Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] problem with createMorph
by André Ribeiro 27 Nov '13

27 Nov '13

Hi Lilla, Thank you for your reply. I have boost installed, yet it is not the version required (v. 1.49). Although, even after installing an older version such as the 1.41 it is not straightforward to use this libboost with freesurfer. The doc from libboost is not easy to understand and even if done correctly you will not be able to use this installation as there is no libboost_program_options.so.5. Nevertheless, I got it to work so here goes the solution that worked for me. >Download libboost v. 1.41 and untar >cd libboost_folder >mkdir libraries >./bootstrap.sh --prefix=./libraries >./bjam install >cd libraries/lib > ln -s libboost_program_options.so.1.41.0 libboost_program_options.so.5 >export LD_LIBRARY_PATH=.../boost_temp/boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH Cheers, Andre Santos Ribeiro On Wed, Nov 27, 2013 at 5:19 PM, Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu>wrote: > > Hi Andre, > > I posted the below on Monday on the list: > > The boost library is installed by default on CentOS platforms. If a user > gets the libboost error then they are using a different platform which > doesn't have boost installed by default. On RedHat systems libboost can be > installed by typing the follwing command: > $>yum install boost-devel" > > The version of libboost that we use for our latest release is 1.41. > > I hope that helps, > > --Lilla > > > On Wed, 27 Nov 2013, André Ribeiro wrote: > > Dear freesurfer experts, >> >> when running the createMorph function an error of shared libraries occur. >> >> createMorph: error while loading shared libraries: >> libboost_program_options.so.5: cannot open shared object file: No such file >> or directory >> >> I searched for such shared library and although I have a different >> version I do not have this specific. >> >> /usr/lib/libboost_program_options-mt.so >> /usr/lib/libboost_program_options.so.1.49.0_orig >> /usr/lib/libboost_program_options-mt.a >> /usr/lib/libboost_program_options.so >> /usr/lib/libboost_program_options.so.1.49.0 >> /usr/lib/libboost_program_options.a >> >> Updating the libboost did not worked and I couldn’t find any useful >> suggestion on the web. >> >> I am running freesurfer under Ubuntu 13.04 I would appreciate any >> suggestion. >> >> Cheers, >> Andre Santos Ribeiro >> >> >> >> > > 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. >

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Retinotopy analysis with blank periods
by Cesar Echavarria 27 Nov '13

27 Nov '13

Hi all, I'm running a retinotopy analysis and I was wondering if there was a way for me to ignore the last x seconds/TRs of a given run. I want to ignore this bit of time because each run started and ended with a 'blank screen' period. I appreciate any tips you guys might give me. Cesar

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Re: [Freesurfer] freeview, mris_preproc, mri_surf2surf, mri_glmfit: wrong home directory
by Bruce Fischl 27 Nov '13

27 Nov '13

Hi Laura freeview by default doesn't use any of the environment variables. You need to give it the full path to the data you are trying to visualize. It included your home dir in the path probably because that was your pwd. cheers Bruce On Wed, 27 Nov 2013, Laura Taylor wrote: > Hi, > > I previously installed set-up and have successfully used freesurfer to run > recon-all and visualize my results in tkmedit and tksurfer. However when I > went to analyze my data and also view it in freeview I have run into a > problem with what my home directory is considered for these applications. > > When I try and load images in freeview from the command line I get the > following error: > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Data/freesurfer > FSFAST_HOME /Data/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Data/freesurfer/subjects > MNI_DIR /Data/freesurfer/mni > woodward@Bambi:~$ freeview -v B60/mri/braimmask.mgz > mghRead(/home/woodward/B60/mri/braimmask.mgz, -1): could not open file > MRIread failed: Unable to read from /home/woodward/B60/mri/braimmask.mgz > mghRead(/home/woodward/B60/mri/braimmask.mgz, -1): could not open file > > This is because freeview is looking for my subject in the computers home > directory (~) which is /home/woodward. > > I get a similar problem when I run i.e. mri_glmfit. When I specify > > --glmdir lh.dx_age.glmdir, it places the output in my home (~) > (/home/woodward) directory and not in my FREESURFER_HOME directory. > mris_preproc and mri_surf2surf also seems to be placing their output in my > computers home directory. > > > I've looked in FreeSurferEnv.sh and I can't seem to find a place to make any > changes. Please let me know if I can edit a path somewhere, or if I need to > write out the full path for the mri_* programs and freeview. > > > Thank you, > > > Laura > > > > > > >

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problem with createMorph
by André Ribeiro 27 Nov '13

27 Nov '13

Dear freesurfer experts, when running the createMorph function an error of shared libraries occur. createMorph: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory I searched for such shared library and although I have a different version I do not have this specific. /usr/lib/libboost_program_options-mt.so /usr/lib/libboost_program_options.so.1.49.0_orig /usr/lib/libboost_program_options-mt.a /usr/lib/libboost_program_options.so /usr/lib/libboost_program_options.so.1.49.0 /usr/lib/libboost_program_options.a Updating the libboost did not worked and I couldn’t find any useful suggestion on the web. I am running freesurfer under Ubuntu 13.04 I would appreciate any suggestion. Cheers, Andre Santos Ribeiro

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Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit
by Clark Fisher 27 Nov '13

27 Nov '13

Hi Doug, I sidestepped the registration issue because I am performing the analysis on 5 ROIs per subject (5x1x1 volumes), which are aligned by design. I'm doing this using the lab's semi-manual NHP processing stream, so usual assumptions you have about which FS-fast steps have been performed may not hold. Just to clarify things, I'll try to outline where I stand more completely. I have a block design study with 3 subjects, and ~30 runs per subject. Each run contains every condition occurs twice in each run. These runs have been collected over 2-3 days for each subject. Within each subject, I aligned all of the different sessions and combined them into a single metasession. Within these 3 metasessions, I defined ROIs, and created new ROI volumes by averaging the time courses within each ROI. From here I have taken 2 approaches. Approach A: Combine all of the ROI volumes (~30 runs X 3 subjects), which are pre-aligned with each other, into a single bold folder. Run selxavg3-sess on this data using my contrasts of interest. Approach B: Keep the ROI volumes from each subject in their own bold folder, and run selxavg3-sess 3 times (once for each subject). Then I used mri_glmfit to attempt fixed effects meta-analysis. Here there's another split. Approach B.1: I ran the contrasts for each individual subject, then used mri_glmfit --osgm on the ces and cesvar volumes of each contrast to test for significance of the contrast over the group. This does not work for F-tests. Approach B.2: I ran an omnibus contrast on each subject separately, and use the ces and cesvar for each condition in each subject. I assembled this for input to mri_glmfit. The fsgd file looks roughly like: GroupDescriptorFile 1 Class Subj1 Class Subj2 Class Subj3 Variables Condition1 Condition2 Condition3 Condition4 Input Subj1-Cond1 Subj1 1 0 0 0 Input Subj1-Cond2 Subj1 0 1 0 0 Input Subj1-Cond3 Subj1 0 0 1 0 Input Subj1-Cond4 Subj1 0 0 0 1 Input Subj1-Cond00 Subj1 0 0 0 0 Input Subj2-Cond1 Subj2 1 0 0 0 Input Subj2-Cond2 Subj2 0 1 0 0 Input Subj2-Cond3 Subj2 0 0 1 0 Input Subj2-Cond4 Subj2 0 0 0 1 Input Subj2-Cond00 Subj2 0 0 0 0 Input Subj3-Cond1 Subj3 1 0 0 0 Input Subj3-Cond2 Subj3 0 1 0 0 Input Subj3-Cond3 Subj3 0 0 1 0 Input Subj3-Cond4 Subj3 0 0 0 1 Input Subj3-Cond00 Subj3 0 0 0 0 Approach B.2 (continued): I then define contrasts comparing conditions (Condition1 vs Condition2, etc.) and run these contrasts using mri_glmfit --C. With this method, I have no problem defining F contrasts (what they are actually testing is another question). My actual experiment is a 6 condition, 2x3 factorial design. The 2 contrasts of interest that I need an F test for are one of the main effects (these contrasts are shown without the 3 leading columns of zeros for the different subjects): 1 1 -1 -1 0 0 1 1 0 0 -1 -1 and the interaction effect: 1 -1 -1 1 0 0 1 -1 0 0 -1 1 I switched to Approach B because I want to scale the condition betas per-subject before running the analysis across all subjects (this is to correct for potentially different levels of a contrast agent). I was worried that if I scaled the raw time courses that are the input to Approach A, that the normalization step built into selxavg3-sess would interact with my manual normalization in ways that would be difficult to figure out. With approach B, I can directly scale the contrast ces and cesvars (B.1) or betas (B.2) for each subject. OK, given all of that background information, what is the best way to approach this? Should I: a) Try to scale the time courses that go into Approach A b) Work with Approach B.1, and live without knowing the significance of my main/interaction effects (not a nice thought) c) Work with Approach B.2 d) Take some other tack If I take Approach B.2, would any violation within-subject independence decrease my power, or artificially inflate my significance? Some loss of power could be acceptable. Thanks for reading all of the way through this, Clark On Nov 26, 2013, at 11:13 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> wrote: Clark, it sounds like what you did (ie, combine different subjects into one folder) would be tricky to analyze correctly because FSFAST will try to register them to the same subject. I could think of a way to do it, but it would be complicated. What is the test that you want to do? An F test is usually something like a logical "or" between two conditions. The RM ANOVA won't do this, but a simple ANOVA would. The problem is that the DOF would be off because it would assume that each data point came from a different subject, and it would not take into account the covariance in the measurements from a single subject. Another approach would be to do separate tests for each condition at the group level, then do a type of conjunction analysis to implement the OR. Let me know if you want to pursue that approach. doug On 11/26/13 4:02 PM, Clark Fisher wrote: Thanks again, I have 3 subjects, and want to tests for effects using data collected across all 3 subjects. The multiple sessions for each subject have already been concatenated into a single BOLD folder (3 folders total: 1 for each subject). I have actually already performed the fixed effects analysis by concatenating all 3 subjects into a single bold folder and re-running the first level analysis. While that works, I now want to try to normalize the data for each subject to minimize the variability introduced by the contrast agent we use, and that would be easier to do by normalizing the outputs of the first level analysis. If I wanted to normalize per-subject and then combine them into a first level analysis, what would be the best way to do this? My naive assumption would have been that using glmfit for this should be very similar to the repeated measures ANOVA example that is on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova) Rather than time points for each subject, I will have the beta from each condition for each subject. In both cases (multiple time points from a single subject and multiple conditions from a single subject/set of runs), the within-subject measurements are not independent. How is my situation different? Cheers, Clark On Nov 26, 2013, at 1:41 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> wrote: Are the different input to glmfit different runs within a session or across sessions? Either way, for within subject analysis, can you put all of the runs into a single "bold" folder? Then it automatically does the FFX analysis across runs, which can include an F-test. The problem is that glmfit expects all the inputs to be independent, which conditions within a run will not be. doug On 11/25/2013 01:35 PM, Clark Fisher wrote: Thanks Doug, I had forgotten that my roadblock was actually in isxconcat_sess, not mri_glmfit. This worked out great. Following this up, how would you recommend calculating the fixed-effects significance of a complex (within subject) contrast with mri_glmfit? For simple contrasts, I have been calculating the contrast at the single subject level, then performing an osgm fixed-effects analysis on the output ces and cesvar volumes for each subject. However, I have some 2D F-contrasts that don't output ces volumes (naturally). One possibility would be to concatenate the ces and cesvar from the omnibus contrasts of each subject, set up an appropriate fsgd (as in http://ftp.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova) and then define the contrasts at the level of mri_glmfit with .mtx files. Would that be the way to go? Thanks, Clark -- 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 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/ 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.

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mris_calc recon-all problem
by Johnson, Eileanoir 27 Nov '13

27 Nov '13

Hi there, I am currently trying to run freesurfer version 5.3.0 on a cluster and am encountering an error when running recon-all. The error is: Writing to ./tmp.mri_nu_correct.mni.2867/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2867/nu2.mnc ./tmp.mri_nu_correct.mni.2867/nu2.mnc mul Linux blue34 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 22057 exited with ERRORS at Wed Nov 27 12:31:54 GMT 2013 Does anyone know what might be causing recon-all to exit at this point? I have attached the full log file. Thanks, Eli Eli Johnson Research Assistant, Track-On UCL Institute of Neurology, Box 104 Queen Square, London, WC1N 3BG Tel:+44(0)207 242 0038

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can I run Monte Carlo simulation without calling mri_glmfit
by Wang, Xin 27 Nov '13

27 Nov '13

Hello, I repeated same mri_glmfit at multiple depth of cortical thickness and merged the maximal values of the sig.mghs for all depths to a merged_sig.mgh (as in Wang X, et al. Neuroimage. 49(4):3075-85; 2010). I need to run Monte Carlo simulation<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/030604.html> on the merged_sig.mgh. I have the .fsgd and .mtx files for this glm design but I don't have a smoothed input image as fs.8.mgh for this merged sig.mgh. Can I modify the mri_glmfit-sim to run the correction without calling fs.8.mgh? Thank you. Xin

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Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
by Bruce Fischl 26 Nov '13

26 Nov '13

Hi Pablo it also depends on how much ram it has. You should be able to run 1 significantly faster using the -openmp 8 flag to recon-all, or 8 (if you have enough ram, probably at least 32G) cheers Bruce On Tue, 26 Nov 2013, pablo najt wrote: > Dear Bruce,Last week I emailed with the question of how many recon -all > separate subjects I could run in parallel with the FS version 5.3 for Centos > 6. You answered that this depends on how many cores my machine has. > I just found out that our workstation has two processors with 4 cores each > (8 cores in total). > Would you be able to tell me how many subjects could I run in parallel with > our workstation? > Thank you for your support, > Pablo > > Date: Thu, 21 Nov 2013 10:47:34 -0500 > From: fischl(a)nmr.mgh.harvard.edu > To: pablonajt(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > Hi Pablo > > it depends on how many cores you have > > Bruce > On Thu, 21 Nov 2013, pablo najt wrote: > > > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I a > m > > wondering up to how many recon -all for separate subjects I can run in > > parallel. With the version of Snow Leopard 32b I was running two at a time > > and it took around 20 hours. Would I be able to run 6 subjects in parallel > ? > > If so would this process still efficient or there is an optimum number? > > Thank you, > > Pablo > > > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > > From: zkaufman(a)nmr.mgh.harvard.edu > > > To: garikoitz(a)gmail.com > > > CC: pablonajt(a)hotmail.com; freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > > CentOS 6 > > > > > > I have to agree with Gari, I see no reason for you to not use the > > > CentOS6 build. > > > > > > -Zeke > > > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any > > > > reason to not use this version in your CentOS 6, if you have some othe > r > > > > requirements maybe Nick or Zeke could help you better, I am just an us > er > > :) > > > > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt(a)hotmail.com > > > > <mailto:pablonajt@hotmail.com>> wrote: > > > > > > > > Dear Gari, > > > > Thank you for the advice. One additional question. > > > > Considering that I will start from scratch the processing in the > > > > CentOS 6, which would be the recommended FS version for CentOS 6? > > > > Thanks, > > > > Pablo > > > > > > > > ---------------------------------------------------------------------- > -- > > > > From: garikoitz(a)gmail.com <mailto:garikoitz@gmail.com> > > > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > > > To: pablonajt(a)hotmail.com <mailto:pablonajt@hotmail.com> > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > and CentOS 6 > > > > > > > > > > > > Hi Pablo, > > > > you shouldn't mix different OS-s or software version in the same > > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > > effects of FreeSurfer version, workstation type, and Macintosh > > > > operating system version on anatomical volume and cortical thickness > > > > measurements. /PloS one/, /7/(6), e38234. > > > > doi:10.1371/journal.pone.0038234). > > > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > > it works too). > > > > regards! > > > > Gari > > > > > > > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt(a)hotmail.com > > > > <mailto:pablonajt@hotmail.com>> wrote: > > > > > > > > Dear FS experts, > > > > I am forwarding my question (please see below), in case it got > > > > lost among the intense flow of messages. > > > > Thank you for your consideration. > > > > Pablo > > > > > > > > ---------------------------------------------------------------------- > -- > > > > From: pablonajt(a)hotmail.com <mailto:pablonajt@hotmail.com> > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > Date: Mon, 18 Nov 2013 16:38:41 +0000 > > > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > and CentOS 6 > > > > > > > > > > > > Dear FS experts, > > > > I have a question about compatibility for running recon-all > > > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > > > SnowLeopard OS X 10.6 (32b Intel). > > > > > > > > I already run recon all- for several of my subjects with a Mac > > > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > > > access to an additional machine (a linux CentOS 6 (64b)) I was > > > > wondering if I could process additional subjects in parallel > > > > with this other machine that are also intended to be included in > > > > the longitudinal stream. > > > > Also, I am not sure about whether I should be installing in the > > > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > > > because of compatibility issues. > > > > Thank you very much for your attention, > > > > Pablo > > > > > > > > > > > > _______________________________________________ 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. > > > > > > > > _______________________________________________ > > > > 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. > > > > > > > > > > > > > > > > _______________________________________________ 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. > > > > > > > > _______________________________________________ > > > > 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. > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ Freesurfer mailing list > Freesurfer(a)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. > >

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talairach_mixed_with_skull.gca file missing in average directory of local version stable5_3_0
by Koene Van Dijk 26 Nov '13

26 Nov '13

Hi there, We've been using this local version of Freesurfer: /cluster/freesurfer/centos6_x86_64/stable5 And this file was relevant: /cluster/freesurfer/centos6_x86_64/stable5/average/talairach_mixed_with_skull.gca We want to switch to the newest version of Freesurfer at the beginning of a new study but we can't find that "talairach_mixed_with_skull.gca" file in the /cluster/freesurfer/centos6_x86_64/stable5_3_0 directory. Is it possible to also include the "talairach_mixed_with_skull.gca" file in: /cluster/freesurfer/centos6_x86_64/stable5_3_0/average/? Thanks, Koene -- Koene R.A. Van Dijk, PhD Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology - Massachusetts General Hospital 149 Thirteenth Street (Suite 2301) Charlestown, MA 02129

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Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit
by Clark Fisher 26 Nov '13

26 Nov '13

Thanks again, I have 3 subjects, and want to tests for effects using data collected across all 3 subjects. The multiple sessions for each subject have already been concatenated into a single BOLD folder (3 folders total: 1 for each subject). I have actually already performed the fixed effects analysis by concatenating all 3 subjects into a single bold folder and re-running the first level analysis. While that works, I now want to try to normalize the data for each subject to minimize the variability introduced by the contrast agent we use, and that would be easier to do by normalizing the outputs of the first level analysis. If I wanted to normalize per-subject and then combine them into a first level analysis, what would be the best way to do this? My naive assumption would have been that using glmfit for this should be very similar to the repeated measures ANOVA example that is on the wiki (http://ftp.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova) Rather than time points for each subject, I will have the beta from each condition for each subject. In both cases (multiple time points from a single subject and multiple conditions from a single subject/set of runs), the within-subject measurements are not independent. How is my situation different? Cheers, Clark On Nov 26, 2013, at 1:41 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > Are the different input to glmfit different runs within a session or across sessions? Either way, for within subject analysis, can you put all of the runs into a single "bold" folder? Then it automatically does the FFX analysis across runs, which can include an F-test. The problem is that glmfit expects all the inputs to be independent, which conditions within a run will not be. > doug > > > On 11/25/2013 01:35 PM, Clark Fisher wrote: >> Thanks Doug, >> >> I had forgotten that my roadblock was actually in isxconcat_sess, not mri_glmfit. This worked out great. >> >> Following this up, how would you recommend calculating the fixed-effects significance of a complex (within subject) contrast with mri_glmfit? For simple contrasts, I have been calculating the contrast at the single subject level, then performing an osgm fixed-effects analysis on the output ces and cesvar volumes for each subject. However, I have some 2D F-contrasts that don't output ces volumes (naturally). >> >> One possibility would be to concatenate the ces and cesvar from the omnibus contrasts of each subject, set up an appropriate fsgd (as in http://ftp.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova) and then define the contrasts at the level of mri_glmfit with .mtx files. Would that be the way to go? >> >> Thanks, >> Clark > > -- > 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/ > > > > 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. >

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