Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

Overlap of vertices in downsampled data
by Ersin Ersözlü 09 Apr '20

09 Apr '20

External Email - Use Caution Hi FreeSurfer experts, We calculated the differences with downsampled -fsaverage6- thickness data between our groups using 'PALM' on the vertex level and got .mgz files as overlays wit h log-p values for each contrast. Now, we would like to test the overlap. We computed a ratio of overlap through 'mri_compute_overlap' within log-p overlay files but it showed labels (-s option) such as unknown and white matter. Is there a way to differentiate vertices that are in cortical regions? And could this labeling be correct? Medical doctoral student University of Munich (LMU) Ersin Ersözlü

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mri_convert input files
by Setiaman, N. 09 Apr '20

09 Apr '20

External Email - Use Caution Hi, I would like to convert my raw scans to nifty. The scans are made on a Philips scanner. I was able to retrieve most of them as DICOM files, but some of them are only available as PAR/REC. Does mri_convert also handle PAR/REC or can I only convert the DICOMS with this tool? Best, Nikita ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Tracula: tract length meaning
by Nazife Ayyıldız 08 Apr '20

08 Apr '20

External Email - Use Caution Dear Tracula experts, I want to compare two groups according to the length statistics from Tracula overall.stats outputs. I just need comprehensive explanations what "tract length" statistics mean and how they are derived and what their reliability is. I checked but I couldn't find detailed information. Are they suitable to use in group comparisons? If so, which one is more suitable to use: average, center, min or max length? I saw in some articles that they used average_length of a tract. If I want to use length statistics do you suggest taking any control variables? I read a message from Anastasia in the archive-list saying that we should be aware that these measures are in their individual DWI spaces. If I understood correctly, I shouldn't use them directly. Should I control the head sizes of the individuals then? How would you do if you wanted to do this kind of comparative analysis? I would really appreciate it if you answer. Thank you very much in advance! Best regards, Nazife -- -Nazife Ayyıldız-

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Re: [Freesurfer] Permutation with Non-Orthogonal Matrices
by Hua, Jessica 07 Apr '20

07 Apr '20

External Email - Use Caution Thanks for your help! I downloaded the patch, and the analysis is now running. Hopefully, I will not run into any other issues with the permutation. Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Recon-all Note Completing
by Ledesma, Jason 07 Apr '20

07 Apr '20

External Email - Use Caution Hi, I am receiving an error when performing recon-all. See attached for recon-all log. Thanks. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)lundquist.org ___________________________________________________________________________________ LUNDQUIST Institute Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ___________________________________________________________________________________

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whether freesurfer version 7 still support GPU
by Frank Robert 07 Apr '20

07 Apr '20

External Email - Use Caution Hello Freesurfer team I checked the freesurfer version 7.0. It says that " but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make)." https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1 But from the hardware setup, it still needs Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers. This makes me confused. Since version 7 does not support GPU anymore, why does it still need the Graphic card? I found GPU may be helpful for some abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not. Thanks Frank

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hippocampus subfield segmentation using Siemen and GE scans
by Kate Marvel 07 Apr '20

07 Apr '20

External Email - Use Caution Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different FOV? Thanks, Kate

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Chorid-plexus in Freesurfer reconall
by Lijun An 07 Apr '20

07 Apr '20

External Email - Use Caution Dear Freesurfer experts, I have a little question about the structure 'chorid-plexus', I am not very deep in brain anatomy and function. Could anyone have a sense of what is the normal range of this structure volume from Freesurfer reconall? I found that mean of 'chorid-plexus' in ADNI is around 1500 mm^3, when I ran reconall for my local subejcts (a local dataset), I found the mean of 'chorid-plexus' is around 800 mm^3. Could anyone give an explanation or a paper I could refer to for this 'chorid-plexus' structure? Thanks so much! Best Regards, An Lijun

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Permutation with Non-Orthogonal Matrices
by Hua, Jessica 06 Apr '20

06 Apr '20

External Email - Use Caution Hi FreeSurfer Experts, As recommended I ran the following command: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs --perm-resid --cwp 0.05 --2spaces And I got the following error message: ERROR: Flag --perm-resid unrecognized. Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Re: [Freesurfer] Install Freesurfer on Ubuntu
by fsbuild 06 Apr '20

06 Apr '20

External Email - Use Caution Hello Stephan, There is some information here about packages to install in order to run freesurfer - see highlighted "apt-get install" commands. https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements I think you will also need to install these packages, libjpeg62_6b2-3_amd64.deb https://drive.google.com/file/d/1Zdd-C3EQEEww180OzxEk1WV0h9obZYkD/view?usp=… libpng12-0_1.2.54-1ubuntu1_amd64.deb https://drive.google.com/file/d/1OWQSWL8a3Y8f1Weiauj9Lr2d3mtvZOm5/view?usp=… We also have an Ubuntu VM you can download.  While you may prefer to run on your own Ubuntu machine, it could also serve as a reference for you to see what we installed on Ubuntu 18.04 (including those extra packages). https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 - R. On Apr 6, 2020, at 16:50, Stephan <stephan.wunderlich22(a)gmail.com> wrote:        External Email - Use Caution        Hi,ist there an official guideline how to install Freesurfer on Ubuntu?Best,Stephan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer April 2020