[Freesurfer] How to threshold an input mutli-volume?
Hi, all. Can mri_threshold threshold an input mutli-volume file? With a seven volumes NIFTI file, all voxels other than in the first volume are set to zero. In addition, the help for mri_threshold options is very limited. There is nothing about the options. Usage: mri_threshold [options] in vol thresh out_vol This program will threshold an input volume Where do I get more detailed description? Best Regards. ___ 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
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
[Freesurfer] Re: Melodic results on Freesurfer average subject
great, thanks Christian. I think Doug has some tools that can be used for this. cheers Bruce On Tue, 7 Jul 2009, Christian F. Beckmann wrote: Hi Bruce Martina, Yes, the easiest is to run melodic temporal concatenation on data pre- processed and warped into a common space by freesurfer. Melodic does not care about the space the data lives in - everything is reshaped into simple matrices anyways. Have a look at the melodic command line call (in the log file) to see how to call melodic with data pre-processed outside the FSL environment. Essentially you just need to create a single ASCII text file containing the N different input files (one per row) and then use melodic -i inputfilenames -o outputdir -a concat [otheroptions] Hope this helps cheers Christian On 7 Jul 2009, at 12:59, Bruce Fischl wrote: Hi Martina, the freesurfer average subject lives in a spherical coordinate system created using nonlinear surface-based warps, so it's very far from any version of the mni. Maybe Steve or Christian can comment on integration, but certainly you would want to do the multi-subject ICA in the surface coordinate system. cheers, Bruce On Tue, 7 Jul 2009, Campanella Martina wrote: Hi Freesurfer, I've run a multi-subject analysis with MELODIC(FSL), resting-state data. Now I'd like to view the results on the Freesurfer average subject (made with make_average_subject)... But... FSL uses mni152 and Freesurfer mni305. Is it true? If so... any suggestion? Thank you Cheers, Martina Campanella ___ Christian F. Beckmann, DPhil Senior Lecturer, Clinical Neuroscience Department Division of Neuroscience and Mental Health Imperial College London, Hammersmith Campus Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548 Email: c.beckm...@imperial.ac.uk http://www.imperial.ac.uk/medicine/people/c.beckmann/ Senior Research Fellow, FMRIB Centre University of Oxford JR Hospital - Oxford OX3 9DU Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717 Email: beckm...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~beckmann ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] WM-hypointensities
Hi all, I don't kown what is WM-hypointensities Is it a volume? I suppose this because WM-hypointensities is in the aseg.stats. thanks Anita di Iasio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM-hypointensities
they are voxels with abnormal appearing white matter On Tue, 7 Jul 2009, Anita di Iasio wrote: Hi all, I don't kown what is WM-hypointensities Is it a volume? I suppose this because WM-hypointensities is in the aseg.stats. thanks Anita di Iasio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ROI
Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all the precentral motor area. Finally I am downsampling the output from vol2roi in order to use it as an FSL target mask in ProbtrackX. When checking the output in FSL, the mask seems to be missaligned with the original T1 image, is it beacuse an error in the header or is it because I am doing something wrong in the process? Thenk you for your help, let me know if you need anything else. -- Natalia Sanchez ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ROI
Hi Natalia, at what stage is it misaligned? Note that we do everything in native space, so unless you apply a transform to the ROI it will not be in tal coords. Also, you might consider using our estimate of M1 from the Zilles/Amunts data instead of drawing it (e.g. lh.BA4a.label). cheers, Bruce On Tue, 7 Jul 2009, Natalia Sanchez wrote: Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all the precentral motor area. Finally I am downsampling the output from vol2roi in order to use it as an FSL target mask in ProbtrackX. When checking the output in FSL, the mask seems to be missaligned with the original T1 image, is it beacuse an error in the header or is it because I am doing something wrong in the process? Thenk you for your help, let me know if you need anything else. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Gaussian random field correction
I've actually implemented that already, but I have not been satisfied with how well the grf results match the simulations. doug jorge luis wrote: There is a very good implementation of surface-based Gaussian Random Field theory (GRF) correction from Keith J. Worsley at: http://www.stat.uchicago.edu/~worsley/surfstat/ The matlab toolbox there provides functions for reading freesurfer surface data. I have compared the results (by means of simulations) with those from freesurfer permutation testing and I think it is a very good alternative. Cheers Jorge Luis Bernal Rusiel Phd Student. Laboratory of functional Neuroscience. University of Pablo de Olavide. Seville. Spain --- El lun, 6/7/09, Jürgen Hänggi j.haen...@psychologie.uzh.ch escribió: De: Jürgen Hänggi j.haen...@psychologie.uzh.ch Asunto: [Freesurfer] Gaussian random field correction Para: Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu Fecha: lunes, 6 julio, 2009 12:11 Dear FS experts Is the GRF correction for multiple comparisons implemented in FS yet and is there any documentation how to use it? Thanks in advance Best regards Jürgen Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 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
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
Re: [Freesurfer] Re: Melodic results on Freesurfer average subject
Use the registration matrix found in $FREESURFER_HOME/average/mni152.register.dat doug Bruce Fischl wrote: great, thanks Christian. I think Doug has some tools that can be used for this. cheers Bruce On Tue, 7 Jul 2009, Christian F. Beckmann wrote: Hi Bruce Martina, Yes, the easiest is to run melodic temporal concatenation on data pre- processed and warped into a common space by freesurfer. Melodic does not care about the space the data lives in - everything is reshaped into simple matrices anyways. Have a look at the melodic command line call (in the log file) to see how to call melodic with data pre-processed outside the FSL environment. Essentially you just need to create a single ASCII text file containing the N different input files (one per row) and then use melodic -i inputfilenames -o outputdir -a concat [otheroptions] Hope this helps cheers Christian On 7 Jul 2009, at 12:59, Bruce Fischl wrote: Hi Martina, the freesurfer average subject lives in a spherical coordinate system created using nonlinear surface-based warps, so it's very far from any version of the mni. Maybe Steve or Christian can comment on integration, but certainly you would want to do the multi-subject ICA in the surface coordinate system. cheers, Bruce On Tue, 7 Jul 2009, Campanella Martina wrote: Hi Freesurfer, I've run a multi-subject analysis with MELODIC(FSL), resting-state data. Now I'd like to view the results on the Freesurfer average subject (made with make_average_subject)... But... FSL uses mni152 and Freesurfer mni305. Is it true? If so... any suggestion? Thank you Cheers, Martina Campanella ___ Christian F. Beckmann, DPhil Senior Lecturer, Clinical Neuroscience Department Division of Neuroscience and Mental Health Imperial College London, Hammersmith Campus Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548 Email: c.beckm...@imperial.ac.uk http://www.imperial.ac.uk/medicine/people/c.beckmann/ Senior Research Fellow, FMRIB Centre University of Oxford JR Hospital - Oxford OX3 9DU Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717 Email: beckm...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~beckmann ___ 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
Re: [Freesurfer] ROI
Sounds like there are a lot of places where something could have gone wrong. Have you checked the output each step of the way or just the final result? doug Natalia Sanchez wrote: Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all the precentral motor area. Finally I am downsampling the output from vol2roi in order to use it as an FSL target mask in ProbtrackX. When checking the output in FSL, the mask seems to be missaligned with the original T1 image, is it beacuse an error in the header or is it because I am doing something wrong in the process? Thenk you for your help, let me know if you need anything else. -- Natalia Sanchez ___ 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
[Freesurfer] citation for appropriateness of using freesurfer with children
Hello- I am using Freesurfer to obtain cortical parcellations for both children (aged 8-11 years) and adults. A reviewer asked for evidence that the parcellation works equally well in children and adults. Has this been tested empirically and published anywhere? I found a post saying not too worry about it for this age range (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06537.html), but reviewers tend to like references to published evidence :) The closest I get are papers by Burgund et al., 2002 and Kang et al., 2003 (http://tinyurl.com/m6v5s5; http://tinyurl.com/kwckol), but those papers do not use Freesurfer. Anything with Freesurfer? Anthony -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: ad...@uchicago.edu Web: http://home.uchicago.edu/~adick/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to Fitting Tensors in dt_recon?
you can apply it to the raw data. The tensor is just assembled from the regression coefficients (betas) in the standard way, ie, a design matrix is constructed with 7 columns. Each column consists of [gx gy gz gx*gy gx*gz gy*gz 1], and the 1st 6 coefficients for the tensor. doug 李猛 wrote: Thank you very much. In fact, I want to insert the bet module before calculating the tensor, eigvals, eigvecs, fa, ra etc in dt_recon. I also know mri_glmfit can create glm-related images. But I can't find the tensor calculation in (mri_glmfit --y $fec --glmdir $OutDir --dti $bvals $bvecs). On Tue, Jul 7, 2009 at 12:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It just takes the log of the input and constructs a design matrix from your bvals and bvecs, then fits a glm. doug ?? wrote: Hi, All. The related item of Fitting Tensors is listed from the dt_recon. # Fit tensors echo #...@#--- | tee -a $LF echo Fitting Tensors | tee -a $LF date | tee -a $LF set cmd = (mri_glmfit --y $fec --glmdir $OutDir); if($#bvals == 0) then set cmd = ($cmd --dti $infodump) else set cmd = ($cmd --dti $bvals $bvecs) endif However, I can't find any description about this argument(--dti) in mri_glmfit. Did the mri_glmfit call the dtifit to fit the tensor from fsl?If not, what is it? -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA -- 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
Re: [Freesurfer] citation for appropriateness of using freesurfer with children
Hi Anthony, Peng Yu had a relatively recent IEEE TMI paper in which we parcellated neonates. The citation (and paper) are on the wiki. cheers, Bruce On Tue, 7 Jul 2009, Anthony Dick wrote: Hello- I am using Freesurfer to obtain cortical parcellations for both children (aged 8-11 years) and adults. A reviewer asked for evidence that the parcellation works equally well in children and adults. Has this been tested empirically and published anywhere? I found a post saying not too worry about it for this age range (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06537.html), but reviewers tend to like references to published evidence :) The closest I get are papers by Burgund et al., 2002 and Kang et al., 2003 (http://tinyurl.com/m6v5s5; http://tinyurl.com/kwckol), but those papers do not use Freesurfer. Anything with Freesurfer? Anthony ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: BUG in multiple comparisons correction for ABS
Hello Doug, Thanks so much for fixing this bug. I tried it and it works perfectly fine and it solves the problem that I had. Many thanks again, Nasim Nasim and Judith (and everyone else), I've found and fixed a bug that was causing the surfcluster results for the mc and perm simulations of absolute abs contrasts. To implement the fix, get Linux 64bit versions of these files and copy them to $FREESURFER_HOME/bin (make backups of the originals:). ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit You can then run something like: mri_glmfit-sim --glmdir yourglmdir --no-sim mc-z.abs The --no-sim option tells it NOT to do the full simulation again, just use the CSDs that are there to recompute the cluster results for each contrast, so it should be done in a matter of minutes. If you've used a permutation, then run mri_glmfit-sim --glmdir yourglmdir --no-sim perm.abs Please let me know if this fixes the problem. doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Citing QDEC
Hello, Could you advise me on how to cite QDEC please? Thank you, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Within group analysis
I am trying to run glm for two different scans of same subjects, ie first year scan vs second year scan. I ran the mris_prepoc and mri_surf2surf and it completed without error. When i run mri_glmfit it gives me error ERROR: gdfReadV1: Input line 1, subjid = 0049_05102006 Found 1 variables, expected. 0 FSGDF Format Error: file = CAA_1stScan_VS_2ndScan_Control_thickness.fsgd, tag=Input Ayaz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Within group analysis
looks like you have a variable on the input line that you did not declare. Check to make sure that your fsgd file has the proper format. Muhammad Ayaz wrote: I am trying to run glm for two different scans of same subjects, ie first year scan vs second year scan. I ran the mris_prepoc and mri_surf2surf and it completed without error. When i run mri_glmfit it gives me error ERROR: gdfReadV1: Input line 1, subjid = 0049_05102006 Found 1 variables, expected. 0 FSGDF Format Error: file = CAA_1stScan_VS_2ndScan_Control_thickness.fsgd, tag=Input Ayaz ___ 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
Re: [Freesurfer] Citing QDEC
It's just a GLM, so you only need to say that you used QDEC and cite our web site (www.surfer.nmr.mgh.harvard.edu) doug nmal...@mclean.harvard.edu wrote: Hello, Could you advise me on how to cite QDEC please? Thank you, Nasim ___ 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
[Freesurfer] restarting after edits to brainmask.mgz and wm.mgz
Hi, I was just wondering if I should use -autorecon2-wm or -autorecon2-pial after making adjustments to both the brainmask.mgz and wm.mgz when restarting freesurfer. -Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 940305 (650)498-4538 http://cibsr.stanford.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] restarting after edits to brainmask.mgz and wm.mgz
autorecon2-wm which is a superset of autorecon2-pial. cheers Bruce On Tue, 7 Jul 2009, Mira Michelle Raman wrote: Hi, I was just wondering if I should use -autorecon2-wm or -autorecon2-pial after making adjustments to both the brainmask.mgz and wm.mgz when restarting freesurfer. -Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 940305 (650)498-4538 http://cibsr.stanford.edu ___ 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] How to threshold an input mutli-volume?
I guess it would be pretty easy to fix to work on multi-frame images. What hardware/software platform are you using? Bruce On Tue, 7 Jul 2009, [UTF-8] ?? wrote: Hi, all. Can mri_threshold threshold an input mutli-volume file? With a seven volumes NIFTI file, all voxels other than in the first volume are set to zero. In addition, the help for mri_threshold options is very limited. There is nothing about the options. Usage: mri_threshold [options] in vol thresh out_vol This program will threshold an input volume Where do I get more detailed description? Best Regards. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to threshold an input mutli-volume?
Thank you in advance for your help. We installed the freesurfer on a ubuntu 8.04 i686 machine. On Wed, Jul 8, 2009 at 9:57 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: I guess it would be pretty easy to fix to work on multi-frame images. What hardware/software platform are you using? Bruce On Tue, 7 Jul 2009, [UTF-8] ?? wrote: Hi, all. Can mri_threshold threshold an input mutli-volume file? With a seven volumes NIFTI file, all voxels other than in the first volume are set to zero. In addition, the help for mri_threshold options is very limited. There is nothing about the options. Usage: mri_threshold [options] in vol thresh out_vol This program will threshold an input volume Where do I get more detailed description? Best Regards. -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
