Freesurfer

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30133 discussions

xhemi installation
by Sofie Valk 08 Jan '14

08 Jan '14

Dear FreeSurfers, I have a question regarding the installation of xhemi (I am using FreeSurfer 5.1) I tried to follow the guide on: https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi to install the necessary files, however the following files do not seem to be present on the ftpserver: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.{… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol.{… What could be wrong? Thank you very much!! Kind regards, Sofie Valk, ... PhD Candidate, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany

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Re: [Freesurfer] pial erosion/downsampling
by Octavian Lie 08 Jan '14

08 Jan '14

Thank you, I want to merge the pial eroded (of white expanded) and downsampled surfaces of the two hemispheres in a new surface (generate a new, continuous, surface/mesh, no holes, no self intersections). The question is whether pial freesurfer atlases and spherical registration would be applicable to this surface too, Octavian On Wed, Jan 8, 2014 at 11:54 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you cc the list? I don't know what you mean by "merge" > > On Wed, 8 Jan 2014, Octavian Lie wrote: > >> Thank you, >> >> I want to merge the pial eroded (of white expanded) and downsampled >> surfaces of the two hemispheres in a new surface. The question is >> whether pial freesurfer atlases and spherical registration would be >> applicable to this surface too, >> Octavian >> >> >> > > > 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. >

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surface reorientation in sinc with volume
by Octavian Lie 08 Jan '14

08 Jan '14

Dear All I reoriented a volume on exporting to analyze format for an application mri_convert -i path to file/T1.mgz --out_orientation PSR -o path to file/T1reoriented.mgz mri_convert -ot analyze -i path to file/T1reoriented.mgz -o path to file/T1reorientedPSR.img I need to reorient from the command line the original pial surfaces (?h.pial) generated from the recon-all process to new surfaces to match the new T1 orientation (T1 reorientedPSR). Thank you, please advise, Octavian

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longitudinal hippocampal subfields analysis
by Salil Soman 08 Jan '14

08 Jan '14

Hi, I have been able to do the longitudinal processing steps for a number of subjects with 3 time points each, and then extract the generated statistics using aparcstats2table and asegstats2table. Is it possible to perform longitudinal analysis of the hippocampal subfields? If so, could someone point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated. Thank you. Salil Soman, MD, MS

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pial erosion/downsampling
by Octavian Lie 08 Jan '14

08 Jan '14

Dear All, 1. I need to erode the ?h.pial surfaces be exactly 3 mm, then 2. I need to downsample each of the eroded surfaces to 7500 vertices each, then (3. Merge the downsampled surfaces (whether or not an intermediary voxelizing step is involved)) I would appreciate any help with command syntax. If this is possible, is there a way to warp/ preserve the relationship of the output with aparc.anot labels and surface based registration /sphere.reg in freesurfer? Trying this route to a 4-layer BEM... Thank you, Octavian

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tksurfer display
by Ray, Siddharth 07 Jan '14

07 Jan '14

Hi, Is there any way in tksurfer GUI display, that I can set a NVtxs threshold to get rid of regions (that came up significant after monte carlo simulation) which have NVtxs less than my input threshold. For eg. In my table below, I don't want postcentral label to appear in my tksurfer view (as I only want to see labels with more than 300 NVtxs). Can I get that label out from my brain pictures? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 3.048 133418 89.23 52.8 -12.9 32.0 0.00020 0.00000 0.00040 186 postcentral 2 2.938 109465 989.46 36.0 17.2 31.1 0.00020 0.00000 0.00040 1066 caudalmiddlefrontal Thanks, -Siddharth

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Re: [Freesurfer] reconall error.
by Bruce Fischl 07 Jan '14

07 Jan '14

Hi Rashmi how did you create this dataset? The non-black background is probably going to cause trouble. Is it an mp2rage or something similar? Could you try replacing the background value (386.997) with 0 and see if that helps. If there are really big defects the topology fixer will take forever, and probably won't generate the correct solution anyway cheers Bruce On Tue, 7 Jan 2014, Rashmi Singh wrote: > Hello FreeSurfer experts, > I am having problem with running reconall. > I am using version 5.1. > Attached is data set on which I ran reconall. > Because I was getting tailrace failure I ran it with –notal-check flag( the > run with -use–mritotal flag failed too, so I used the –notal check flag ) > Recon all ran OK, but its has got stuck at a point (topology detection > stage) and its not moving forward (my terminal shows that its still running) > May you please help me troubleshoot this issue. > > Thanks, > Rashmi > >

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Postdoc fellowships available in engineering at USC - know any good candidates? (fwd)
by Bruce Fischl 07 Jan '14

07 Jan '14

FYI ---------- Forwarded message ---------- Date: Tue, 07 Jan 2014 10:35:41 -0800 From: Richard Leahy <leahy(a)ee.usc.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Postdoc fellowships available in engineering at USC - know any good candidates? USC has a new and generous engineering postdoctoral fellowship program (deadline January 31st, details attached) for PhD students/recent grads planning on an academic career. If you have any students (or know of others) about to or recently graduated who might be interested in working in the area of neuroimaging imaging at USC, can you please forward the attached and ask them to get in touch with me at their earliest convenience. We have a substantial and growing program in brain imaging at USC, with three faculty in EE (myself, Krishna Nayak and Justin Haldar) with primary research interests in medical imaging and a major focus on the brain. We have access to 3T MRI with simultaneous EEG on the main university park campus where the EE dept is housed as well as research and clinical scanners at the health science campus and Childrens' Hospital LA. We will also have a 7T scanner online sometime in the next 12 months. There is excellent potential to collaborate with neuroimaging faculty in gerontology, psychology, neuroscience and the medical school. We are also particularly interested in candidates with interests in statistics, computer vision, machine learning and graph-based analysis and their application to medical image analysis. I would be happy to discuss this opportunity with any students you feel would benefit from this position. Please do encourage any qualified students to apply and to contact me to discuss potential research topics. best regards Richard. -- _____________________________________ Richard M. Leahy, Professor Signal and Image Processing Institute Department of Electrical Engineering University of Southern California 3740 McClintock Ave, EEB400, MC 2564 Los Angeles, CA90089-2564. 213 740 4659 (t) 213 740 4651 (f) http://neuroimage.usc.edu _____________________________________

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seeking a post-doc (fwd)
by Bruce Fischl 07 Jan '14

07 Jan '14

FYI Dear Colleagues, I hope this finds you well! I wanted to pass along an ad for a post-doc position on a motion correction project. We're having a tough time finding someone with both a strong interest in clinical autism research and technical sophistication with data analysis. Please pass this around and let me know if you can think of anyone or if you have suggestions on where to advertise. We did advertise at SFN. The position is available immediately. Thanks for your consideration and best wishes for a happy new year, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging and Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 1.111 Charlestown, MA 02129 email: dara(a)nmr.mgh.harvard.edu phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Cannot run unpacksdcmdir on buckner_data/014-anon
by Anders Olsen 07 Jan '14

07 Jan '14

Hello FreeSurfer team. I am currently trying to learn the general usage of FreeSurfer and have run into problems with unpacking DICOM files. When I run: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -scanonly ~/fs_subjects/014-anon/scan.info It completes and gives me the following output: 14 anon ok 256 256 128 001.dcm I then try to unpack slice number 14 by running: unpacksdcmdir -src ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon -targ ~/fs_subjects/014-anon -fsfast -run 14 bold nii f.nii And it gives me the message: ERROR: reading ~/freesurfer_dicom/buckner_data/tutorial_subjs/014-anon/001.dcm tag 28 30 I have done md5sum buckner_data-tutorial_subjs.tar.gz and got the hash: 14618f42ffa6b21d5714f37e159357c4 which matches the md5sum in ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5su… Am I doing something wrong or is there a problem with the dcm files in the test data? -- Venlig hilsen | Kind regards Anders Dreisig Olsen anders.d.olsen(a)gmail.com <mailto:anders.d.olsen@gmail.com>

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