Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

Re: [Freesurfer] Set Up question
by Douglas N Greve 10 Jun '13

10 Jun '13

Hi David, Just put the commands into your .cshrc file (or .bashrc if you're using bash). Also, please post questions to the FS list instead of us directly so that it gets logged in our archive, other people can answer, and everyone can see the answer. Thanks! doug On 06/10/2013 04:39 PM, David Dalton wrote: > Thank you so much! Do you also know how to get FreeSurfer to run > automatically when I open the terminal? Right now I have to run the > startup sequence every time. > > Thanks, > David > > > On Mon, Jun 10, 2013 at 2:42 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi David, it is not a problem if you're not going to run FS-FAST. > If it > bugs you, you can > setenv NO_FSFAST 1 > in your cshrc file prior to sourcing the FS env > > doug > > > > > On 06/10/2013 03:35 PM, David Dalton wrote: > > Hello FreeSurfer experts, > > > > I recently downloaded and installed FreeSurfer on my Mac > computer, but > > I have a few questions about the startup. > > > > 1. When I run FreeSurfer, I get the following. I know the Wiki says > > to ignore the warning, and FreeSurfer does run normally after this, > > but I wanted to be sure it really was not a problem. > > > > [SiriasBook:/] csirias% setenv FREESURFER_HOME > Applications/freesurfer/ > > [SiriasBook:/] csirias% source > Applications/freesurfer/SetUpFreeSurfer.csh > > -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME Applications/freesurfer/ > > FSFAST_HOME Applications/freesurfer//fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR Applications/freesurfer//subjects > > > > WARNING: The /Users/csirias/matlab/startup.m file does not > appear to be > > configured correctly. You may not be able > > to run the FS-FAST programs > > Try adding the following lines to /Users/csirias/matlab/startup.m > > -----------------cut--------------------- > > fshome = getenv('FREESURFER_HOME'); > > fsmatlab = sprintf('%s/matlab',fshome); > > if (exist(fsmatlab) == 7) > > path(path,fsmatlab); > > end > > clear fshome fsmatlab; > > fsfasthome = getenv('FSFAST_HOME'); > > fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); > > if (exist(fsfasttoolbox) == 7) > > path(path,fsfasttoolbox); > > end > > clear fsfasthome fsfasttoolbox; > > -----------------cut--------------------- > > > > MNI_DIR Applications/freesurfer//mni > > [SiriasBook:/] csirias% > > > > > > 2. When I type in 'freeview' to the command line, I get several > other > > messages as the program opens. I am not sure if they are a problem, > > but here they are. I seem to be able to run freeview despite these > > messages, but some others have told me that these messages do not > > appear on their computers, so I am wondering why they appear. > > > > [SiriasBook:/] csirias% freeview > > 2013-06-10 12:22:57.739 Freeview[1200:303] invalid drawable > > 2013-06-10 12:22:57.740 Freeview[1200:303] invalid drawable > > 2013-06-10 12:22:57.754 Freeview[1200:303] invalid drawable > > 2013-06-10 12:22:57.755 Freeview[1200:303] invalid drawable > > 2013-06-10 12:22:57.768 Freeview[1200:303] invalid drawable > > 2013-06-10 12:22:57.769 Freeview[1200:303] invalid drawable > > 2013-06-10 12:22:57.781 Freeview[1200:303] invalid drawable > > 2013-06-10 12:22:57.782 Freeview[1200:303] invalid drawable > > > > 3. And my last question. How do I run FreeSurfer automatically > when I > > open the terminal window? I would like to just type 'freeview' into > > the command line to have the program run, but I currently have > to type > > > > setenv FREESURFER_HOME Applications/freesurfer/ > > > > followed by > > > > source Applications/freesurfer/SetUpFreeSurfer.csh > > > > in order for the program to run. > > > > Thank you so much for any help you can give! Like I said, the > program > > appears to run normally despite the messages, but I just want to > know > > why they are appearing. The last question is more of a > convenience issue. > > > > Thanks, > > David > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

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AR2 Error
by Erin Browning 10 Jun '13

10 Jun '13

Hi everyone-- I emailed the other day about hyperintensity after running motioncor. We've skipped motioncor in our processing now, but we keep getting this error while running AR2. \n mri_ca_register -invert-and-save transforms/talairach.m3z \n mri passed volume size is different from the one used to create M3D data Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z gunzip -c transforms/talairach.m3z Inverting GCAM ERROR: mri_ca_register with non-zero status 0 Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s freesurfer exited with ERRORS at Wed Jun 5 19:32:56 CDT 2013 I tried rerunning recon-all -s freesurfer -talairach before running AR2, and that didn't fix the error. What's going wrong? Thanks, Erin Browning

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Neuroinformatics Database (NIDB) 4.2.0 released
by Greg Book 10 Jun '13

10 Jun '13

This is an announcement that Neuroinformatics Database version 4.2.0 has been released. This version includes many performance enhancements and new features. There is also a demo server available with some sample MR data and the ABIDE dataset hosted for users who want to test the database without needing to install it locally. General features: * store any binary or text data, including MR (any dicom modality), EEG, SNP, video, audio, images, etc. * store assessment/clinical measure values (DSM code, etc, only values, not full assessments) * real-time QC for MR data, with values stored in the database * automatic pipeline processing of any image data, with results stored in the database * query and retrieve any of the above data and dump to local/remote FTP, NFS share, or export in NiDB format * additionally: DICOM receiver, store family pedigree information, store MR behavioral data, download stats, reports New features: * sharing of imaging data between NiDB instances, while maintaining anonymity and eliminating subject duplication * improved pipelines: testing mechanism for new pipelines, creating/editing scripts, and second level pipelines * query performance improved on pipeline results: 4.4 million result values retrieved in 107 seconds. * methods for creating new back-end NiDB modules Download version 4.2.0 in .tar.gz format or VirtualBox VM: http://nidb.sourceforge.net. We'll be presenting at HBM in Seattle next week, so stop by! NiDB is developed by and with support from the Olin Neuropsychiatry Research Center at Hartford Hospital/Institute of Living.

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Set Up question
by David Dalton 10 Jun '13

10 Jun '13

Hello FreeSurfer experts, I recently downloaded and installed FreeSurfer on my Mac computer, but I have a few questions about the startup. 1. When I run FreeSurfer, I get the following. I know the Wiki says to ignore the warning, and FreeSurfer does run normally after this, but I wanted to be sure it really was not a problem. [SiriasBook:/] csirias% setenv FREESURFER_HOME Applications/freesurfer/ [SiriasBook:/] csirias% source Applications/freesurfer/SetUpFreeSurfer.csh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Applications/freesurfer/ FSFAST_HOME Applications/freesurfer//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR Applications/freesurfer//subjects WARNING: The /Users/csirias/matlab/startup.m file does not appear to be configured correctly. You may not be able to run the FS-FAST programs Try adding the following lines to /Users/csirias/matlab/startup.m -----------------cut--------------------- fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; -----------------cut--------------------- MNI_DIR Applications/freesurfer//mni [SiriasBook:/] csirias% 2. When I type in 'freeview' to the command line, I get several other messages as the program opens. I am not sure if they are a problem, but here they are. I seem to be able to run freeview despite these messages, but some others have told me that these messages do not appear on their computers, so I am wondering why they appear. [SiriasBook:/] csirias% freeview 2013-06-10 12:22:57.739 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.740 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.754 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.755 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.768 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.769 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.781 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.782 Freeview[1200:303] invalid drawable 3. And my last question. How do I run FreeSurfer automatically when I open the terminal window? I would like to just type 'freeview' into the command line to have the program run, but I currently have to type setenv FREESURFER_HOME Applications/freesurfer/ followed by source Applications/freesurfer/SetUpFreeSurfer.csh in order for the program to run. Thank you so much for any help you can give! Like I said, the program appears to run normally despite the messages, but I just want to know why they are appearing. The last question is more of a convenience issue. Thanks, David

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Re: [Freesurfer] AR2 Error
by Douglas N Greve 10 Jun '13

10 Jun '13

There is no indication in this log file that you ran autorecon3 doug On 06/07/2013 02:51 PM, Erin Browning wrote: > Here's the log. I ran mri_add_xform_to_header after it failed again > last time and am currently rerunning AR2+3 on it, so you can probably > ignore the latest modifications to it. > > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=iowkgmv > > We're running Mac OSX 10.6.8. > > Thanks, > Erin > > > On Fri, Jun 7, 2013 at 12:22 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hmmm, I don't know. I think that something strange is happening. > Can you > send me the new recon-all.log file? Also, tell me what platform > you are > using and I'll send you a new version of mri_segstats > > doug > > > > On 06/07/2013 01:14 PM, Erin Browning wrote: > > Could it be that since we skip motioncor, we skip the > > mri_add_xform_to_header program as well? Should I be running that > > separately? > > > > Thanks, > > Erin Browning > > > > > > On Fri, Jun 7, 2013 at 11:54 AM, Erin Browning <brownin8(a)uwm.edu > <mailto:brownin8@uwm.edu> > > <mailto:brownin8@uwm.edu <mailto:brownin8@uwm.edu>>> wrote: > > > > Hi Doug-- > > > > Running: > > > > recon-all -s freesurfer -autorecon2 -autorecon3 > > > > produced the same error. Could you send me the new version > of the > > program? > > > > Thanks! > > Erin Browning > > > > > > On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve > > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > > > OK, this is a known problem when running recon-all with > > -autorecon1 > > -autorecon2 but not autorecon3. If you run it with > > -autorecon3, then it > > should run all the way through without a problem. > > Alternatively, I can > > give you a new version of the offending program > (mri_segstats) > > that will > > allow you to use just ar1 and ar2. > > > > doug > > > > > > > > > > On 06/06/2013 03:46 PM, Erin Browning wrote: > > > Here is the log file. > > > > > > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=zrh2oi9> > > > > > > Thank you! > > > > > > > > > On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning > > <brownin8(a)uwm.edu <mailto:brownin8@uwm.edu> > <mailto:brownin8@uwm.edu <mailto:brownin8@uwm.edu>> > > > <mailto:brownin8@uwm.edu <mailto:brownin8@uwm.edu> > <mailto:brownin8@uwm.edu <mailto:brownin8@uwm.edu>>>> wrote: > > > > > > Yes, it was. I tried copy and pasting it and just > > attaching the > > > log file. Can I paste urls here? I'll just upload > it to > > pastebin > > > or something like that. > > > > > > > > > On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve > > > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > That's weird, people upload their recon-all.log > > files all the > > > time. Was > > > the email kicked back to you? > > > > > > On 06/06/2013 03:27 PM, Erin Browning wrote: > > > > The log file for recon-all is too large. How > > should I send it? > > > > > > > > > > > > On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve > > > > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > > > Hi Erin, thanks for reposting. Can you > post the > > > recon-all.log file? > > > > doug > > > > > > > > > > > > On 06/06/2013 02:37 PM, Erin Browning wrote: > > > > > Hi everyone-- > > > > > > > > > > I emailed the other day about > hyperintensity > > after running > > > > motioncor. > > > > > We've skipped motioncor in our processing > > now, but we > > > keep getting > > > > > this error while running AR2. > > > > > > > > > > \n mri_ca_register -invert-and-save > > > transforms/talairach.m3z \n > > > > > mri passed volume size is different > from the > > one used > > > to create > > > > M3D data > > > > > Loading, Inverting, Saving, Exiting ... > > > > > Reading transforms/talairach.m3z > > > > > gunzip -c transforms/talairach.m3z > > > > > Inverting GCAM > > > > > ERROR: mri_ca_register with non-zero > status 0 > > > > > Darwin cerebrum.uwm.edu > <http://cerebrum.uwm.edu> > > <http://cerebrum.uwm.edu> <http://cerebrum.uwm.edu> > > > <http://cerebrum.uwm.edu> > > > > <http://cerebrum.uwm.edu> 10.8.0 Darwin > Kernel > > > > > Version 10.8.0: Tue Jun 7 16:33:36 > PDT 2011; > > > > > root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > > > recon-all -s freesurfer exited with ERRORS > > at Wed Jun 5 > > > > 19:32:56 CDT 2013 > > > > > > > > > > I tried rerunning recon-all -s freesurfer > > -talairach > > > before running > > > > > AR2, and that didn't fix the error. What's > > going wrong? > > > > > > > > > > Thanks, > > > > > Erin Browning > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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 > > > > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > > > Phone Number: 617-724-2358 > > > > Fax: 617-726-7422 > > > > > > > > Bugs: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > FileDrop: > > https://gate.nmr.mgh.harvard.edu/filedrop2 > > > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > Outgoing: > > > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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 > > > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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 > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 greve(a)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/

2 9

Hippocampal subfields intensity
by Marcos Martins da Silva 10 Jun '13

10 Jun '13

Hi, Freesurfer Experts After usual processing with recon-all -all we get the aseg.stats file with several data including intensity values like: normMean normStdDev normMin normMax normRange Left-Hippocampus 77.8939 7.5748 46.0000 105.0000 59.0000 How could I get similar results for each hippocampal subfield, assuming I also generated all posterior*.mgz files corresponding to each subfield? I guess I should first binarize each of the subfields file with a threshold=127 to map all the pertinent voxels, and then use these files as masks over nu.mgz and calculate the intensities values. But I do not know the best way to accomplish this after the binarize step. Thank you in advance for any help. Marcos

2 1

OptSeq first time
by fMRI 10 Jun '13

10 Jun '13

Hello all, This is my first question in this list and it is about OptSeq2. I am nee to this command. In brief, I wish to insert the following but Some of them I could not handle it: My experiment has three conditions although I will later specify them as one condition: Moving hand at three different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects. My design will have two columns : main effect of moving hand and the 1 order. My contrast will be like this [1 0; 0 1] This is what I would like to optimize using OptSeq2: Event design 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this 2) TR 3 3) volumes 150 4) 45 hand movement; 15 at each target level ( I could not do this ) 5) each movement lasts for 3 seconds I am not sure whether I should use null events or the Period between movement is enough. Also my main aim is to optimize the best design in terms of detection. Please any guide or help Thanks AS

3 4

Re: [Freesurfer] white matter volume per lobe...
by Gonzalo Rojas Costa 10 Jun '13

10 Jun '13

Hi Doug: I used the instructions that you told me to get the white matter per each lobule... But, I got the grey colored region (red arrow)... Which neuroanatomical area is ?... Sincerely, Gonzalo Rojas Costa > Message: 15 > Date: Mon, 27 May 2013 22:41:41 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] white matter volume per lobe... > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <51A41965.6050808(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > you will need to run mri_annotation2label and specify the output to be > an annotation file instead of a segmentation. Then you will have to run > mri_aparc2aseg, specifying your lobes annotation as well as --labelwm > (look in the recon-all.log file for an example of how wmparc.mgz is > created). Then run mri_segstats (you can also get an example from the > recon-all.log file). > doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 7

Surface area measurement method
by Andreas Berger 10 Jun '13

10 Jun '13

Hello FreeSurfers, after reading this [1] paper about measuring surface area, i realized i don't know what the default way of measuring surface area is in FreeSurfer. Is it similar to what's described in the paper? Could you point me to the right documentation or publication? Forgive me if i've overlooked it, i found something for thickness, but not for area. To clarify, i don't mean parcellation-based areas, i mean the measure that i find in /surf/hemi.area. thanks, regards, Andreas [1] Measuring and comparing brain cortical surface area and other areal quantities. Winkler AM, Sabuncu MR, Yeo BT, Fischl B, Greve DN, Kochunov P, Nichols TE, Blangero J, Glahn DC (2012). Neuroimage 61(4):1428-43

2 3

surface stream steps
by Joshua Lee 10 Jun '13

10 Jun '13

Dear Freesurfers, >From the Wiki Freesurfer surface stream follows something like: 1. Affine registration to Tal. 2. Bias correction and skull stripping 3. Classify WM 4. Cut hemisphere planes 5. Tile WM surface 6. Refine WM surface following GM-WM intensity gradients 7. Nudge (nudge?) WM surface to follow the GM-CSF gradient to generate pial surface 8. Labeling Data Set 9. Stats May I ask which couple of these steps tend to be the most computationally taxing/longest to complete? Also, I'm not sure I understand #7. Is the WM surface scaled in some sense to approximate the GM-CSF boundary, or is this just a refinement step like #6 of a surface that already approximates the GM-CSF boundary? Thanks, I've spent most of my time working with the sub-cortical stream. - Joshua

2 1

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