Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 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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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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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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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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Problem with conversion to mgz
by Hemant Bokil 28 Feb '12

28 Feb '12

I am trying to convert some dicom slices to mgz but am getting errors. From the errors it appears that mri_convert is looking for some metadata and that this metadata is corrupted. The MRs themselves look fine when I view them in Matlab. The full screen dump is below: mri_convert -it dicom -ot mgz DICOM_MR_DATA/MR2/MR20000.DICOM MR2 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from DICOM_MR_DATA/MR2/MR20000.DICOM... Starting DICOMRead2() dcmfile = DICOM_MR_DATA/MR2/MR20000.DICOM dcmdir = DICOM_MR_DATA/MR2 Ref Series No = 3 Found 83 files, checking for dicoms Found 80 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 80 nslices = 1 ndcmfiles = 80 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=40.00, TE=8.00, TI=0.00, flip angle=40.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -1.094 -0.000 nan nan; -0.000 -1.094 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000;

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Frontal signal drop out
by Mahinda Yogarajah 24 Feb '12

24 Feb '12

Dear Experts, Sorry if this is a repost, but I was not sure it got posted. I have a few subjects that I want to salvage and use where there appears to be significant signal inhomogeniety in the last few frontal slices (see T1.mgz in attached figure 1). Despite the use of control points (placed with careful adjustments of windowing parameters), I still can't encompass all of the the gyri right at the front (see brainmask.mgz coronal slice in figure 2). I would really appreciate some advice on how to proceed from here. Is placing white matter voxels in wm.mgz a possible solution ? Or is there another solution ? Thanks. M

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ICV
by Dusan Hirjak 23 Feb '12

23 Feb '12

Dear Freesurfer experts, I am a beginner in using Freesurfer. I was wondering if ICV should be treated as a potential confounder (such as age, education, chlorpromazine equivalents and duration of illness) in the statistical analysis of volumetric data/cortical thickness? Thanks in advance! Dusan

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mris_make_face_parcellation
by Franz Liem 13 Feb '12

13 Feb '12

Dear Freesurfers, I have some questions regarding mris_make_face_parcellation (and possibly found one error in the .tri file). (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0). I would like to make a high res parcellation of several subjects and used ic3.tri. Parcels should correspond across subjects. I computed mris_make_face_parcellation ../surf/lh.sphere $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot 1. It seems not to make a difference whether I choose .sphere or .sphere.reg as input, the resulting parcellations are identical (i checked by comparing vertex label values in matlab; .inflated deviates a bit, but not substantially). According to Bruce (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18509.html) "You want to use either ?h.sphere if you want it to be uniform in subject space or ?h.sphere.reg if you want the parcels to correspond across subjects" Could anybody tell me how the parcellation is performed exactly? I thought it was performed on the input surf (the input surf is parcellated into (e.g.) 642 equally sized parcels), which should lead to different results at .sphere and .sphere.reg, shouldn't it? Alternatively, would it be better to mris_make_face_parcellation the fsaverage and mri_surf2surf the high res parcellation onto each subject to get cross-subject correspondency (I tried this. It didn't look that great with this command: mri_surf2surf --srcsubject fsaverage --sval-annot ic3.annot --trgsubject subject1 --tval ic3s03.annot --hemi lh )? To recap, what is the best strategy to arrive with cross-subject-corresponing parcellations? Performing mris_make_face_parcellation with ?h.sphere.reg for each subject individually? 2. There seems to be duplicate structNames/annotationValues when applying mris_make_face_parcellation with ic3.tri In fsaverage at least the following labelnames are given to two spatially separated labels. ic3.tri_vertex_25 (cluster 1 around vertex 41132, cluster 2 around vertex 157199) ic3.tri_vertex_42 (cluster 1 around vertex 137845, cluster 2 around vertex 155417) How come? Thanks for you help, Franz

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Freesurfer January 2012