[Freesurfer] map parcellations into DWI space?
External Email - Use Caution Dear FreeSurfer experts: I am trying to map ./mri/aparc.a2009s+aseg.mgz and ./mri/aparc+aseg.mgz into DTI file. Let's say, we have a DTI file with its b-vectors: ./bvals ./bvecs ./data.nii.gz I am trying to use the command from this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat So I used the command : mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz --o dk-in-rawavg.mgz --regheader aparc+aseg.mgz The output file seems not very reasonable. Could you help me with this? Yerong == Can you be more specific about which files you want to map into your DWI space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You will need a registration file which you can obtain with bbregister On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: [Hide Quoted Text] External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Notebook specification
External Email - Use Caution Dear Freesurfer Members, First I would like to introduce myself my name is Mustafa Amin, and I’m planning to do a study to measure the volume of prefrontal cortex, hippocampus, and ventricle of patients with schizophrenia comparing them with control in Medan Indonesia. I read and saw information that freesurfer is capable in doing the measurement, however I am still not sure about what kind of notebook specification that I need to download and install it. For my knowledge, this is the first study that will be done in Indonesia so every explanation and further information about freesurfer and the notebook will make me very grateful. I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here that can share the minimum requirements of the notebook, it will help me a lot to choose which one to buy. Thank you in advance. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] voxel cordinates
External Email - Use Caution Dear Freesurfer experts I am using freesurfer version 6.0. I have extracted ROI's from the aseg.mgz file. Now is it possible to get the cordinates of each voxel for a particular ROI? Thanks in advance Regards Research student ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Notebook specification
External Email - Use Caution I would not recommend to buy a notebook to run FreeSurfer. If you want to run many subjects, it takes a lot of time (between 10 and 20 h per subject and processor roughly), so you want many cores and also roughly 2GB of RAM per subject that you are running in parallel. So you want powerful hardware in general. But whatever CPU and amount of RAM you decide on: it's gonna cost A LOT more if you want it inside a laptop. And the processing power you want for a large study (several hundred subjects) cannot be achieved with any laptop I would say, no matter how much you pay. In general I would suggest a desktop or workstation PC with 16 GB RAM or more and at least 8 cores. If you have many subjects, you may be better off with 16-24 cores and maybe 32 GB of RAM. If you want even more details and my personal opinion: a desktop PC with AMDs Threadripper CPU seems like an excellent choice for FreeSurfer these days if you look at bang for the buck. Intel also offers CPUs with many cores, but at a way higher price, and you should not need the extra memory bandwith for FreeSurfer, so in my opinion they are not worth it for this specific task. If you are building a general-purpose server for parallel computing, this may differ. In case you may at some point in the future want to run other neuroimaging software that works on the GPU (like the eddy correction tool from FSL or whatever): most of these programs are based on CUDA, so if you are getting a graphics card, getting an nVidia card won't hurt. Tim (I am not affiliated with any of the mentioned companies, nor with any other hardware company.) > On December 30, 2018 at 9:46 AM mustafa amin wrote: > > > External Email - Use Caution > > Dear Freesurfer Members, > > First I would like to introduce myself my name is Mustafa Amin, and I’m > planning to do a study to measure the volume of prefrontal cortex, > hippocampus, and ventricle of patients with schizophrenia comparing them with > control in Medan Indonesia. I read and saw information that freesurfer is > capable in doing the measurement, however I am still not sure about what kind > of notebook specification that I need to download and install it. For my > knowledge, this is the first study that will be done in Indonesia so every > explanation and further information about freesurfer and the notebook will > make me very grateful. > > I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and > full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here > that can share the minimum requirements of the notebook, it will help me a > lot to choose which one to buy. Thank you in advance. > > Yours faithfully, > > Mustafa M. Amin > Consultant Psychiatrist in Biological Psychiatry > Department of Psychiatry > Faculty of Medicine > Universitas Sumatera Utara > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Notebook specification
External Email - Use Caution One last thing I forgot: you could maybe check whether you can get access to some super computer. Maybe some university you know has one and you can request access (maybe even for free). It's nice to have your own server, but access to a 2nd system is good to have as well. Best, Tim > On December 30, 2018 at 9:46 AM mustafa amin wrote: > > > External Email - Use Caution > > Dear Freesurfer Members, > > First I would like to introduce myself my name is Mustafa Amin, and I’m > planning to do a study to measure the volume of prefrontal cortex, > hippocampus, and ventricle of patients with schizophrenia comparing them with > control in Medan Indonesia. I read and saw information that freesurfer is > capable in doing the measurement, however I am still not sure about what kind > of notebook specification that I need to download and install it. For my > knowledge, this is the first study that will be done in Indonesia so every > explanation and further information about freesurfer and the notebook will > make me very grateful. > > I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and > full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here > that can share the minimum requirements of the notebook, it will help me a > lot to choose which one to buy. Thank you in advance. > > Yours faithfully, > > Mustafa M. Amin > Consultant Psychiatrist in Biological Psychiatry > Department of Psychiatry > Faculty of Medicine > Universitas Sumatera Utara > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Notebook specification
External Email - Use Caution Dear Mustafa, The Open Science Grid has freesurfer 5.3 and 6.0 installations and provides a simple user interface to upload scans, run freesurfer on them using OSG computing resources, and download the results. This facility was designed to meet the kinds of requirements you describe. Check out the link below to learn about it. If you decide to use it, the OSG has a good ticket system which provides help. https://support.opensciencegrid.org/support/solutions/articles/1208483-introduction-to-fsurf-and-freesurfer Best - Don -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ts...@rcmd.org Sent: Sunday, December 30, 2018 10:20 AM To: Freesurfer support list Subject: Re: [Freesurfer] Notebook specification External Email - Use Caution One last thing I forgot: you could maybe check whether you can get access to some super computer. Maybe some university you know has one and you can request access (maybe even for free). It's nice to have your own server, but access to a 2nd system is good to have as well. Best, Tim > On December 30, 2018 at 9:46 AM mustafa amin wrote: > > > External Email - Use Caution > > Dear Freesurfer Members, > > First I would like to introduce myself my name is Mustafa Amin, and I’m > planning to do a study to measure the volume of prefrontal cortex, > hippocampus, and ventricle of patients with schizophrenia comparing them with > control in Medan Indonesia. I read and saw information that freesurfer is > capable in doing the measurement, however I am still not sure about what kind > of notebook specification that I need to download and install it. For my > knowledge, this is the first study that will be done in Indonesia so every > explanation and further information about freesurfer and the notebook will > make me very grateful. > > I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and > full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here > that can share the minimum requirements of the notebook, it will help me a > lot to choose which one to buy. Thank you in advance. > > Yours faithfully, > > Mustafa M. Amin > Consultant Psychiatrist in Biological Psychiatry Department of > Psychiatry Faculty of Medicine Universitas Sumatera Utara > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
