[Freesurfer] white matter snr
Hi, I would like to know whether it is a good idea to use the snr measure from *wm-anat-snr *as a covariate in lme (or glm) analyses? I find significant effects of snr on cortical area and thickness. Am I right in thinking I should be more cautious about interpreting findings in regions where wm snr has a strong/significant effect on the dependent variable? Also, if I use it in an lme model, would it be permissible to use it as a random factor? And finally, is there any similar snr measure for gray matter? (There is of course a wm/gm contrast measure but it is not very thoroughly documented.) Thank you! yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) Trondheim, Norway ___ 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] Speeding Freesurfer
My impression is that CUDA drivers are not available for AMD FirePro graphics boards. Aren't they? Sorry, I dont know the answer to that question. In regard to the next release of freesurfer, my guestimate would be between 1-2 months. -Zeke On 12/03/2014 02:12 AM, Francesco Cardinale wrote: Zeke, Thank you for your prompt response. I've been using for a long time my own bash script that parallelizes the simultaneous computation of the hemisphere-specific steps. Moreover, I re-organized the pipeline for obtaining the pial reconstruction asap. I'm happy to know that next release of Freesurfer will support openmp under MacOS X. Can you roughly estimate when it will be available? I also tried with VMWare Fusion and a VM with CentOS 6.6, and it mapped 12 virtual cores on the real cores. The time needed for CAREG was reduced by about 2/3. My impression is that CUDA drivers are not available for AMD FirePro graphics boards. Aren't they? Thanks again Cico Francesco Cardinale Neurosurgeon Claudio Munari Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia phone 0039 02 64442917 fax 0039 02 64442868 e-mail francesco.cardin...@ospedaleniguarda.it mailto:francesco.cardin...@ospedaleniguarda.it Il giorno 02/dic/2014, alle ore 15:59, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu ha scritto: Francesco, There are ways to speed up single subject processing time by parrallelizing the parts of the recon-all stream that deal with the left and right hemisphere so they get processed simultaneously. This would require a custom script and thus is a bit more complicated than a single call to recon-all. But I can provide you the skeleton of such a script if you like. We no longer support CUDA but it is included in the 5.3 release and people have reported success using it. The gpu can be used along with the openmp flag to further quicken processing time, but only on CentOS machines, as openmp is not supported on the Mac build of freesurfer v5.3. However, the next release of freesurfer WILL support openmp on the Mac side. -Zeke On 11/27/2014 04:31 AM, Francesco Cardinale wrote: Dear Freesurfer experts, I've been using Freesurfer on Mac computers for some years with great satisfaction. I just bought a monster computer, a Mac Pro with 12-core Xeon E5, 64 Gb RAM, GPU AMD FirePro D700. This is, out of doubt, a marvellous machine to compute many subjects simultaneously, but quite often we need to run one single subject as fast as possible. What can I do? OpenMP optimization is available only for CentOS, isn't it? What about CentOS in a VM, will it be able to exploit multithreading, or is it necessary to configure a multiboot machine with BootCamp? Any suggestions to do that? Moreover, what about CUDA and GPU acceleration? Is it available for FirePro graphic cards? Any other suggestions? Anything really new in the field with the next version of Freesurfer? Thanks a lot Francesco Cardinale, MD Neurosurgeon Claudio Munari Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia x-apple-data-detectors://0/0 phone 0039 02 64442917 tel:0039%2002%2064442917 fax 0039 02 64442868 tel:0039%2002%2064442868 e-mail francesco.cardin...@ospedaleniguarda.it mailto:francesco.cardin...@ospedaleniguarda.it mailto:francesco.cardin...@ospedaleniguarda.it ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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] Speeding Freesurfer
CUDA is specific to NVIDIA graphics devices. http://www.nvidia.com/object/cuda_home_new.html On Thu, Dec 4, 2014 at 10:10 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: My impression is that CUDA drivers are not available for AMD FirePro graphics boards. Aren't they? Sorry, I dont know the answer to that question. In regard to the next release of freesurfer, my guestimate would be between 1-2 months. -Zeke On 12/03/2014 02:12 AM, Francesco Cardinale wrote: Zeke, Thank you for your prompt response. I've been using for a long time my own bash script that parallelizes the simultaneous computation of the hemisphere-specific steps. Moreover, I re-organized the pipeline for obtaining the pial reconstruction asap. I'm happy to know that next release of Freesurfer will support openmp under MacOS X. Can you roughly estimate when it will be available? I also tried with VMWare Fusion and a VM with CentOS 6.6, and it mapped 12 virtual cores on the real cores. The time needed for CAREG was reduced by about 2/3. My impression is that CUDA drivers are not available for AMD FirePro graphics boards. Aren't they? Thanks again Cico Francesco Cardinale Neurosurgeon Claudio Munari Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia phone 0039 02 64442917 fax 0039 02 64442868 e-mail francesco.cardin...@ospedaleniguarda.it mailto:francesco.cardin...@ospedaleniguarda.it Il giorno 02/dic/2014, alle ore 15:59, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu ha scritto: Francesco, There are ways to speed up single subject processing time by parrallelizing the parts of the recon-all stream that deal with the left and right hemisphere so they get processed simultaneously. This would require a custom script and thus is a bit more complicated than a single call to recon-all. But I can provide you the skeleton of such a script if you like. We no longer support CUDA but it is included in the 5.3 release and people have reported success using it. The gpu can be used along with the openmp flag to further quicken processing time, but only on CentOS machines, as openmp is not supported on the Mac build of freesurfer v5.3. However, the next release of freesurfer WILL support openmp on the Mac side. -Zeke On 11/27/2014 04:31 AM, Francesco Cardinale wrote: Dear Freesurfer experts, I've been using Freesurfer on Mac computers for some years with great satisfaction. I just bought a monster computer, a Mac Pro with 12-core Xeon E5, 64 Gb RAM, GPU AMD FirePro D700. This is, out of doubt, a marvellous machine to compute many subjects simultaneously, but quite often we need to run one single subject as fast as possible. What can I do? OpenMP optimization is available only for CentOS, isn't it? What about CentOS in a VM, will it be able to exploit multithreading, or is it necessary to configure a multiboot machine with BootCamp? Any suggestions to do that? Moreover, what about CUDA and GPU acceleration? Is it available for FirePro graphic cards? Any other suggestions? Anything really new in the field with the next version of Freesurfer? Thanks a lot Francesco Cardinale, MD Neurosurgeon Claudio Munari Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda Ca' Granda Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia x-apple-data-detectors://0/0 phone 0039 02 64442917 tel:0039%2002%2064442917 fax 0039 02 64442868 tel:0039%2002%2064442868 e-mail francesco.cardin...@ospedaleniguarda.it mailto:francesco.cardin...@ospedaleniguarda.it mailto:francesco.cardin...@ospedaleniguarda.it ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] --pca flag on mri_glmfit
Dear Freesurfer experts, Potentially super-noob question here, but I'm curious about the --pca flag on mri_glmfit. I can see that it does PCA/SVD on the dataset? in question and saves the residuals to the glmdir specified, but I was unable to find anything in the documentation describing what exactly it is doing. I got sdiag.mat, stats.dat (with some rather large eigenvalues, on the order of 40k, but they might look more normal once I demean my variables), a u.mtx, a v.mgh surface overlay, and an error log (stating MatlabRead: readHeder returned NULL, ImageRead (/path/glmdir/pca-eres/sdiag.mat) failed. When I loaded the v.mgh, it looked rather binarized (with red and blue colors covering the entire cortex mask for that hemi). May I ask how it is computing these eigenvalues? What the sdiag and u.mtx files are used for? And what is being displayed in the v.mgh (is it components? if so, what do these components reflect?). And most importantly, is this meant primarily for functional data or can it be applied to mophometric data? If it can be used for the latter, what is being fed into the PCA/SVD to determine spatial components? -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpdera...@gmail.com, faus...@uab.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Some questions about fsaverage
Hello, I am currently working with cortical thickness and more particularly with the fsaverage. Since the thickness has the same number of voxel, I would like to correspond the voxels with some ROI, for instance the Desikan-Killiany Atlas https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation or the Brodmann area http://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps. Are they any label or text files which correspond a ROI with the indices of the voxels in fsaverage ? Thanks in advance for you help, Alexandre ___ 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] Some questions about fsaverage
you can use mri_annotation2label to convert each annotation into a label. The label is a text file with a list of indices. doug On 12/04/2014 02:25 PM, Alexandre Routier wrote: Hello, I am currently working with cortical thickness and more particularly with the fsaverage. Since the thickness has the same number of voxel, I would like to correspond the voxels with some ROI, for instance the Desikan-Killiany Atlas https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation or the Brodmann area http://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps. Are they any label or text files which correspond a ROI with the indices of the voxels in fsaverage ? Thanks in advance for you help, Alexandre ___ 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] --pca flag on mri_glmfit
It performs pca/svd on the residuals. The sdiag.mat I think includes the singular values but also the percent variance explained by each component and the cumulative explained by all components upto and including that component. You probably just need to change the overlay thresholds on the v.mgh to make it look more reasonable. The range of the singular values depends on your data so you can't just look at them and decide they are too big. The u.mtx are the temporal components. doug On 12/04/2014 11:10 AM, Thomas DeRamus wrote: Dear Freesurfer experts, Potentially super-noob question here, but I'm curious about the --pca flag on mri_glmfit. I can see that it does PCA/SVD on the dataset? in question and saves the residuals to the glmdir specified, but I was unable to find anything in the documentation describing what exactly it is doing. I got sdiag.mat, stats.dat (with some rather large eigenvalues, on the order of 40k, but they might look more normal once I demean my variables), a u.mtx, a v.mgh surface overlay, and an error log (stating MatlabRead: readHeder returned NULL, ImageRead (/path/glmdir/pca-eres/sdiag.mat) failed. When I loaded the v.mgh, it looked rather binarized (with red and blue colors covering the entire cortex mask for that hemi). May I ask how it is computing these eigenvalues? What the sdiag and u.mtx files are used for? And what is being displayed in the v.mgh (is it components? if so, what do these components reflect?). And most importantly, is this meant primarily for functional data or can it be applied to mophometric data? If it can be used for the latter, what is being fed into the PCA/SVD to determine spatial components? -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 _Phone_: 205-934-0971 _Email:_ tpdera...@gmail.com mailto:tpdera...@gmail.com, faus...@uab.edu mailto:faus...@uab.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_surfcluster problem
It cannot read the .w file as input. There is no need to use .w files (despite what it might say). On 12/03/2014 12:22 AM, wangzhiwei3233 wrote: *The command I used is* /mri_surfcluster --in sig.w --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 30 --sum area100.pos.cluster.summary --o area100.pos.cluster.w --thmin 1.3/ *Teriminal output is * /thsign = pos, id = 1/ /version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $/ /hemi = lh/ /srcid = sig.w / /srcsubjid = fsaverage/ /srcsurf= white/ /srcframe = 0/ /thsign = pos/ /thmin = 1.3/ /thmax = -1/ /fdr= -1/ /minarea= 30/ /xfmfile= talairach.xfm/ /nth = -1/ /outid= area100.pos.cluster.w paint/ /sumfile = area100.pos.cluster.summary/ /subjectsdir= /isilon/work/FBIP/0_projects/freesurfer/subjects/ /FixMNI = 1/ /- XFM matrix (RAS2RAS) ---/ //isilon/work/FBIP/0_projects/Pinna/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm/ / 1.000 0.000 0.000 0.000;/ / 0.000 1.000 0.000 0.000;/ / 0.000 0.000 1.000 0.000;/ / 0.000 0.000 0.000 1.000;/ // /Reading source surface /isilon/work/FBIP/0_projects/freesurfer/subjects/fsaverage/surf/lh.white/ /Done reading source surface/ /Reading annotation /isilon/work/FBIP/0_projects/freesurfer/subjects/fsaverage/label/lh.aparc.annot/ /reading colortable from annotation file.../ /colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)/ /Computing metric properties/ /Loading source values/ /mri_read(): couldn't determine type of file /isilon/work/FBIP/0_projects/PROJECT/GROUP_27SUB/fsaverage.lh/c1/g2v0.weight/high+low/sig.w/ /ERROR: could not read sig.w as type / At 2014-12-03 13:03:45, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: That is the right command line. What is the terminal output? On 12/2/14 8:01 AM, wangzhiwei3233 wrote: Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum area50.pos.cluster.summary --o area50.pos.cluster.nii.gz --thmin 1.3 However, I found that the command did not set the non-cluster vertices to zero. The help of mri_surfcluster says that this command currently only supports paint (or w) format for input and output. I converted the sig.nii.gz to sig.w using / mri_surf2surf --s fsaverage --hemi lh --sval sig.nii.gz --tval sig.w --trg_type paint./ But command mri_surfcluster could not read the paint file. Could anyone help me? Thanks! Zhiwei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface
Thank you, Doug. Can I just check that projdist is the same as projabs but with a different name? Just in case I'm using an old/wrong version, here's the last line from the mri_vol2surf help output: $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $ From that help and your email I'm looking to run: mri_vol2surf --mov input_volume \ --o $output_name \ --projdist -2 \ --interp nearest \ --surf pial \ --hemi lh Which will give me values that are 2mm toward white matter from the pial surface. Thanks again for all the help! Kx On 3 December 2014 at 04:48, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can spec the surface to be pial (instead of the default white). Then spec --projabs to specify the distance into cortex (using negative numbers). doug On 11/27/14 1:24 PM, Kirstie Whitaker wrote: Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2surf (or another tool!). The point is that I'd like to be agnostic about exactly where the grey/white matter boundary lies. I've had a look through the help for mri_vol2surf and nothing's jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.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] mri_vol2surf --prodist measuring from pial surface
Sorry - if anyone's looking at this in the future, you also need --regheader subID in the command: mri_vol2surf --mov input_volume \ --o $output_name \ --projdist -2 \ --interp nearest \ --surf pial \ --hemi lh \ --regheader subid Kx On 4 December 2014 at 20:41, Kirstie Whitaker kw...@cam.ac.uk wrote: Thank you, Doug. Can I just check that projdist is the same as projabs but with a different name? Just in case I'm using an old/wrong version, here's the last line from the mri_vol2surf help output: $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $ From that help and your email I'm looking to run: mri_vol2surf --mov input_volume \ --o $output_name \ --projdist -2 \ --interp nearest \ --surf pial \ --hemi lh Which will give me values that are 2mm toward white matter from the pial surface. Thanks again for all the help! Kx On 3 December 2014 at 04:48, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can spec the surface to be pial (instead of the default white). Then spec --projabs to specify the distance into cortex (using negative numbers). doug On 11/27/14 1:24 PM, Kirstie Whitaker wrote: Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2surf (or another tool!). The point is that I'd like to be agnostic about exactly where the grey/white matter boundary lies. I've had a look through the help for mri_vol2surf and nothing's jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.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] mri_vol2surf --prodist measuring from pial surface
Yes doug On 12/04/2014 03:41 PM, Kirstie Whitaker wrote: Thank you, Doug. Can I just check that projdist is the same as projabs but with a different name? Just in case I'm using an old/wrong version, here's the last line from the mri_vol2surf help output: $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $ From that help and your email I'm looking to run: mri_vol2surf --mov input_volume \ --o $output_name \ --projdist -2 \ --interp nearest \ --surf pial \ --hemi lh Which will give me values that are 2mm toward white matter from the pial surface. Thanks again for all the help! Kx On 3 December 2014 at 04:48, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: You can spec the surface to be pial (instead of the default white). Then spec --projabs to specify the distance into cortex (using negative numbers). doug On 11/27/14 1:24 PM, Kirstie Whitaker wrote: Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2surf (or another tool!). The point is that I'd like to be agnostic about exactly where the grey/white matter boundary lies. I've had a look through the help for mri_vol2surf and nothing's jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 tel:%2B44%207583%20535%20307 *Website:* www.kirstiewhitaker.com http://www.kirstiewhitaker.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com http://www.kirstiewhitaker.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
Re: [Freesurfer] Some questions about fsaverage
Hi Alexandre I'm not entirely sure what you are asking, but the fsaverage Brodmann areas and parcellations should all be stored in the directory: $FREESURFER_HOME/subjects/fsaverage/label cheers Bruce On Thu, 4 Dec 2014, Alexandre Routier wrote: Hello, I am currently working with cortical thickness and more particularly with the fsaverage. Since the thickness has the same number of voxel, I would like to correspond the voxels with some ROI, for instance the Desikan-Killiany Atlas or the Brodmann area. Are they any label or text files which correspond a ROI with the indices of the voxels in fsaverage ? Thanks in advance for you help, Alexandre ___ 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.
