[Freesurfer] Algebraic operations with scalars
Dear Freesurfer experts, I would like to make some algebraic operations with scalars, such as ?h.thickness or sig.mgh. They are referred to the same surface, of course. How can I export the thickness values to a spreadsheet? (?h.thickness 2 table) How can I export the significance values to a spreadsheet? (sig.mgh 2 table) All my best Cico Francesco Cardinale, MD 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> ___ 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] Algebraic operations with scalars
Thanks a lot! Cico Francesco Cardinale, MD 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 > Il giorno 31 mag 2016, alle ore 19:39, Douglas N Greve > ha scritto: > > You can use mri_convert, like > > mri_convert lh.thickness --ascii lh.thickness.txt > > this will create a text file with a single column, one row for each > vertex. You can also use > > > mri_convert lh.thickness --ascii+crsf lh.thickness.txt > > This will create 5 columns, the first being the column number, then row > number, then slice number, then frame number, then thickness value. In > this case, the column number will be the vertex number, and the row, > slice, and frame will always be 0. > > > >> On 05/29/2016 12:19 PM, Francesco Cardinale wrote: >> Dear Freesurfer experts, >> >> I would like to make some algebraic operations with scalars, such as >> ?h.thickness or sig.mgh. They are referred to the same surface, of course. >> >> How can I export the thickness values to a spreadsheet? (?h.thickness >> 2 table) >> >> How can I export the significance values to a spreadsheet? (sig.mgh 2 >> table) >> >> All my best >> >> Cico >> >> Francesco Cardinale, MD >> >> 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> >> >> >> >> >> ___ >> 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.
[Freesurfer] the "Configure Overlay Display" dialog is clipped on low resolution monitors.
Dear Freesurfer developers, the "Configure Overlay Display" dialog is clipped on low resolution monitors with FS version 5.3.0 for MAC. This bug affected the version 5.1.0 and you released a fix for it, but now it's not available anymore on the website. Best regards Cico Cardinale___ 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] Statistical analyses with QDEC
Dear Freesurfer experts, I have some questions about statistical analyses. How to adjust for sex and age? I use the precompiled Freesurfer 5.3.0 MacOSX version, and its tool QDEC to compare cortical thickness between two groups. I would like to use age and sex as nuisance factors. No problem with the age, but I don’t see the sex in the list of usable variables if I code it as a categorical variable (male / female). On the opposite, If I code it as numbers (male = 1, female = 2) I can use it, but how can I declare that it is a factor and not a continuous numerical variable? I don’t want that “female” affects the fitting of the GLM with a value that means “male” * 2. What about the use of other morphometric properties as nuisance factors? For example, how could I use sulcality or LGI as nuisance factors? Is it possible to use more than one scalar simultaneously? Similarly to question 2, is it possible to use home-made *.mgh scalars as a nuisance factors? How? Do the command-line tools allow such analyses better than QDEC? Related to my questions, which features do they add? In this field of interest, are there any major advantages coming with Freesurfer 6.0? Thanks a lot and best regards Cico Francesco Cardinale, MD 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>___ 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] Statistical analyses with QDEC
Dear Freesurfer experts, I have some questions about statistical analyses. How to adjust for sex and age? I use the precompiled Freesurfer 5.3.0 MacOSX version, and its tool QDEC to compare cortical thickness between two groups. I would like to use age and sex as nuisance factors. No problem with the age, but I don’t see the sex in the list of usable variables if I code it as a categorical variable (male / female). On the opposite, If I code it as numbers (male = 1, female = 2) I can use it, but how can I declare that it is a factor and not a continuous numerical variable? I don’t want that “female” affects the fitting of the GLM with a value that means “male” * 2. What about the use of other morphometric properties as nuisance factors? For example, how could I use sulcality or LGI as nuisance factors? Is it possible to use more than one scalar simultaneously? Similarly to question 2, is it possible to use home-made *.mgh scalars as a nuisance factors? How? Do the command-line tools allow such analyses better than QDEC? Related to my questions, which features do they add? In this field of interest, are there any major advantages coming with Freesurfer 6.0? Thanks a lot and best regards Cico___ 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] Parallelization in MAC
Dear Freesurfer experts, Does the parallelization work with Freesurfer 6.0 under MacOS? Best regards Francesco Cardinale, MD 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 13 feb 2017, alle ore 23:13, Francis Tyson Thomas > ha scritto: > > Hi, > > I have run recon-all with both -parallel enabled (including different openmp > threads) and disabled and I'm not able to get processing times same as the > information provided in recon-all help. The CPU used is Dual Intel Xeon > E5-2623 v3 paired with 32GB DDR4 RAM. Is the configuration presented in > recon-all help a dual cpu configuration? > > Following are the runtimes I have obtained, > > no parallelization : 7 hrs and 58 > mins > -parallel (coarse parallelization) : 4 hrs and 39 mins > -parallel (fine parallelization; -openmp 8): 4 hrs and 34 mins > -parallel (fine parallelization; -openmp 14) : 4 hrs and 37 mins > > Somehow varying the number of threads is having no effect in the execution > time of recon-all as can been seen from the processing times. If you can > explain what could be possibly going wrong here, it will help me in speeding > it up further. > > Thanks, > Tyson > ___ > 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] Speeding Freesurfer
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 phone 0039 02 64442917 fax 0039 02 64442868 e-mail francesco.cardin...@ospedaleniguarda.it___ 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
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 > Il giorno 02/dic/2014, alle ore 15:59, Z K 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 >> >> phone 0039 02 64442917 >> fax 0039 02 64442868 >> e-mail francesco.cardin...@ospedaleniguarda.it >> <mailto:francesco.cardin...@ospedaleniguarda.it> >> >> >> ___ >> 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 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] Clipping of tksurfer's "Configure Overlay Display" window in OSX
Hi Bruno, Another workaround is to activate the "full screen" X11 option. Ciao 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 > Il giorno 20/dic/2014, alle ore 21:22, Enzo Tagliazucchi > ha scritto: > > Hi Bruno, > > thanks - did not know that space bar was a shortcut for "apply"! > > I'll try to see if I can solve the clipping issue with the .tcl file you > sent, although the space bar shortcut pretty much solves it. > > best wishes, > > Enzo > >> On Sat, Dec 20, 2014 at 9:15 PM, Bruce Fischl >> wrote: >> Hi Enzo, >> >> I think that the space bar is usually the keyboard short cut for apply - >> have you tried that? Sorry, we don't do any development on tksurfer anymore, >> but we can post a new tksurfer.tcl if that helps (I'll attach one to this >> email, but I don't know that it fixes your problem) >> >> cheers >> Bruce >> >> On Sat, 20 Dec 2014, Enzo Tagliazucchi wrote: >> >>> Dear Freesurfer Team and users, >>> this has been brought to attention before in recent times, but I'm not aware >>> of any solution. >>> >>> the "Configure Overlay Display" tksurfer menu (freesurfer 5.3.0) does not >>> fit on screen (is "clipped") in OSX 10.8.5 using XQuartz 2.7.5. This is in a >>> MacBook Pro 15'' using the max resolution of 1440x900. >>> >>> As a result, it is impossible to interact with the lower part of the menu >>> box, in particular, it is not possible to hit the "Apply button". Please >>> note that this severely limits the usability of tksurfer. >>> >>> Apparently, a solution was available for download at the link I'm copying >>> below, but the folder is now empty. Thank you very much for your help. >>> >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksu >>> rfer.tcl >>> >>> Enzo Tagliazucchi. >>> >> >> ___ >> 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 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.
