Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Multi-echo FLASH
by Jon Houck 02 May '14

02 May '14

Hi all, I'm building a scan protocol for what is primarily a MEG study, which needs T1 information for co-registration and T1/T2 information to construct an accurate BEM from the inner skull surface. It seems like the two multi-echo FLASH sequences at 5 and 30 degrees would give me all of the information that I need without an MPRAGE, but I'm not sure how well the two MEFs work in the standard Freesurfer pipeline. Would it be reasonable to acquire no MPRAGE but two MEF sequences at 5 and 30 degrees, combine them following the method from https://surfer.nmr.mgh.harvard.edu/fswiki/MEF, and send the resulting T1 to recon-all? With my scan time constraints, the alternative would be to acquire a multi-echo MPRAGE and a single 5-degree MEF. Thanks for any help on what is probably a naïve question. Jon Houck

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Re: [Freesurfer] using multiple cores
by Lukas.Scheef＠ukb.uni-bonn.de 02 May '14

02 May '14

Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas > Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 > > Hi Luke > > what version of FS are you running? We see significant speedups. Try > running top in a unix terminal and seeing if the cpu usage of > mri_ca_register (during autorecon2, the longest single step) is morethan 100% > > cheers > Bruce > > On Fri, 2 May 2014, lukas.sch...(a)ukb.uni-bonn.de wrote: > > > > Hi folks! > > > > I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not > > see any accelartion when processing a single data set with or without the > > flag -openmp flag set. > > > > recon-all -s ernie_1 -all > > > > leads to ~6,4h processing time. > > > > Unfortunately > > recon-all -s ernie_2 -all -openmp 4 > > > > did not change anything. Do I miss anything? Do I have to prepare my system > > in a special way? Or run any scripts in advance? > > > > (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) > > > > Best wishes, > > > > Luke

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using multiple cores
by Lukas.Scheef＠ukb.uni-bonn.de 02 May '14

02 May '14

Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon-all -s ernie_2 -all -openmp 4 did not change anything. Do I miss anything? Do I have to prepare my system in a special way? Or run any scripts in advance? (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS version) Best wishes, Luke

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Hippocampal subfields on 1.5 Tesla
by Alan Francis 01 May '14

01 May '14

Hi Bruce and FreeSurfers: I have received a manuscript to review for possible publication. The authors have used the subfields algorithm on 1.5T scans and obtained a parcellation with values. They have drawn some major conclusions on the basis of the findings. My understanding is that this method can only be done on 3T. Is the 1.5T results valid? Please advice. thanks, Alan Francis

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Plot Histograms
by Dídac Vidal 01 May '14

01 May '14

Hi! I would like to plot an histogram with values from sig.mgh across all cortical mantle (as represented in qdec or in tksurfer-overlay options). Which function would allow me to obtain/create histograms from *mgh files? I also would like to obtain a similar histogram, but restricted to a cortical label. How I could do that? Thanks in advance -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Faculty of Medicine University of barcelona

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Constraining fMRI data with a surface label generates a bfloat file?
by JacobML＠nmr.mgh.harvard.edu 01 May '14

01 May '14

Hello Freesurfer Experts, Using func2roi (in stable3), we constrained our functional data with specific surface labels and t thresholds, and over-threshold masks were outputted as .bfloat files. Does this mean these masks are in volume format and that the volumetric functional data was mapped to the surface but then back to the volume again when the mask was created? We would now like to project these masks onto the fsaverage brain (for viewing). Can you please let me know how this may be accomplished? It seems mri_convert can not transpose .bfloat to .label, but I imagine there is a way! Thank you again for the help. Jacob

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Rendering in 3ds Max?
by Dorian P. 01 May '14

01 May '14

Hi list, Anybody has ever tried to bring Freesurfer pial surfaces for render in 3D studio max? I would be curious on the procedure to follow, more specifically on which file to export/import/convert. Thank you. Dorian TJU

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cortical thickness limit
by Hayyah Clairman 01 May '14

01 May '14

Hello, I have done some comparative cortical thickness analyses in children using FreeSurfer and noticed that the maximum regional thickness value is 5.0. I was wondering if there is an explanation for this limit. Perhaps this is because FreeSurfer was designed for adults? Thank you, Hayyah ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) 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.

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installing freesurfer on mac
by Demanuele, Charmaine 01 May '14

01 May '14

Hi, I am trying to install freesurfer on my mac, and I got a license key, which I need to save as ".license" file. However, the mac is not allowing me to do so. I tried saving the file in linux and importing to the mac but this failed too. I also tried saving it as freesurfer.license instead of just .license but I get the error: [Charmaines-MacBook-Pro:/Applications/freesurfer] Charm% tkmedit bert orig.mgz Couldn't create output file .xdebug_tkmedit-------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. Any ideas? Thanks very much, Best, Charmaine --------------------------------------------------------------------------------------- Charmaine Demanuele, Ph.D. Psychiatric Neuroimaging Athinoula A. Martinos Center for Biomedical Imaging Harvard Medical School 149 13th Street Charlestown Navy Yard Charlestown, MA 02129 phone: +1617-724-3170 email: charmd(a)nmr.mgh.harvard.edu <tel:617-726-4078>

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Re: [Freesurfer] Question regarding IGI
by Marie Schaer 30 Apr '14

30 Apr '14

Hi Virendra, Where does this surface come from? You didn't get this one after running the default recon-all, right? Looking at it I noticed a lots of holes and many small unconnected components on the medial aspect. I ran mris_euler_number and got a total of 68 defects, so I'm afraid you'll not be able to run lGI with this surface as the lGI code expect a single continuous surface with no holes. And beside the issue of running lGI until the end, I'm concerned that neither cortical thickness not cortical folding can be reliably estimated based on this surface, and that you'll have trouble registering it to an average template. Best, Marie On Apr 30, 2014, at 3:08 PM, Virendra Mishra <virendra.mishra(a)utsouthwestern.edu<mailto:virendra.mishra@utsouthwestern.edu>> wrote: Hello Marie and other freesurfer users, I am trying to compute IGI for the attached file but at the step of mri_path2label , the code goes into an infinite loop and it is not able to create .label file even for the first .path file. I will be very thankful if you can help me debug this issue. Thank you, Sincerely, Virendra. ________________________________ UT Southwestern Medical Center The future of medicine, today. <lh.pial>

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