Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

Cortical thickness/surface area in volume-defined ROIs
by Anita van Loenhoud 29 Nov '13

29 Nov '13

Dear Freesurfer experts, I want to use volume-defined ROIs (obtained in a VBM study) to extract mean thickness and surface area, in a total group of 138 participants. I followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few questions regarding this analysis: 1. The volume-defined ROI (i.e. orange dot) appears normal on my avg152_T1 and fsaverage. After the vol2surf-step, however, a few problems arise. The new ROIs look very different: one ROI actually consists of two clusters close to each other, one is very small and two ROIs have completely disappeared. Does anyone know why this happened? 2. When I want to obtain surface area data instead of thickness data, is it sufficient to replace 'thickness' with 'area' in the surf2surf command (it seems to work, but I want to check)? So: --sval lh.area \ --tval lh.area.fsaverage.mgh \ 3. mri_segstats creates separate files for each ROI in each participant. When I want to have all thickness and area ROI data in one file, can I use asegstats2table, meas mean (it seems to work, but I want to check)? Any help would be very much appreciated! Anita

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nii format input for recon-all
by Rujing Zha 29 Nov '13

29 Nov '13

Dear all, I have done the recon-all for DICOM format input of all subjects. Part of subjects extracted brain volume not very perfectly. I want to use brain volumes nifti format which have strip the skull and neck well. My question is how to use the brain volume in nii format to segment and next recon-all analysis. Thanks. All the best. 2013-11-29 Rujing Zha

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Re: [Freesurfer] freeview, mris_preproc, mri_surf2surf, mri_glmfit: wrong home directory
by Douglas Greve 28 Nov '13

28 Nov '13

you don't need to supply the full path to the inputs of mris_preproc, but you must for the output of mris_preproc as well as the input and output of surf2surf and glmfit On 11/28/13 1:25 PM, Laura Taylor wrote: > Thanks, Bruce... > > Do you know if you also have to specify the full path for the location > of _input _/and /_output_ files in mris_preproc, mri_surf2surf, and > mri_glmfit? > > By default, when I ran the above programs, my output files were placed > in my computers home directory and not my freesurfer home directory (I > did not specify full pathnames). > > However, mris_preproc seemed to be able to read in my target > (--target) (fsaverage) without needing a full pathname, and > mri_surf2surf also seemed to be able to read in my subject (--s) > without needing a full pathname. > > Please let me know if I have this right (especially regarding reading > in input files). > > Thank you, > > Laura > > On Wed, Nov 27, 2013 at 11:53 AM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > 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 > > > > > > > > > > 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

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Re: [Freesurfer] mris_calc recon-all problem
by Johnson, Eileanoir 28 Nov '13

28 Nov '13

It is happening on every subject; the disk isn't full. I checked the MRI folder, and some of the files (nu.mgz, brainmask.mgz) weren't outputted. For one participant who had also been processed on another computer I copied these files onto the cluster and it seems to run ok once these files are in the folder. I found a similar problem (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027257.h…) and have asked the team who maintain the cluster to try this solution as I don't have the right permissions. Hopefully this will solve the issue. Thanks for your help, Eileanoir -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rudolph Pienaar Sent: 28 November 2013 00:47 To: Douglas N Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_calc recon-all problem Not sure if it's relevant, but the syntax for mris_calc in this case is: mris_calc -o <outputFile> <file1> mul <file2> Your log is missing <file2> so the syntax doesn't make sense and mris_calc will fail... On 11/27/13, 18:10 , Douglas N Greve wrote: > > Does it happen on every subject? Any chance that the disk is full? > > On 11/27/2013 07:43 AM, Johnson, Eileanoir wrote: >> >> 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 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA _______________________________________________ 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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Re: [Freesurfer] Freesurfer course troubleshooting presentation slides
by Douglas N Greve 27 Nov '13

27 Nov '13

Are these this right one? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/freesurfer.fa… On 11/27/2013 03:55 AM, Janosch Linkersdörfer wrote: > Hi, > > thank you very much for providing the lectures of the last Freesurfer course as videos! I am just watching them, and it seem that the .ppt file provided for the troubleshooting lecture does not match the slides used in the video. > > It would be great if you could provide the slides used in the video! > > Thanks, > > J > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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/

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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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Freesurfer November 2013