Re: [Freesurfer] make_average_subject error about limit
Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit. And, when I type the following command: mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.noise_0.5- 1.glmdir The terminal shows: ERROR: Option --cortex unknown Would you tell me what’s wrong? And how do I do to solve this error? Thank you in advance! Feng-Xian On Tue, 07 Jul 2009 11:49:32 -0400, Douglas N Greve wrote Is there a space between -- and hemi? caching is just a way to speed some analyses by pre-smoothing and sampling to the standard space. doug Feng-Xian wrote: Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and some contrast matrices and put them into my analysis dir. After that, I start to run group analysis. But, when I type the following commands: mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh -- meas thickness --out lh.noise_0.5-1-5.thickness.00.mgh The terminal shows: ERROR: flag -- not recognized Now, I have two problems want to ask. 1) What's wrong about the commands that I type? And, how to solve the problem? 2) I found this commands from the FreeSurfer web. And, I'm confused about that two ways to do analysis. One is cached (qcached) data, and the other is uncached data. What's way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis, and, I want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't understand the differences from them. Thank you in advance! Feng-Xian On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote in general, it is not necessary to run make_average_subject prior to performing an analysis. using the default average subject that freesurfer provides, named 'fsaverage', is sufficient for most cases, because it doesnt affect the analysis, its only used as a target upon which to project results. the 'fsaverage' subject is in the $FREESURFER_HOME/subjects dir, and you should copy it to your own SUBJECTS_DIR prior to performing any group analysis. Nick On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote: Hi, I know I wont to do QDEC now, so I want to change the method of group analysis from QDEC to the web you tell me. But, I did QDEC before. Before I do DODS, should I do make_average_subject to view the result of my subjects? Or, I have another method to view the results?? Thank you in advance! Feng-Xian On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote Feng-xian, I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work with three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples: http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and note one of them is 1 Factor, 3 Levels. Nick On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s subjid -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian - Chang Gung University Mail Server
Re: [Freesurfer] make_average_subject error about limit
You probably have an older version that does not recoginze --cortex. Try --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label instead Feng-Xian wrote: Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit. And, when I type the following command: mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.noise_0.5- 1.glmdir The terminal shows: ERROR: Option --cortex unknown Would you tell me what’s wrong? And how do I do to solve this error? Thank you in advance! Feng-Xian On Tue, 07 Jul 2009 11:49:32 -0400, Douglas N Greve wrote Is there a space between -- and hemi? caching is just a way to speed some analyses by pre-smoothing and sampling to the standard space. doug Feng-Xian wrote: Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and some contrast matrices and put them into my analysis dir. After that, I start to run group analysis. But, when I type the following commands: mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh -- meas thickness --out lh.noise_0.5-1-5.thickness.00.mgh The terminal shows: ERROR: flag -- not recognized Now, I have two problems want to ask. 1) What's wrong about the commands that I type? And, how to solve the problem? 2) I found this commands from the FreeSurfer web. And, I'm confused about that two ways to do analysis. One is cached (qcached) data, and the other is uncached data. What's way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis, and, I want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't understand the differences from them. Thank you in advance! Feng-Xian On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote in general, it is not necessary to run make_average_subject prior to performing an analysis. using the default average subject that freesurfer provides, named 'fsaverage', is sufficient for most cases, because it doesnt affect the analysis, its only used as a target upon which to project results. the 'fsaverage' subject is in the $FREESURFER_HOME/subjects dir, and you should copy it to your own SUBJECTS_DIR prior to performing any group analysis. Nick On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote: Hi, I know I wont to do QDEC now, so I want to change the method of group analysis from QDEC to the web you tell me. But, I did QDEC before. Before I do DODS, should I do make_average_subject to view the result of my subjects? Or, I have another method to view the results?? Thank you in advance! Feng-Xian On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote Feng-xian, I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work with three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples: http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and note one of them is 1 Factor, 3 Levels. Nick On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s subjid -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong
Re: [Freesurfer] make_average_subject error about limit
Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and some contrast matrices and put them into my analysis dir. After that, I start to run group analysis. But, when I type the following commands: mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas thickness --out lh.noise_0.5-1-5.thickness.00.mgh The terminal shows: ERROR: flag -- not recognized Now, I have two problems want to ask. 1) What's wrong about the commands that I type? And, how to solve the problem? 2) I found this commands from the FreeSurfer web. And, I'm confused about that two ways to do analysis. One is cached (qcached) data, and the other is uncached data. What's way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis, and, I want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't understand the differences from them. Thank you in advance! Feng-Xian On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote in general, it is not necessary to run make_average_subject prior to performing an analysis. using the default average subject that freesurfer provides, named 'fsaverage', is sufficient for most cases, because it doesnt affect the analysis, its only used as a target upon which to project results. the 'fsaverage' subject is in the $FREESURFER_HOME/subjects dir, and you should copy it to your own SUBJECTS_DIR prior to performing any group analysis. Nick On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote: Hi, I know I wont to do QDEC now, so I want to change the method of group analysis from QDEC to the web you tell me. But, I did QDEC before. Before I do DODS, should I do make_average_subject to view the result of my subjects? Or, I have another method to view the results?? Thank you in advance! Feng-Xian On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote Feng-xian, I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work with three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples: http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and note one of them is 1 Factor, 3 Levels. Nick On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s subjid -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] make_average_subject error about limit
Is there a space between -- and hemi? caching is just a way to speed some analyses by pre-smoothing and sampling to the standard space. doug Feng-Xian wrote: Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and some contrast matrices and put them into my analysis dir. After that, I start to run group analysis. But, when I type the following commands: mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas thickness --out lh.noise_0.5-1-5.thickness.00.mgh The terminal shows: ERROR: flag -- not recognized Now, I have two problems want to ask. 1) What's wrong about the commands that I type? And, how to solve the problem? 2) I found this commands from the FreeSurfer web. And, I'm confused about that two ways to do analysis. One is cached (qcached) data, and the other is uncached data. What's way is suitable to my subjects? (My subjects is one factor and three levels, had run QDEC before, but QDEC is not good job to analysis, and, I want to change the analysis method from QDEC to DODS) So, which way do I choose to analysis my subjects?? Idon't understand the differences from them. Thank you in advance! Feng-Xian On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote in general, it is not necessary to run make_average_subject prior to performing an analysis. using the default average subject that freesurfer provides, named 'fsaverage', is sufficient for most cases, because it doesnt affect the analysis, its only used as a target upon which to project results. the 'fsaverage' subject is in the $FREESURFER_HOME/subjects dir, and you should copy it to your own SUBJECTS_DIR prior to performing any group analysis. Nick On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote: Hi, I know I wont to do QDEC now, so I want to change the method of group analysis from QDEC to the web you tell me. But, I did QDEC before. Before I do DODS, should I do make_average_subject to view the result of my subjects? Or, I have another method to view the results?? Thank you in advance! Feng-Xian On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote Feng-xian, I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work with three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples: http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and note one of them is 1 Factor, 3 Levels. Nick On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s subjid -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas
[Freesurfer] make_average_subject error about limit
Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s subjid -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject error about limit
Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s subjid -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ 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
Re: [Freesurfer] make_average_subject error about limit
Feng-xian, I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work with three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples: http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and note one of them is 1 Factor, 3 Levels. Nick On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s subjid -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ 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
Re: [Freesurfer] make_average_subject error about limit
You don't *have to* to run make_average_subject to do your analysis, only if you want to view the results on a map with the curvature patterns averaged over your subjects. As for the limit error, how old is your version of freesurfer? That line was removed about 1.5 years ago... doug Feng-Xian wrote: Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s subjid -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to DODS. I had a fsaverage file when I running QDEC, but the fsaverage did not use my subjects to make. So, can I use the fsaverage file to run DODS? If not, I should make a new fsaverage with my subjects. But, I encounter the problem about make_average_subject. When I type: make_average_subject --subects subjid1 subjid2 ... the terminal show that: limit: descriptors: Can't remove limit What's wrong about the command I type? And, how to solve the problem? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
