Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

selxavg3 problems - missing mcextreg files
by Adam Nitenson 07 Oct '10

07 Oct '10

Hi all, I'm having an issue with selxavg3-sess in Stable 4. I've run all commands up to this point without error. Here was the command I used selxavg3-sess -s FB0011099AA -analysis fmcsm5_functionals and the error: ERROR: cannot find volume matching /autofs/cluster/roffman/users/folate_subjects/FB0011099AA/bold/015/mcextreg ERROR: loading nonpar reg /autofs/cluster/roffman/users/folate_subjects/FB0011099AA/bold/015/mcextreg >From looking at the other bold folders...it's clear that I'm missing the "mcextreg" files in /cluster/roffman/users/folate_subjects/FB0011099AA/bold/015 which seems to halt the command What is the best way to recover these files for this one BOLD folder? Thanks, Adam Nitenson PS Here is the additional computer info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /cluster/roffman/users/folate_subjects PWD: /cluster/roffman/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /cluster/roffman/users/folate_subjects cd /cluster/roffman/users/folate_subjects

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zero cortical thickness in the lingual and precuneus
by Wang, Xin 07 Oct '10

07 Oct '10

Hello, Dr. Fischl, I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0. My questions are 1) Do you have any additional suggestion to fix this bug? 2) If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex. Thank you in advance, Xin Wang ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

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memory needed to run a freesurfer stream
by Nathan Dankner 07 Oct '10

07 Oct '10

Hi all, I was curious as to approximately how much memory is required to run a surface through autorecon 1 and 2, and autorecon 2 and 3. I'm running them on a new server where I have to request resources, so a ballpark figure is really all I need. Thanks! Nathan

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Defining cluster threshold
by Jacobs H (NP) 07 Oct '10

07 Oct '10

Hi FreeSurfers, I have done my DTI analyses (dt_recon with TBSS) and the statistical analyses in FreeSurfer. Now I have defined the clustersize with mri_volcluster, but I find this rather arbitrary. Is there a way to calculate a minimum size cluster threshold (by using for example a Monte Carlo simulation)? Thanks! Heidi

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tksurfer
by Oya, Hiroyuki 07 Oct '10

07 Oct '10

Dear all, Can tksurfer load both hemispheres at once from command line input? Hiroyuki

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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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