Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0
by Andrew Bock 08 Mar '13

08 Mar '13

Hello, I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock(a)u.washington.edu

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entorhinal cortex volume question
by Cat Chong 29 Jan '13

29 Jan '13

Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine

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selxavg3 error : NaN in Xtmp.mat file
by Sid Kundu 07 Dec '12

07 Dec '12

Hi Doug, I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error: Saving X matrix to /home/sidkundu/freesurfer/sessions/Heading-TTP/LMV2010_N19_Heading-TTP/bold/TTP-analysis-3/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 248) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I looked at the generated Xtmp.mat file and it shows the design matrix X has all zeros in 2 columns, resulting in NaNs in the same columns for Xn, and corresponding NaNs in XtX. I'm wondering what would cause this or why it would only occur for only one subject. _________________________________ Sid Kundu Biomedical Engineering Boston University

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flipping surface data
by kelsi 04 Dec '12

04 Dec '12

Hi Freesurfers, Is there a tool to flip the orientation of surface data to the opposite hemisphere? We are working with stroke patients, and I would like to do analysis of the contralesional hemisphere of all the patients. However, this requires putting them on the same hemisphere for ttests, etc. I saw an earlier thread online about a program for flipping in the works, I was just wondering if this is now possible? Thank you! Kelsi

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Re: [Freesurfer] integrating FSL and Freesurfer
by noam Schneck 09 Oct '12

09 Oct '12

Hi Doug Here are more detailed versions of my first two questions. 1) I used tkmedit to look at the mean_func produced by a gfeat analysis of one subject's three functional runs overlayed onto the anatomical image produced by recon-all on that same subject(bert/mri/orig.mgz). The registration matrix I used was the anat2std.dat that was produced by running reg-feat2anat on all three of the feat analyses from the individual runs. When I did this I saw that the mean_func image was outside the boundaries of the anatomical image. Correspondingly, when I overlayed the zstat.nii.gz from the gfeat analysis onto the anatomical image I had activation outside of the anatomical image brain. 2) Originally, I ran BBR on a subject that I had run Recon-all for. I used BBR to register the example_func.nii.gz to the bert/mri/orig.mgz. I had BBR output an fsl.mat. I then used ApplyXFM in fsl to apply BBR's fsl.mat to register the example_func.nii.gz onto a T1 image that had been created by converting bert/mri/brainmask.mgz into niftii with mri_convert. I tried it again, this time converting the orig.mgz to niftii. In both cases the example_func in T1 space image produced by ApplyXFM is rotated about 90 degrees and also inverted. This is viewed in fslview, The corresponding T1 images created by mri_convert are not. What can I do to allow me to use BBR's fsl.mat within ApplyXFM?

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Error with mri_volcluster
by Antonella Kis 01 Oct '12

01 Oct '12

Dear Doug, I was running the mri_glmfit-sim \ --glmdir GroupAnalysis_abs.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign abs \ --cwpvalthresh .05 just to get an idea of how my FA Group Analysis data is looking and I got an error before to get the permcsd.sig.cluster.summary file from the mri_volcluster: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh ERROR: cannot find /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/fsaverage/mri/aparc+aseg.mgz I replaced the fsaverage/mri/aparc+aseg.mgz with the cvs_avg35/mri/aseg.mgz and to get the cluster summary I was running: mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh but then I am getting the following error: NOT Adjusting threshold for 1-tailed test Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt INFO: loading mask volume: GroupAnalysis_abs.glmdir/mask.mgh INFO: MRIbinarize01(): nhits = 961260 Found 961260 voxels in mask ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file. Can you please help me to solve this problem. I am not sure what to do. Thank you very much! Antonella PS. Just to remember you that I registered my FA data over the CVS space but I have for each subject from dt_recom the register.dat file so I suppose I need to keeo the fsaverage in the --reg COMMAND-LINE ARGUMENTS.

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label transformation to MNI space
by Linda Douw 05 Jul '12

05 Jul '12

Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Linda Douw, PhD.

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/path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
by Xiangzhen Kong 08 Jun '12

08 Jun '12

Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv -f /xxx/dmri/dwi_orig_flip.mghdti.bvecs /xxxx/dmri/bvecs mv: cannot stat `/xxx/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz' and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM data? My data is from a siemens scanner. Thanks! Xiangzhen 2012-02-03 Xiangzhen Kong

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Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> 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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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Comparing Cortical Thickness
by Jeff Sadino 03 May '12

03 May '12

Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline? I ran make_average_subject on each group. To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino

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Freesurfer February 2012