Freesurfer October 2010

freesurfer@nmr.mgh.harvard.edu

100 participants
129 discussions

Two PhD positions in multimodality neuroimaging
by Michels Lars 07 Oct '10

07 Oct '10

Applications are invited for two doctoral research positions in a multimodality neuroimaging project funded by the Zürich Institute of Human Physiology (ZIHP), to start on the 1st of January 2011. The project will investigate the major physiological and metabolic markers of typical and atypical brain development, using a combination of advanced brain imaging, e.g. simultaneous EEG and functional MRI, perfusion MRI, and MR-spectroscopy methods. Candidates should hold a Master's degree in neuroimaging, neuroscience, neurobiology, neuropsychology, neurophysiology, or physics, or a related field. Fluency in English, good oral and written German, and the ability to work within a multidisciplinary team are essential. Some experience of MRI, EEG or other brain imaging methods is an advantage. Salaries are in accordance with the Swiss National Research Foundation: 1st year: 40'800.- 2nd year: 43'800.- 3rd year: 46'800.- For further information about the project please contact: Dr. Lars Michels (lars.michels(a)kispi.uzh.ch) To apply please send your CV with a covering letter including a description of your research interests, a copy of your academic degree(s), and two academic referees to the address below. Reviews of applications will begin on the 25th of October and will continue until the positions are occupied. Dr. Lars Michels MR-Zentrum University Children's Hospital Steinwiesstrasse 75 8032 Zürich Switzerland

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Re: [Freesurfer] Pial Edit on Atrophied Brain
by Soon Hock Wei 06 Oct '10

06 Oct '10

Dear All: Just to follow up with my previous enquiry, is there any suggestion/advice over this pial edit issue? In addition, I would like to ask one more question if possible: I understand that the pial surface is created by expanding the WM surface. Hence, is there any parameter (maybe to mris_make_surfaces command) that I can adjust to allow for more expansion? Meaning the pial boundary will be "pushed" further from WM surface? I know the end-result maybe be worse but just for the sake of curiosity. Thanks! Regards, Hock Wei SOON -----Original Message----- From: Soon Hock Wei Sent: Tuesday, September 28, 2010 8:49 AM To: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] Pial Edit on Atrophied Brain Hi: Thanks for the reply! Attached is the image. Regards, Hock Wei SOON -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 27, 2010 11:49 PM To: Soon Hock Wei Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Pial Edit on Atrophied Brain could you send us an image to illustrate what you mean? On Mon, 27 Sep 2010, Soon Hock Wei wrote: > Dear All: > > I am working on MRI images of subjects suffered from dementia. In severe > cases, atrophy is observed where the white matter loss causes reduced > white/gray differentiation. Hence, the pial surface generated from the > autorecon2 does not include what is clearly atrophied cortical tissue > without the underlying white matter. > > I could not find any way to manually correct for this pial surface (i.e. > to expand the surface outward to include the atrophied cortical tissue). > The nearest wm surface is far away due to white matter loss. Can anyone > please give me some advices? > > Any suggestion is appreciated. > > Regards, > Hock Wei SOON > > 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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Re: [Freesurfer] spmregister error
by Chindhuri Selvadurai 06 Oct '10

06 Oct '10

Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for other users. Any help would be appreciated! Thanks, Chindhuri ________________________________________________ Re: [Freesurfer] spmregister error Douglas N Greve Fri, 30 Jul 2010 09:58:18 -0700 Yes, that should work. doug Adam Nitenson wrote: > Hi Sandra, > > I just had this same problem about a week ago. The solution which > worked for me was adding the following line of text into the startup.m > file in your matlab folder: > > path(path,'/usr/pubsw/common/spm/spm5'); > > I'm not sure it matter exactly where you put it. I put mine in the last > row in the FreeSurfer FAST section, under the line beginning with "clear". > > Hope that helps! > > -Adam > > > > >> Hello, >> >> When running spmregister-sess (standard environment was sourced) I >> encountered this error: >> >> ERROR: matlab exited with errors >> ERROR: cannot find spm_coreg.m. Make sure that the SPM >> package is in your matlab path (check ~/matlab/startup) >> ERROR: spm_coreg >> >> ERROR: spmregister failed >> __________________________________________________________ >> >> Our information: >> >> >> FREESURFER_HOME: /usr/local/freesurfer/stable4 >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 >> >> RedHat release: CentOS release 5.3 (Final) >> >> Kernel info: Linux 2.6.18-128.7.1.el5 x86_64 >> >> NMR Center info (/space/freesurfer exists): >> >> machine: purkinje >> >> SUBJECTS_DIR: /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons >> >> PWD: /cluster/ablood/1/DMRF_ASL >> >> ssh purkinje >> setenv SUBJECTS_DIR /cluster/ablood/1/DMRF_ASL/DMRF_ASL_recons >> cd /cluster/ablood/1/DMRF_ASL >> __________________________________________________________________ >> >> >> We appreciate any help you can give us!! >> >> Thanks, >> >> Sandra >> Mood and Motor Control Laboratory >> Athinoula Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> 120 6th St. >> Charlestown, MA 02129 >> Tel: 617-643-6245 >> Fax: 617-726-1351 >> Email: swoodm...(a)partners.org >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital > _______________________________________________ > 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 gr...(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 _______________________________________________ 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. * [Freesurfer] spmregister error swoodman o Re: [Freesurfer] spmregister error Adam Nitenson + Re: [Freesurfer] spmregister error Douglas N Greve # Re: [Freesurfer] spmregister error swoodman

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Problem with reading GE dicom and reducing the resolution
by Shahin 06 Oct '10

06 Oct '10

Hi, I have received a dataset of high resolution monkey structural scans (0.5 mm * 0.5mm * 0.5mm) collected by GE machines. Now I have two problems that I appreciate if you help me with them, 1- mri_convert can not convert these files to mgh format and I don't now why. Error message says that they are not dicom while even the linux machine detects them as dicom. 2- How can I reduce the resolution to 1mm rather than 0.5 to further use them with freesurfer? I have attached one of those dicom files to this e-mail. Apparently their name format is also very different from ours. Best Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] Annoying mri_convert
by Wayne Su 05 Oct '10

05 Oct '10

Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer. Wayne On 05/10/10 10:44 AM, "Wayne Su" <wsu(a)interchange.ubc.ca> wrote: > Hello Freesurfer Users, > > I am feeling very bad when I am using mri_convert. There are two problems: > 1. When I converted a file in mgz format to nii.gz format, and did some > volume calculation (mask and addition) by using fslmaths from FSL, then > converted back to mgz. If the image type is uchar, it works fine. If the > image type is int, the intensities changed. The 0¹ value is changed to > 2.1e+09¹, others also in very large number (look like read the data from > wrong place). Here is the code I used: > > ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz > -odt int > ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add > right_vect_mask aparc+aseg > ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz > -odt int > > If no fslmaths calculation, convert back to mgz right way, no problem > found. > > 2. when the conform is used, some head were rotated a little bit, but not for > others. I am wondering how to avoid the rotation? > > Regards, > Wayne > > _______________________________________________ > 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.

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Clusters - Qdec 1.4
by Fernanda Palhano 05 Oct '10

05 Oct '10

Hello All, Does anyone know if it's possible to automatically create labels for the clusters found with the new feature in Qdec 1.4, *Find Clusters and Goto Max*? I want to map the clusters onto all my subjects and then use * mris_anatomical_stats* to get average thickness and st. deviation for each one. Thanks in advance, Fernanda Palhano

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Meaning of volumes
by Ed Gronenschild 05 Oct '10

05 Oct '10

Hi, What exactly is the definition of - Brain Mask Volume - Brain Segmentation Volume as listed in the aseg.stats file? Moreover, and correct me if I'm wrong, the Intracranial volume is the scaled intracranial volume of the MNI template. Is the latter intracranial volume just a number or is it available in 3D as an image file? I would like to know how it is defined. Kind regards, Ed

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BEM surfaces
by Alexander Hunold 04 Oct '10

04 Oct '10

Dear experts, Currently I am playing around with the mri_watershed algorithm. After processing the T1.mgz from "bert" I got 256 COR files plus the COR-.info with the direction cosine information. <mri_watershed -surf -useSRAS $SUBJECTS_DIR/bert/mri/T1.mgz $SUBJECTS_DIR/bert/bem/> Output in bert/bem/: COR-.info, COR-001 . COR-256 How can extract the information of these files which I need to proceed .mesh files in Matlab? Thank you so much in advance. Sincerely, Alexander

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normal brain volume ?...
by Gonzalo Rojas Costa 04 Oct '10

04 Oct '10

Hi: I am quantifying the brain volume of some MS patients (BrainSegVol-ventricles-cerebelum-brain_stem)... There exist any paper that shows normal brain volume ?... There exisst any other way to compute the brain volume ?... Sincerely, Gonzalo Rojas Costa

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QDEC 5.0 with data from 4.x recon-all data
by Mira Michelle Raman 04 Oct '10

04 Oct '10

Hi, I was wondering if it were possible/advisable to use data processed and cached using earlier versions of FreeSurfe with the new 5.0 QDEC, since it has enhanced capabilities. Sincerely, Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University

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Freesurfer October 2010