Freesurfer

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30088 discussions

Crippled fiber tracts in healthy subjects (TRACULA)
by Ansgar Furst 15 Mar '12

15 Mar '12

Hi, We are using the ADNI Acc 3D FSPGR for structurals and 30 directional (5 B0s) repeat sequence for DTI which so far rendered really nice results. However, recently I encountered data from several healthy young subjects where the TRACULA fiber tract estimations would suggest severely crippled tracts which, however, is not consistent with the FA maps. using

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export hippocampal subfields using mri_binarize
by Catarina Duarte 15 Mar '12

15 Mar '12

Hi all, I am trying to export the hippocampal subfields generated in Freesurfer 5.1. To do that I use mri_binarize with a minimum voxel threshold of 150 and a maximum of 255. However, some of these regions appear overlapped. Why does this happen if a minimum threshold of 150 correponds to a probability higher than 50%? Thank you in advance. Best, Catarina Duarte

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Q: Tkmedit
by Yiyu Chou 15 Mar '12

15 Mar '12

Dear FS users, Please have a look at the attached fig: As shown on the left (using Tkmedit), you will see some "straight lines", but they were not shown if using other software package (ex: mipav - on the right). Do you know what might be wrong on tkmedit ? Thanks in advance !! Regards, Yi-Yu

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WG: Save segmentation results as nifi files
by Fellhauer, Iven 15 Mar '12

15 Mar '12

________________________________________ Von: Fellhauer, Iven Gesendet: Donnerstag, 15. März 2012 10:29 Bis: Douglas N Greve Betreff: AW: [Freesurfer] WG: Save segmentation results as nifi files Dear all, in which space are the output files stored? If they are not stored in MNI space, which steps are necessary to convert these images into MNI space. Best regards, Iven Fellhauer ________________________________________ Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Gesendet: Dienstag, 31. Januar 2012 18:33 Bis: Fellhauer, Iven Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] WG: Save segmentation results as nifi files There's not a separate GM, WM, and CSF. You can create these from the segmentations with mri_binarize. In general, it is run something like this: mri_binarize --i aparc+aseg.mgz --match id1 id2 --o output.nii where id1 and id2 are structure codes from $FREESURFER_HOME/FreeSurferColorLUT.txt For all WM use: 2, 41, 77, 7, 46, 251-255 For all ventricular CSF and choroid plexus use: 4, 5, 14, 45, 44, 72, 31, 63, 15 For GM, use all the above plus 0, then add the --inv option to invert the mask (basically creating a mask of everything that is not GM and inverting it). doug Fellhauer, Iven wrote: > Hi Bruce > > And thank you for your hint, but where are the files for GM, WM and CFS stored in the Freesurfer output directory structur? > > Best regards, > > Iven > > > -----Ursprüngliche Nachricht----- > Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Gesendet: Montag, 30. Januar 2012 15:20 > An: Fellhauer, Iven > Cc: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] Save segmentation results as nifi files > > Hi Ivan > > you can convert any volume to any supported output type using mri_convert. It will figure out the format from the extension, so: > > mri_convert aseg.mgz aseg.nii.gz > > or > > mri_convert aseg.mgz aseg.nii > > should do the trick > > cheers > Bruce > > > > On Mon, > 30 Jan 2012, Fellhauer, Iven wrote: > > >> Dear all, >> >> >> >> I run recon-all with the ?autorecon1 and ?autorecon2 options. Now I >> want to store the segmentation results in a spm like way. One nifti >> file for each matter. Can I do this with freesurfer? And how can I do >> this with freesurfer? >> >> >> >> Best regards, >> >> >> >> Iven Fellhauer >> >> >> >> ---------------------------------------------------------------- >> >> Universitätsklinikum Heidelberg >> >> Zentrum für Psychosoziale Medizin >> >> Klinik für Allgemeine Psychiatrie >> >> Sektion für Gerontopsychiatrie >> >> Voßstr. 4 >> >> 69115 Heidelberg >> >> Tel.: +49 (0) 6221 - 56 7578 >> >> Email: iven.fellhauer(a)med.uni-heidelberg.de >> >> >> >> >> >> > > > 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 > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Cluster-Size in Qdec
by Dusan Hirjak 14 Mar '12

14 Mar '12

Dear Freesurfer experts, I am a beginner in using Freesurfer. I did an explorative study where I correlated cotical thickness with different neuropsychological parameters: I found positive correlations between cortical thickness and higher scores on different neuropsychological scales in different brain regions. However, some of these brain regions (clusters) with cortical thinning are only covering a very small surface area (blue color). I was now wondering if there is a possibility in Qdec to manually define the minimal and maximal cluster size, which I want to show? Thanks in advance! Dusan

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Coordinate Transform
by Tianyi Qian 14 Mar '12

14 Mar '12

Dear Freesurfer experts, How can I transfer the coordinate in individual space into MNI space. I don't want to transfer the whole volume, I only need to transfer the coordinate of some points. Thanks, -- Tianyi Qian

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Qdec
by Ahmed, F, Me <fahmed＠sun.ac.za> 14 Mar '12

14 Mar '12

Hello Freesurfer experts, I'm trying to run the tutorial of Qdec and am using the tutorial data set "buckner_data-tutorial_subjs.tar.gz". I started running the Qdec tutorial ok, I managed to load the Qdec.table.dat file ok and everything looked ok. Then when I pressed the tab 'Generate Stats Data Tables' I got this error window popping up below: And in the terminal window it also said: asegstats2table --meas volume --tablefile /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/qdec/stats_tables/aseg.volume.stats.dat --subjects 140 049 141 084 021 093 080 091 040 017 138 106 108 092 124 129 103 130 039 123 095 067 004 133 097 073 149 045 136 144 032 131 145 111 102 074 114 008 128 099 Building the table.. SUBJECTS_DIR : /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs ERROR: cannot find /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/140/stats/aseg.stats Use --skip flag if you want to continue in such cases I can't seem to locate the aseg.stats file in the tutorial data set. Did I not extract the file properly or something? Should it be there? Thanks, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

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intersection between ROI masks
by Miranka Wirth 14 Mar '12

14 Mar '12

Dear freesurfers, how can I compute the intersection between binarized masks? Thank you for your support, Miranka

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Freesurfer: surf2vol?
by Florsek 14 Mar '12

14 Mar '12

Dear all, we have performed a cluster analysis in Qdec and found a significant vertex-cluster after correction for multiple testing using the Monte Carlo simulation. Our aim is to map the vertices to an atlas which is different from that of Desikan. To do that we need the volume-based information of the significant cluster. To transform the surface-based information into volume-based information we need to conduct the "surf2volume"-command, right? What I don't understand is what the required flags such as "--surfval" and "--volreg" need to contain. For example what is meant with "source of the surface values and format" (surfval) or "matrix that maps XYZ in the reference anatomical to XYZ in the functional volume" (volreg). Where can I get these files? Do I have to run tkregister2 for each proband? Thank you very much for your help in advance! Best regards, Florian -- Florian Siedek Doctoral Scientist Institute of Human Genetics Department of Genomics Life& Brain Center University of Bonn Sigmund-Freud-Strasse 25 D-53127 Bonn Germany Email: florsek(a)gmail.com

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Vertex index information for a sphere.reg file
by Ji hoon Oh 14 Mar '12

14 Mar '12

Dear FreeSurfer, Hi, I have a label with vertex index, RAS and overlay values, and want to add spherical coordinates to them as presented in tksurfer. I found following archives that are related to this question, but I couldn't find any vertex index (number) information in a sphere.reg file. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00627.html) I converted ?h.sphere.reg file into ?h.sphere.reg.asc using *mris_convert* command, and imported it to MATLAB using *read_asc.m* file (without face data). They had [x,y,z] coordinates in columns, but did not provide vertex index information. I wonder if there is a way to read the vertex index from a sphere.reg file, or there are other methods that read both vertex index and spherical coordinates. Thank you, Jihoon Oh -- --------------------------------------------------------------- Jihoon Oh, M.D. Ph.D. candidate, Bio and Brain Engineering Korea Advanced Institute for Science and Technology (KAIST) E-mail: ojihoon(a)gmail.com ---------------------------------------------------------------

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