[Freesurfer] Freesurfer flips brains?

wrong assumption on neurological vs radiological convention, or what is going on? Thanks in advance, best, Frank ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freesurfer flips brains?

ional and I realign that one, but that makes for one extra step where it can go wrong. Don't think this is related to the flip, but I also have a few alignment problems for other subjects. Thanks a lot in advance, best, Frank - "Douglas N Greve&qu

Re: [Freesurfer] Freesurfer flips brains?

d now the changes are far less severe (only a small shift still) and most importantly: no flip anymore. Do I now need to reconvert my all my surfaces? I don't hope, but I'm at least glad I have this one fixed. best, Frank - "Douglas N Greve" schreef:

Re: [Freesurfer] Freesurfer flips brains?

Hi Dan, Sure. It was in my earlier e-mail of today: I use tksurfer, see below. For this last test, I used the SPM display function though, that now shows them to both have the same orientation, so appears to be okay. Or am I still missing something? best, Frank Hi

Re: [Freesurfer] Freesurfer flips brains?

ollow the sulci/gyrii), but apparently there is a strong gradient in there and it is quite dotted, so it ends up not showing me all gyrii, just a subset, and a bit scattered. Is there a better way? Thanks again, hope also this is useful for others, best, Frank - "D

[Freesurfer] loading data to matlab?

, I have all the files already in matlab, now I just need to know how this conversion works. Specifying -noreshape apparently isn't the entire story. Thanks a lot in advance, kind regards, Frank ___ Freesurfer mailing

[Freesurfer] license error

hanks, -- ** Frank J. Kanayet, Ph.D. Stanford University 420 Jordan Hall, Room 342 ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati

[Freesurfer] Postdoc Position at the Dynamic Memory Lab at UC Davis

Postdoctoral Researcher: The Dynamic Memory Lab (C. Ranganath, PI) at the University of California, Davis, now has an open position for a funded postdoctoral researcher. We currently are running studies that involve multimodal imaging (EEG, fMRI, ECoG, Diffusion Imaging, MR Spectroscopy) as well a

[Freesurfer] Freesurfer software in stroke study

Frank Yu ___ Freesurfer mailing list Freesurfer@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

Re: [Freesurfer] problem of using freesurfer

Frank Yu On Mon, Oct 3, 2016 at 12:24 PM, Douglas N Greve wrote: > you can get it from here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg > > On 10/03/2016 12:46 PM, Hsin-Tsung Lee wrote: > > Dear Dr. Bruce > > I have one more question, does t

[Freesurfer] mri_coreg question

eve/mri_coreg> \local\user\freesurfer\bin\mri_coreg can not execute binary file? I use sudo chmod u+x mri_coreg to make it executable. Do you know why? Frank Yu Douglas N Greve Oct 3 to freesurfer you can get it from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg On

Re: [Freesurfer] problem of using freesurfer

I usesudo chmod u+x mri_coreg, so it should can be run. Frank Yu On Thu, Dec 15, 2016 at 10:51 AM, Frank Robert wrote: > > I download mri_coreg from this website to put it on my virtual machine > ubuntu \local\user\freesurfer\bin directory. But I run it and it say

Re: [Freesurfer] mri_coreg question

Hello ZK Yes, Ubuntu is 32-bit. I installed it half-year ago, only had such version. Does FreeSurfer provide 64-bit ubuntu version on Windows? Best Regards Frank Yu On Thu, Dec 15, 2016 at 3:18 PM, Z K wrote: > My guess is that your Ubuntu virtual machine is 32bit? If so it will not &

[Freesurfer] questions about registration tool in Freesurfer

st Regards Frank Yu ___ Freesurfer mailing list Freesurfer@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 w

[Freesurfer] ROI masks created in FreeSurfer used in FSL??

different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue. Many thanks in adva

[Freesurfer] Question about 7T MRI Datasets with isotropic voxels of 0, 7 mm

in a loss of quality. If so, is it possible to change Freesurfers settings to obtain optimal results from the segmentation? Any help would be greatly appreciated,   best regards, Valentin Frank ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??

Hi Gari, Thanks so much for the tips! @ Doug: I basically followed the instructions on this site<http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/>to obtain my ROIs. Any thoughts? Many thanks! Frank On Thu, Jan 9, 2014 at 1

Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??

On Jan 9, 2014, at 9:24 AM, Douglas N Greve wrote: > Frank, can you send the commands you used and the terminal output? > doug > > On 01/09/2014 04:35 AM, Frank Hsieh wrote: >> Hi Gari, Thanks so much for the tips! >> @ Doug:

[Freesurfer] Source Code not accessible

Hello, I tried to get freesurfer's source code after registering and receiving the password for the read-only-cvs. The login command from https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS is simply failing with a timeout like this: # cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fsc

[Freesurfer] Exporting mask file into Brainvoyager

Hello, I'm trying to use anatomical regions of a subject labeled by freesurfer as an fMRI mask in brainvoyager. I'm using mri_convert to change aparc+aseg.mgz to a nifti, and then changing that into a brainvoyager vmr file. However, the vmr file in brainvoyager looks wrong (see attached screensho

[Freesurfer] PostDoc and MD/PhD positions in Zürich – Real-time fMRI neurofeedback

cultural and outdoor activities and a very high quality of life. Interested applicants should send their CV, a brief statement of research interests, and contact information for 2-3 references. Please feel free to contact me with any questions. Best wishes, Frank -- Prof. Dr. Frank Scharnowski

[Freesurfer] Processing of young children using Freesurfer

also read about that it is advised to run freesurfer with patient age >5 but maybe someone has an idea how to solve this. As far as I get from the step it crashes at the intensity correction step? Do I need to calculate some sort of template maybe ? Any comments welcome Yours Fr

Re: [Freesurfer] Processing of young children using Freesurfer

Hi again, just an update, I treid this all again with an older child (109 years) but same thing happens. Logfile attached. Yours Frank PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim

Re: [Freesurfer] Processing of young children using Freesurfer

Hi Bruce, thanks for the reply. Here comes the output (see attached). I just downloaded the VM with freesurfer from your website, fyi. Yours Frank PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Facult

Re: [Freesurfer] Processing of young children using Freesurfer

Hi, did you find a hint why my installation of freesurfer is not processing the data at that stage ? It seems to be a general problem, we tried also with other data sets of elder people etc .. Any help appreciated. Yours Frank PD Dr. Frank Zoellner Group Leader "MR

[Freesurfer] Save-the-Date: Feb 12-13, 2015, Real-time Functional Imaging and Neurofeedback Conference, Gainesville, Florida

s, your co-organizers, Ranganatha Sitaram, University of Florida Sven Haller, University of Geneva Jarrod Lewis-Peacock, University of Texas at Austin Frank Scharnowski, University of Geneva Luke Stoeckel, Harvard University / National Institutes of Health James Sulzer, University of Texas at Austin Nikolau

[Freesurfer] Surface X, Y, Z to Tailarach or Volume Index

ch or Volume index? I read the information on conversions between surface Talairach and Volume Index, that works, but this case is different: I am actually referring to the 3D locations of the vertices. Hopefully someone can help me, thanks a lot in advance,          best,                  

[Freesurfer] Run Recon-all Parallel on Linux

External Email - Use Caution Dear Freesurfer experts, May I know how to run Recon-all in parallel on Linux? I have read some source said that can use "gnu parallel" to complete it. But they do not describe it in detail how to perform it. Regar

Re: [Freesurfer] Run Recon-all Parallel on Linux

w.) But I couldn't find any similar information on the Linux platform. Regards Frank On Jan 3, 2020 11:15 PM, Bruce Fischl wrote: Hi Frank do you mean completing a single recon faster? The easiest way to do that is to use the -openmp flag, and set to the number of threads/cores you want to use

Re: [Freesurfer] Run Recon-all Parallel on Linux

External Email - Use Caution Dear Tim, Sorry, I am a Linux code beginner. I installed the GNU parallel in my Linux. May I know how to adapt the script of “ run_reconall_parallel_wrapper.bash” to my own need? Thank you. Regards Frank > On Jan 4, 2020, at 6:12 PM, Tim Schä

[Freesurfer] why topology fix almost takes 4 days to finish job

. but if I use recon-all -i T1_MPRAGE image rather than recon-all -i T1_MPRAGE image -t2 T2-FLAIR-Image. It will take about 15h, why this make such big difference? Many thanks. Frank ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] freesurfer- recon-all "exited with ERRORS"

download at: https://www.dropbox.com/s/bxb2vyhz3koo83s/recon-all.log-%20Terminal%20Output%20log%2020%20Jan%202020%20.txt?dl=0 Regards Frank --- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mai

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution Dear Tim, Is it the FOV of my T1 image will affect the process Recon-all? If yes, how would it impact my output results? Regards Frank From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim Schäfer

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution Dear Tim, The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will affect the process Recon-all? If yes, how would it impact my output results? Regards Frank From: freesurfer-boun

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution Dear Tim, The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series will affect the process Recon-all? If yes, how would it impact my output results? Regards Frank From: freesurfer-boun

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution Dear Douglas , How could I find out the root cause of this recon-all "exited with ERRORS"? Does it mean there are flaws in the generated output? Or I could ignore this error warning? Thank you. Rega

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

%20exited%20with%20ERROR%2020%20Jan%202020%20.txt?dl=0 Zip file of the entire subject dir: https://www.dropbox.com/s/r1uvd2ngyap7klp/subject%20dir%20%28exited%20with%20ERRORS%29.zip?dl=0 Please take your time. Thank you very much. Regards Frank

[Freesurfer] whether freesurfer version 7 still support GPU

abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not. Thanks Frank ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] whether freesurfer version 7 still support GPU

External Email - Use Caution Hello Dr. Hoopes Does it mean that in Beta version 7, there is no GPU capability. But stable version 7 still support the existing GPU capacity.. Is it correct? BR Frank On Tue, Apr 7, 2020 at 10:06 AM Hoopes, Andrew wrote: > Hi Fr

[Freesurfer] Recon-all error output

https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0 Thank you. Regards Frank --- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mail : cyfr...@hku.hk<mailto:cyfr.

[Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

oftware of "dicom2" stated that it could perform the conversion but their manual guide are too hard for me to understand. May I know there are any easier method to perform the conversion? Thank you. Regards Frank --- FRANK C Y CHAU Research assistant D

Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

664USaf7wm-rYvZD1PdnBFUqk34qxJYdEBCwIrIk4eWdmIyPoNsKCQlNg6QRNIQuCWgXupp_1_paHiS5DskWDrNsTXjaZmpjTyTuEQBGEhwrj8HJ9E9AhTSnvJYMQgCDHhUk5hpr6BKf7r38LOVd55215Eypj-tg08IGyPxN2w/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting --- Regards Frank From: frees

[Freesurfer] intensity normalization fails?

structural looks just fine. Is there a way to correct for this? Many thanks for your help, frank <>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-

Re: [Freesurfer] intensity normalization fails?

Hi Bruce, It is the orig.mgz (cannot check right now if the nu is also dark). Many thanks, frank 2010/6/18 Bruce Fischl : > Hi Frank, > is it the orig.mgz that is dark, or the nu? > > cheers > Bruce > > On Fri, 18 Jun 2010, Frank Scharnowski wrote: > >> Dear Frees

Re: [Freesurfer] Retinotopic mapping of only polar data

ng almost the entire second 20s. Is this the correct thing to do, or should I rather keep everything / make sure I have an exact number of periods for each stimulus? Thanks a lot in advance, kind regards, Frank On Mon, 2010-01-18 at 17:32 -0500, Douglas N Greve wrote: &g

Re: [Freesurfer] infantFS: expected outputs

atlas… Yours Frank adj. Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent Systems in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621

Re: [Freesurfer] infantFS: expected outputs

in the atlas? Thanks in advance Yours Frank --- adjunct Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent System in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0

Re: [Freesurfer] infantFS: expected outputs

External Email - Use Caution Hi, I have another question. I set ccseg option to get CC stats but they do not show in the final aseg.stats file though it seem that the CC segemntnation is performend ? Yours Frank adj. Prof. Dr. Frank Zoellner Acting head

[Freesurfer] creating a freesurfer guix package definition (aka compiling from source)

External Email - Use Caution Hi, I'm trying to create a freesurfer (v7.3.3) package definition for guix. I have some problems during freesurfers configure step though. I'm using the following definitions to build freesurfer (this may not help much if you don't know guix, but you