Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

aparc+aseg.mgz recovery
by Daria Boratyn 25 Apr '14

25 Apr '14

Hi all, I accidentally damaged my aparc+aseg.mgz file. Is there any way to recover this without rerunning recon-all? Thanks so much! Daria

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FreeSurfer on MacBook Pro
by Ebraheem, Ahmed 25 Apr '14

25 Apr '14

Dear Sir/Madame, I am trying to install and run Freesurfer on my new MacBook Pro 15.4" Retina 2880x1800 2.3GHZ Intel QC i7 Intel Iris Graphics 16GB RAM 512GB SSD ME294LL/A I am not sure why it's not running but I noticed that my OS is Mavericks and the download page says: Lion OX X 10.7 (64b Intel) or SnowLeopard OS X 10.6 (32b Intel) Could you please advise me on how to install and run Freesurfer on my machine? Thank you very much, Ahmed Ahmed Ebraheem, MBChB., M.Sc., Ph.D Concussion Fellow Neurology Division Toronto Western Hospital ahmed.ebraheem(a)uhn.ca This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

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recon-all subject -qcache in a different version of freesurfer?
by Yizhou Ma 25 Apr '14

25 Apr '14

Dear Freesurfer experts, I have processed my images and done analysis with cortical thickness using FS510. Now that I want to do vertex-wise analysis with surface area and volume, I learned that there is a bug in FS510 with this. ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.h… ) Before I go on to use recon-all subject -qcache in FS530 to generate vertex-wise surface area and volume maps, I want to make sure that this would not cause concerns about use of mixed versions of Freesurfer, or concerns about interpreting my cortical thickness and surface area/volume findings together. And if it does, what should I do? Thanks a lot, Cherry

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Invalid license for recon-all
by Teodorescu, Roxana 25 Apr '14

25 Apr '14

Dear FreeSurfer experts, I have FreeSurfer installed on an Ubuntu system and I got the following error: ERROR: Invalid FreeSurfer license key found in license file /media/datas/study_tools/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment FreeSurfer was previously working on this computer without any errors. I have not been using it for a while and now I got this error. I got a new license and even though the .license file is updated and recon help works I still get the same error. Can you please help. Thank you. Roxana.

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openmp/mkl support in tracula
by Satrajit Ghosh 25 Apr '14

25 Apr '14

hi a.y., is there any part of tracula that currently benefits from openmp or mkl availability? cheers, satra

2 1

convert volume-based mni152 space into fsaverage surface space(MNI305)
by charujing123 25 Apr '14

25 Apr '14

Hi FS experts and users, I created a mask volume, whose space is in MNI152 space. And I want to convert this volume into surface-based in fsaverage. How can I realize this? Thanks All the best. Rujing Zha 2014-04-22 charujing123

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Regarding mri_path2label in computation of gyrification index
by Virendra Mishra 24 Apr '14

24 Apr '14

Hi, I am trying to compute gyrification index step by step for my dataset using the guidelines outlined on the website to compute lgi. I'm stuck at the step of mri_path2label command. What is the exact command to create a?h.pial.*.label file from?h.pial.*.path and?h.pial.*.center file? mri_path2label --(?) ?h.pial.*.path ?h.pial.*. center ?h.pial.*.label If I use --singlepath I could create *. label files but the results don't match the output created from recon_all -compute_lgi. Secondly, what is the meaning of the error MRIS‎alloc:nfaces=-8<0. Thank you for any help. Sincerely Virendra ________________________________ UT Southwestern Medical Center The future of medicine, today.

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mri_glmfit | constructing the "C.txt" and FSGD files
by Baker, Justin T.,M.D.,Ph.D. 24 Apr '14

24 Apr '14

Hi all, I'm trying to run what should be a very simple cortical thickness regression analysis in mri_glmfit, but could use some help with putting together my "C.txt" and FSGD files. I have two classes (e.g. Patient, Control) and two nuisance variables (i.e. Age, Gender). My FSGD file looks like this: GroupDescriptorFile 1 Title FS_Thickness Class Patient Class Control Variables Age Gender Input 130725_GB49NP Patient 18 1 Input 130620_HU64KP Patient 21 2 ... And my "C.txt" file looks like: 1 -1 0 0 0 0 ...which I'm pretty sure is wrong, but I don't quite understand what the columns mean, so any light shed would be appreciated! -Justin

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Re: [Freesurfer] mri_glmfit | constructing the "C.txt" and FSGD files
by Baker, Justin T.,M.D.,Ph.D. 24 Apr '14

24 Apr '14

Hi Freesurfer et al., Since no one has responded to my email below, I'll assume my question is poorly formed. I'm trying to compose an appropriate contrast matrix (what I've called the "C.txt" file) for a regression of surface thickness categorical comparison (two categories) with two nuisance variables. Can someone clarify what each column of the contrast file represents and how to set it up for this? I'm having trouble finding documentation of this. It is my hope that when I call: mri_glmfit --fsgd fsgd.txt --y lh.TEMP.mgh --C C.txt --surf fsaverage lh --cortex --glmdir lh.TEMP.output I am prepping to run a regression looking at the relationship between Patient status (i.e. 1 or 0) and cortical thickness, partialing out age and gender. Thanks in advance for any help you can offer, Justin On Apr 23, 2014, at 3:40 PM, Justin Baker <jtbaker(a)partners.org> wrote: > Hi all, > > I'm trying to run what should be a very simple cortical thickness regression analysis in mri_glmfit, but could use some help with putting together my "C.txt" and FSGD files. > I have two classes (e.g. Patient, Control) and two nuisance variables (i.e. Age, Gender). > > My FSGD file looks like this: > GroupDescriptorFile 1 > Title FS_Thickness > Class Patient > Class Control > Variables Age Gender > Input 130725_GB49NP Patient 18 1 > Input 130620_HU64KP Patient 21 2 > ... > > And my "C.txt" file looks like: > 1 -1 0 0 0 0 > ...which I'm pretty sure is wrong, but I don't quite understand what the columns mean, so any light shed would be appreciated! > > -Justin

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FS QA Tools: Output, html and .gif Files
by Jessica Bernard 24 Apr '14

24 Apr '14

Hi All, I've been running the Freesurfer QA Tools on some new data, and have been having some difficulties with the outputs. I am running this using the -snaps-detailed flag. In the past, we have had .html links, but also detailed .gif files for each person. We've consistently had trouble with the .html links, but the .gif files have been perfectly fine. However, when running new individuals, not only are the images broken in the .html output, but there are no gif files (which are preferred). Is there an additional command that needs to be added to generate the detailed gif files as well? Sorry if this is a rather basic question. I recently took over the Freesurfer QA process, and am relatively new to the functions, and my predecessor does not know how they created the gif files (the first batch of QA was run 6 months ago with our first wave of data collection). Thanks in advance for any help you may be able to provide. Best Wishes, Jessica

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