Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30085 discussions

Re: [Freesurfer] Mris_make_face_parcellation
by Jürgen Hänggi 16 Dec '09

16 Dec '09

Hi Bruce I attached a figure that illustrates my problem. I would like to known which parcellations in the right panel (that are denoted only by numbers) are located in the fusiform gyrus parcellation shown in the left panel (aparc.a2005s). Any suggestions are welcome Thanks Jürgen On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: > I guess I'm not sure what you're trying to do. If you give > mris_make_face_parcellation the sphere.reg file as input then the > triangles will be in register across subjects. > > On Wed, 16 Dec 2009, Jürgen > Hänggi wrote: > >> Hi Bruce >> >> Yes, mris_divide_parcellation produces thin stripes as parcels. I prefer the >> triangles produced by mris_make_face_parcellation. >> >> Thanks >> Regards >> Jürgen >> >> >> On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: >> >>> Hi Jurgen, >>> >>> you might try using mris_divide_parcellation instead, which divides up a >>> specified set of annotation units (if you give it a configuration file). >>> >>> cheers >>> Bruce >>> On >>> Tue, 15 Dec 2009, Jürgen Hänggi wrote: >>> >>>> Dear FS experts >>>> >>>> When using mris_make_face_parcellation is it possible to restrict the face >>>> parcellation to a parcellation found in aparc.a2005s, e.g. to the >>>> precentral >>>> gyrus. >>>> >>>> Or is there another way to decide which micro-parcellation produced by >>>> mris_make_face_parcellation belong to which parcellation in aparc.a2005s? >>>> >>>> Thanks in advance >>>> Regards >>>> Jürgen >>>> >>>> --------------------------------------------------------------------------->>>> - >>>> Jürgen Hänggi, Ph.D. >>>> Division Neuropsychology >>>> Institute of Psychology >>>> University of Zurich >>>> Binzmuehlestrasse 14, PO Box 25 >>>> 8050 Zurich, Switzerland >>>> 0041 44 635 73 97 (phone office) >>>> 0041 76 445 86 84 (phone mobile) >>>> 0041 44 635 74 09 (fax office) >>>> BIN 4.D.04 (office room number) >>>> j.haenggi[at]psychologie.uzh.ch (email) >>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>> http://www.juergenhaenggi.ch (private website) >>>> >>>> This e-mail (and any attachment/s) contains confidential and/or privileged >>>> information. If you are not the intended recipient (or have received this >>>> e-mail in error) please notify the sender immediately and destroy this >>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>> material in this e-mail is strictly forbidden. >>>> --------------------------------------------------------------------------->>>> - >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> >> >> ---------------------------------------------------------------------------- >> Jürgen Hänggi, Ph.D. >> Division Neuropsychology >> Institute of Psychology >> University of Zurich >> Binzmuehlestrasse 14, PO Box 25 >> 8050 Zurich, Switzerland >> 0041 44 635 73 97 (phone office) >> 0041 76 445 86 84 (phone mobile) >> 0041 44 635 74 09 (fax office) >> BIN 4.D.04 (office room number) >> j.haenggi[at]psychologie.uzh.ch (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> >> This e-mail (and any attachment/s) contains confidential and/or privileged >> information. If you are not the intended recipient (or have received this >> e-mail in error) please notify the sender immediately and destroy this >> e-mail. Any unauthorised copying, disclosure or distribution of the >> material in this e-mail is strictly forbidden. >> ---------------------------------------------------------------------------- >> >> >> >> >> >> ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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insula infarct and pial boundary understimation of gray matter
by Durazzo, Timothy 16 Dec '09

16 Dec '09

Dear Experts, Occasionally, we have patients with clear cortical or subcort. gray matter infarcts. If the infarct is large enough, in some cases the pial line bends in away from the outer boundary of viable gray matter and in toward the infarct (i.e., area of decreased contrast). In the attached power point, I show a case where there is a left (radiologic convention) rostral insula infarct and the pial line dives in toward the infarct, but the adjacent main surface line looks like it is only very slightly underestimating the white matter boundary. This occurs on six contiguous slices, but the infarct is only apparent of three. This individual was run on a 1.5T scanner and processed with FS v4.5. The area of attenuation is apparent on his raw MPR and is bright on T2, so this is not an artifact in FS. I'm reluctant to use control points or change the WM boundary because it appears to be overall correct. Is there any way to fix this? Thanks a lot. - Tim Timothy C. Durazzo, PhD Assistant Professor Department of Radiology and Biomedical Imaging University of California, San Francisco Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center (415) 221-4810 x4157

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Saving color changes
by nlucena＠artsci.wustl.edu 15 Dec '09

15 Dec '09

I'm manually changing freesurfer's region colors in tksurfer but can't seem to save the changes. Is there a way to either save these changes, or an alternate method for replacing the default colors freesurfer uses in its cortical segmentation in a way that can be applied to each hemisphere and saved?

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[freesurfer] recon-all taking an unusually very long time
by David Qixiang Chen 15 Dec '09

15 Dec '09

Hi, We are having one scan going through recon-all that is taking way longer than ordinary. Other scans took about 20-30 hours to calculate, while this particular scan is taking 3+ days and has still not being completed. Just wondering how often something like this happens, and if there's any known problems with this sort of thing. Here's the mri_info output: Starting DICOMRead2() dcmfile = /media/HIPPO/scans/normals/C11/T1/C11_0.dcm dcmdir = /media/HIPPO/scans/normals/C11/T1 Ref Series No = 3 Found 162 files, checking for dicoms Found 160 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 160 ndcmfiles = 160 PE Dir = ROW (dicom read) Volume information for C11_0.dcm type: dicom dimensions: 256 x 256 x 160 voxel sizes: 0.9375, 0.9375, 1.0000 type: SHORT (4) fov: 240.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 11.96 msec, TE: 5.05 msec, TI: 300.00 msec, flip angle: 20.00 degrees nframes: 1 ras xform not present xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = 5.3850 : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 30.3850 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 27.4266 Orientation : ??? Primary Slice Direction: unknown voxel to ras transform: -0.9375 0.0000 -0.0000 125.3850 0.0000 -0.9375 -0.0000 150.3850 0.0000 0.0000 1.0000 -52.5734 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.878906 ras to voxel transform: -1.0667 0.0000 0.0000 133.7440 0.0000 -1.0667 0.0000 160.4107 -0.0000 -0.0000 1.0000 52.5734 0.0000 0.0000 0.0000 1.0000

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Mris_make_face_parcellation
by Jürgen Hänggi 15 Dec '09

15 Dec '09

Dear FS experts When using mris_make_face_parcellation is it possible to restrict the face parcellation to a parcellation found in aparc.a2005s, e.g. to the precentral gyrus. Or is there another way to decide which micro-parcellation produced by mris_make_face_parcellation belong to which parcellation in aparc.a2005s? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Stats from cluster labels
by Dankner, Nathan (NIH/NIMH) [F] 15 Dec '09

15 Dec '09

Hi all, I was curious as to whether I would be able to pull stats (i.e. Average cortical thickness) from a cluster after cluster correction. Is this possible, and if so, how would I go about doing it? Thanks, Nathan

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QDEC error
by Weisinger, Brian (NIH/OD) [E] 15 Dec '09

15 Dec '09

I am trying to use qdec but it gave me this error. I don’t understand what is wrong because it read the diagnosis factor level of COS & NV but then says subject 00308 has invalid level of COS in diagnosis column. Any ideas? CHP-MP2:freesurfer brianweisinger$ qdec & [1] 7902 CHP-MP2:freesurfer brianweisinger$ Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat... Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 24 Reading discrete factor levels from config file /Applications/freesurfer/subjects/qdec/gender.levels 'Female','Male', done Reading discrete factor levels from config file /Applications/freesurfer/subjects/qdec/diagnosis.levels 'COS','NV', done ERROR: Subject 00308 has an invalid level 'COS' in the diagnosis column INFO: If 'diagnosis' is a discrete factor, then create a file named 'diagnosis.levels' containing the valid factor names one per line. Error loading the data table.

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Strange occipital dip
by Bahadur, Kandy (NIH/NIMH) [F] 15 Dec '09

15 Dec '09

Hello, I am very new to freesurfer and might not have seen enough surfaces to know the answer to this question. But, I went through autorecon1 and autorecon2 with my volumes, and when I looked at the surface to inspect it, I found a weird , relatively large dip around the parietal and occiptal lobes. We are only interested in occipital (we cut that plane out and flatten it), so I am concerned that this dip might interfere with the data. When I looked at that point in the editor, nothing weird or abnormal showed up. I have attached a picture of the RH, where I see this abnormal dip. Can you let me know if this is normal or not? Also, the freesurfer manual nicely illustrates where I need to make the cuts to cut out the occipital lobe for the left hemisphere, but I don't really see any guidelines for cutting out the occipital lobe for the right hemisphere. Any suggestions? Thanks, Kandy -- Kandy Anasha Bahadur National Institute of Mental Health/ National Institute of Health Laboratory of Brain and Cognition 10 Center Drive, Building 10/4C212 Bethesda, MD 20892 Phone: 301-435-4945 Email: bahadurk(a)mail.nih.gov

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Error mri_label2vo
by Ribes Delphine 15 Dec '09

15 Dec '09

Hi FreeSurfer users, I've tried the following from my $SUBJECT_DIR/SubjectX/mri directory: mri_label2vol --seg aseg.mgz --regheader rawavg.mgz --o aseg-in-rawavg.mgz --temp aseg.mgz I have the following error in return: ERROR: Option --regheader unknown Any ideas where does it comes? Thanks a lot, Have a good day, Delphine ________________________________________ De : Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Date d'envoi : mardi 3 novembre 2009 18:48 À : Ribes Delphine Cc : freesurfer(a)nmr.mgh.harvard.edu Objet : Re: [Freesurfer] RE : RE : Skull Stripping Free surfer Check out this page and see if it answers your questions https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat Ribes Delphine wrote: > Hi, > > I've tested to use directly mri_watershed but then you have to set the seeds for watershed initiaization. > > The idea is to create an automatic pipeline (as I have a bunch of data to process) and get the results into the subject space coordinate. > > In subjects directories, I've seen one called transform. Inside this directory, there is some file with (I suppose) the affine transform applied. Is there a freeSurfer command to do the inverse transform? > Also there is a "conformalization" to put all volume in 256 cube with 1mm cube spacing. Is there a command in FreeSurfer to get back the original volume? > > After the inverse affine transform and the inverse conformalization, I will have (hopefully), my skullstrip volume into his original space coordinate? > > Thanks > Delphine > > > > De : Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Date d'envoi : mardi 3 novembre 2009 15:09 > À : Ribes Delphine > Cc : freesurfer(a)nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] RE : Skull Stripping Free surfer > > yes, it's possible. You'll need to download and install freesurfer, then > try out the mri_watershed command (or just run recon-all on your data, > mri_watershed is one of the steps it runs) > On Tue, 3 Nov 2009, Ribes > Delphine wrote: > > >> Hi, >> >> Looking at Literature, HWA algorithm seems to perform well for my kind of data. Also the results I've got seems to confirm this hypothesis. But if possible I would like to siwcth of the affine registration. >> >> So yes I would like only to do skull strip using HWA algorithm. Is it possible to do so in freesurfer? :-) >> >> Thanks >> >> ________________________________________ >> De : Pedro Paulo de Magalhães Oliveira Junior [ppj(a)netfilter.com.br] >> Date d'envoi : mardi 3 novembre 2009 13:43 >> À : Ribes Delphine >> Cc : freesurfer(a)nmr.mgh.harvard.edu >> Objet : Re: [Freesurfer] Skull Stripping Free surfer >> >> Using FreeSurfer just for Skull Striping is like killing an ant with an MP5 :) >> >> Are you sure you just want to skull strip? >> >> >> 2009/11/3 Ribes Delphine <delphine.ribes(a)epfl.ch<mailto:delphine.ribes@epfl.ch>> >> Dear Users, >> >> I've just started using FreeSurfer. I would like to use it for skull-stripping. >> >> I've created a batch file to process all my subjects. >> and I am basically using the command line: >> >> recon-all -autorecon1 -skullstrip -s subj1 >> >> I would like to know if there is a way to only do skull-stripping and not doing the Talairach Transform and then INU correction? >> >> I would like to have the skulll-stripp volume in the same space coordinate as originally? >> >> Otherwise, I am doing skull-stripping of T1 weighted images of normal elderly subejcts. Is there any specific recommandation for skull-stripping parameters? >> >> Thanks a lot, >> Delphine >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > _______________________________________________ > 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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qdec output
by Guang Zeng 15 Dec '09

15 Dec '09

Hi, there, Does anyone can give me link or paper which explains all the QDEC output file, such as F.mgh, gamma.mgh, beta.mgh ....... What are they, how are they related? Thanks a lot! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/

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