com wrote: Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable sum(X(1:207,4).*X(1:207,5)) but not hugely non-zero so maybe just rounding errors? On Jul 9, 2013, at 4:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 07/09/2013 04:11 PM, Joseph Dien wrote: Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a derivative boost amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com mailto:jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ 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. Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com// ___ Freesurfer mailing list
[Freesurfer] Basic question for running recon-all on ios
Hi Freesurfer users, I am new to Freesurfer and have run into difficulty with running the recon-all command in terminal on osx. When I type in the command bellow recon-all –i IM-0001-0001.dcm –subject bert –all I receive ERROR: Flag i unrecognized. Also the usage info on recon-all does not list -i as far as I can see. Has it been replaced by a different flag? On a different note. Has anyone tried to install freesurfer on a second partition with the drive name containing a space character? I have two drives installed on my mac with the second drive foolishly labeled Second Drive. When I tried to install the bash script (export and source commands) it ran into trouble recognising the space character between second and drive. I had to change the name to Second_Drive which unfortunately mucks up other apps that use the reference to that original name fine. Any words of wisdom would be greatly appreciated. Thanks in advance Pascal ___ 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] Basic question for running recon-all on ios
Hello Pascal, What exactly are you trying to achieve? If you would like to make 001.mgz, then use recon-all -i IM-0001-0001.dcm -s bert. If you would like to reconstruct the surfaces and the volumes (after doing the first step), try recon-all -s subject -all. As far as I am concerned, freesurfer is not very good at recognizing spaces. I completely abandoned space keys altogether. Sincerely, Ye On Tue, Jul 9, 2013 at 4:57 PM, Pascal Bou-Haidar pasca...@gmail.comwrote: Hi Freesurfer users, I am new to Freesurfer and have run into difficulty with running the recon-all command in terminal on osx. When I type in the command bellow recon-all –i IM-0001-0001.dcm –subject bert –all I receive ERROR: Flag i unrecognized. Also the usage info on recon-all does not list -i as far as I can see. Has it been replaced by a different flag? On a different note. Has anyone tried to install freesurfer on a second partition with the drive name containing a space character? I have two drives installed on my mac with the second drive foolishly labeled Second Drive. When I tried to install the bash script (export and source commands) it ran into trouble recognising the space character between second and drive. I had to change the name to Second_Drive which unfortunately mucks up other apps that use the reference to that original name fine. Any words of wisdom would be greatly appreciated. Thanks in advance Pascal ___ 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] Questions regarding QDEC
Dear Prof. Greve I have additional (and probably silly) questions. 1) Is there much difference between result of monte-carlo null-z simulation (QDEC GUI) analysis and that of clusterwise correction for multiple comparisons using 1 permutations? I'm guessing similar results between both methods; however I'm wondering whether significant clusters from the former processing might disappeared when using the latter process, or vice versa? 2) Does QDEC analysis automatically produce *.glmdir files for each contrast? If not, how can I make *.glmdir from the QDEC (not using the mri_glmfit command)? Thank you for your kindness Kim 2013/7/9 Douglas N Greve gr...@nmr.mgh.harvard.edu On 07/07/2013 01:36 PM, jh kim wrote: Dear FreeSurfer experts... Please be patient with a newbie's questions. For the first time, I'm trying to analyze between-group differences in cortical thickness (controls vs. patients) by using FS 5.1.0 and QDEC. I've read through the online manual and mailing lists; however, I cannot figure out the following queries. 1) I selected 'group' (con, pat) as a fixed factor (gender is not applicable because all are females), and demeaned age as a continuous covariate. After analyzing using DODS option, several questions are shown in the Display GUI panel. Does the question Does the average thickness differ between con and pat? mean between-group difference of cortical thickness after *controlling for the effect of age*? Yes, it controls for all your other factors. 2) Should I include average cortical thickness of the left or right cortex (calculated from the command, mris_anatomical_stats -l lh.cortex.label -f subid.txt subid lh)as a nuisance variable? I know this issue has been addressed many times before, and it is generally recommended not to include as a nuisance factor. However, in case of statistically significant difference in mean cortical thickness of one hemisphere (unpaired two sample t-test by SPSS), is it still not necessary to include it as a nuisance factor? From the similar points of view, how about volume and surface area analyses (include or not total cortical volume and total surface area as a nuisance factor, respectively) ? I don't have a strong opinion about removing the global mean thickness, but I think others (Mike Harms?) recommend to do so. For volume and surface area, you probably want to normalize by the ICV. 3) I found several significant clusters that are corrected for multiple comparisons using Monte Carlo simulation (corrected P 0.01) in the bottom of Display panel. I assume that this procedures take 10,000 permutations by default. Am I right? It is 10k iterations of generating white noise (not a permutation test unless you specified that explicitly). 4) Last question, how can I extract individual value (cortical thickness per subject) from the significant clusters? I want to do this 'all-at-once'. Please let me know the command. There should already be a file in the output folder called something.y.ocn.dat that has a row for each input subject and a column for each cluster. doug Apology for bothering you. Any comments would be greatly appreciated. Thanks. Kim ___ 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. ___ 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.
