Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30091 discussions

longitudinal analysis
by Joy-Loi Chepkoech 19 Mar '13

19 Mar '13

Hello FreeSurfer experts, I am currently trying to systematically investigate the differences in cortical and subcortical estimates that occur when performing recon-all on one scan, or when averaging across scans of varying quality with regard to movement. I have a list of subjects that each have been processed (recon-all) twice (once with one scan and once with two scans), and would like to run some FreeSurfer statistical analysis on them. Is it feasible to set up a longitudinal analysis similar to the one described here: (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)? If it is, could someone assist me in setting this analysis up? (I have tried following the tutorial, where I on each subject set "0 years" for one scan, and "1 year" for two scans in the QDEC table, but the results from the QDEC analysis don't seem to agree with previous SPSS results that I have). Thank you, Joy-Loi

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interpreting clusters from 2 and 3 way interactions
by Laura M. Tully 18 Mar '13

18 Mar '13

Hi Freesurfer experts, I'm hoping you can help me understand how to interpret interactions in clusters identified in whole brain analysis using glmfit and glmfit-sim. Below I describe what I've done and what I'd like to be able to do. Any suggestions would be most appreciated! - I have two groups (patients, controls) and a behavioral variable of interest (social functioning). I am interested in cortical thickness differences between groups (main effect of group), whether cortical thickness relate to social functioning across the group (main effect of social functioning), and whether this relationship differs by group (group x social functioning interaction). - I ran whole brain analysis using mri_glmfit with group and functioning as variables of interest whilst controlling for/regressing out gender, age, and mean thickness. i.e. 4 classes (conmale,confemale, ptmale, ptfemale) and 3 continuous variables (age, AvgThickness, Functioning) = 16 regressors. - I tested the group x functioning interaction with the following contrast - is it correct? 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 - I then ran mri_glmfit-sim to identify clusters that survive multiple comparisons. This revealed 4 clusters (3 in LH; 1 in RH) that represent regions showing significant group x functioning interaction. - I visualized the clusters in tksurfer, and by loading the y.fsgd file was able to visualize the plotted data to get a sense of the interaction, but this is as much as I know in terms of how to examine interactions in the cluster data...... My specifc questions include: - I understand that the values in xxx.sig.cluster.mgh overlay reflect log10 p values, the signs of which indicate the direction of the relationship (i.e. -3 = negative correlation between thickness & variable) but I'm not sure how to interpret this in the context of an interaction with group? - I understand that the values in xxx.y.ocn.dat contain the average thickness value for each subject in that cluster and that in a simple between groups test this data could be used to conduct post hoc t-tests to show the direction of the difference, but again I'm not sure how to use this data in the context of the interaction. What do the values represent in a group x variable interaction? Ideally, I'd like to extract the contrast estimates for each subject in the group x functioning contrast and plot it in another program and conduct pairwise comparisons (t-tests) in order to get a better understanding of the interaction). I'm not sure how to do this - is it possible? My thinking is that I do something similar in fMRI analysis in spm where I can plot the contrasts in a significant cluster and then extract both the average contrast estimates for each group and the contrast estimates for each individual subject. Thanks in advance! Laura. -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltully(a)mednet.ucla.edu ltully(a)fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

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subcortseg error - ?h.white surfaces not available
by A. Yamamoto 18 Mar '13

18 Mar '13

Hi, After upgrading to FreeSurfer 5.2.0, the command with "-subcortseg" flag exited with the following error. MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white): could not open file I confirmed that the "-autorecon1" stage finished without error. In v5.1.0 it worked fine, so I'm wondering if there is any change in mri_segstats?? FYI, I have attached the last part of recon-all.log file. Thanks for your help. Akio

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Problems with recon-all
by Marcos Martins da Silva 18 Mar '13

18 Mar '13

I installed virtualbox 4.2.8 and CentOS6 (kernel 2.6.32-358.2.1.el6.x86_64). Got tkmedit and tksurfer working on CentOS VM. Recon-all starts and run for sometime but stop with errors a bit later. On bright side I noticed freeview works great both on centos VM and on Fedora 18. At your site, I read freeview may substitute tkmedit and tksurfer when the former come to offer all needed functionality. It follows the errors I got on recon-all.Thanks in advance for your help. _______________________________________ recon-all -s bert -autorecon1 running loop to estimate saturation parameter: A or b constain NAN or infinity values!! _______________________________________ recon-all -s bert -all talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log _______________________________________ The log indicated above shows: imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

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wrong registration
by stdp82＠virgilio.it 18 Mar '13

18 Mar '13

Hi list, I'm noting that registration of DWI and T1 images for some subject is wrong (in the .mincost the first value is netx to 1.1). Before recall new recon-all, trace-all .. what do you advise me? Stefano

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Re: [Freesurfer] LGI
by Marie Schaer 18 Mar '13

18 Mar '13

Hi Jon, I guess you don't have the image processing toolbox installed with matlab? fspecial is a matlab function comprised in this toolbox… I am afraid that lGI with not run without it. Marie On Mar 18, 2013, at 12:03 PM, Jon Wieser <wieser(a)uwm.edu> wrote: > I added the matlab bin directory to my PATH. > > > getmatlab > /Applications/MATLAB_R2012b.app/bin/matlab > > > > I ran : > recon-all -s freesurfer -localGI > and got the following: > > Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0001 > Actual FREESURFER_HOME /Applications/freesurfer > -rw-rw-rw- 1 wieser admin 450426 Mar 18 13:58 /Studies/MJMRI/MJ0001/freesurfer/scripts/recon-all.log > Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > /Studies/MJMRI/MJ0001/freesurfer/surf > #-------------------------------------------- > #@# Local Gyrification Index lh Mon Mar 18 13:59:36 CDT 2013 > \n mris_compute_lgi --i lh.pial \n > ================= > rm -Rf /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial > ================= > ================= > mkdir -p /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial > ================= > ================= > mris_fill -c -r 1 lh.pial /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz > ================= > reading surface from lh.pial... > writing filled volume to /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... > conforming output volume > setting resolution for intermediate calculations to 1.0000 > ================= > make_outer_surface('/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit > ================= > > < M A T L A B (R) > > Copyright 1984-2012 The MathWorks, Inc. > R2012b (8.0.0.783) 64-bit (maci64) > August 22, 2012 > > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com. > >>> reading filled volume... > closing volume... > Undefined function 'fspecial' for input arguments of type 'char'. > > Error in make_outer_surface (line 31) > Gaussian = fspecial('gaussian',[2 2],1); > >>> > ERROR: make_outer_surface did not create output file '/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! > Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > > recon-all -s freesurfer exited with ERRORS at Mon Mar 18 13:59:49 CDT 2013 > > For more details, see the log file /Studies/MJMRI/MJ0001/freesurfer/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > ----- Original Message ----- > From: "Marie Schaer" <Marie.Schaer(a)unige.ch> > To: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, March 18, 2013 1:07:54 PM > Subject: Re: [Freesurfer] LGI > > > > > > > Hi Jon, > > > It looks like the matlab path is not set on your machine. Can you set the $PATH environment variable to include the path to the matlab functions as well? You can try to launch the command "getmatlab", if you get the answer that matlab is not installed, it means that the $PATH environment variable is not properly set. You can also look on the mailing list, there are a few explanations about this path issue, among which the following one: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html > > > > Let me know if you don't find how to make it work. > > > Best, > > > Marie > > > > > On Mar 18, 2013, at 10:44 AM, Jon Wieser < wieser(a)uwm.edu > > wrote: > > > i am trying to computer the LGI local gyrification index with freesurfer. I have Matlab on my machine. > I got the following error: > > > recon-all -s freesurfer -localGI > Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 > Actual FREESURFER_HOME /Applications/freesurfer > -rw-rw-r-- 1 wieser admin 506264 Mar 18 12:37 /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log > Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > /Studies/MJMRI/MJ0012/freesurfer/surf > #-------------------------------------------- > #@# Local Gyrification Index lh Mon Mar 18 12:43:04 CDT 2013 > \n mris_compute_lgi --i lh.pial \n > ERROR: Matlab is required to run mris_compute_lgi! > Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > > recon-all -s freesurfer exited with ERRORS at Mon Mar 18 12:43:04 CDT 2013 > > For more details, see the log file /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > JOn > > -- > Jon Wieser > Research Specialist > UW-Milwaukee > Psychology Department, Pearse Hall Rm 366 > 2441 East Hartford Ave > Milwaukee, WI 53211 > Phone: 414-229-7145 > Fax: 414-229-5219 > _______________________________________________ > 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. > > > > _______________________________________________ > 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. > > -- > Jon Wieser > Research Specialist > UW-Milwaukee > Psychology Department, Pearse Hall Rm 366 > 2441 East Hartford Ave > Milwaukee, WI 53211 > Phone: 414-229-7145 > Fax: 414-229-5219

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mris_preproc
by Mariam Sood 18 Mar '13

18 Mar '13

Hello All, I am trying to do a cross-subject surface based analysis of data analysed using FSL. I am following the instructions in the following tutorial link. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer Each of my subject data comprises of two runs. My question is related to how to use mris_preproc to combine them. Can I combine together each of the runs of multiple subjects as below? mris_preproc --target fsaverage --hemi lh \ --out $OUT_DIR/xrun/lh.varcope$c.mgh \ --iv $subj[1]/run1.feat/stats/varcope$c.nii.gz $subj[1]/run1.feat/reg/freesurfer/anat2exf.register.dat \ --iv $subj[1]/run2.feat/stats/varcope$c.nii.gz $subj[1]/run2.feat/reg/freesurfer/anat2exf.register.dat \ --iv $subj[2]/run1.feat/stats/varcope$c.nii.gz $subj[2]/run1.feat/reg/freesurfer/anat2exf.register.dat \ --iv $subj[2]/run2.feat/stats/varcope$c.nii.gz $subj[2]/run2.feat/reg/freesurfer/anat2exf.register.dat I understand that I can combine the gfeat output of each subject using mris_preproc. I am preferring above method as I believe it is more accurate. Please correct me if I am wrong. Many thanks, Mariam.

2 1

Adding low-res T2 and PD images in the recon-all stream - any advantages?
by Nicola Toschi 18 Mar '13

18 Mar '13

Hello List, on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution. Would you recommend passing these (T2+PD) to the recon-all stream anyway - would they add value/accuracy to the segmentation/parcellation (or would they possibly decrease accuracy)? Thanks in advance, Nicola

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LGI
by Jon Wieser 18 Mar '13

18 Mar '13

i am trying to computer the LGI local gyrification index with freesurfer. I have Matlab on my machine. I got the following error: recon-all -s freesurfer -localGI Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 wieser admin 506264 Mar 18 12:37 /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 /Studies/MJMRI/MJ0012/freesurfer/surf #-------------------------------------------- #@# Local Gyrification Index lh Mon Mar 18 12:43:04 CDT 2013 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 recon-all -s freesurfer exited with ERRORS at Mon Mar 18 12:43:04 CDT 2013 For more details, see the log file /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting JOn -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

2 1

make a volume template from the surface-based template for non-human primates
by Longchuan Li 18 Mar '13

18 Mar '13

Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks in advance! Longchuan

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