Re: [Freesurfer] Failed to download Freesurfer from ftp, server seems empty

Hi Minos we are having major hardware issues that we hope to have resolved tonight. Try again tomorrow cheers Bruce On Wed, 29 Jun 2016, C. Minos Niu wrote: > Hello, > > I tried to have my new students download and install Freesurfer from >

[Freesurfer] Problem while using the -localGI

Dear Freesurfer experts, I am having trouble using the -localGI option to smoothen the pial surface. When I use the command like: recon-all -s ABC -localGI I got the following error: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current

Re: [Freesurfer] Question about FreeSurfer

Hi Dorsa as I said, if you rerun don't include the -i. And please include the full command and output pasted into the email thanks Bruce On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote: Hi, Thanks for the help. I ran the following code and I got errors. I have attached the log. recon-all

Re: [Freesurfer] Question about FreeSurfer

Hi Dorsa can you just copy and paste the text into the email? It's much easier than trying to look at images of text. Your recon-all command finished successfully. Essentially you didn't tell it to do anything except import the data and create the subject dir. Typically you want to give the

Re: [Freesurfer] freeview display problem

Ok, you should try updating your graphics card driver. There is also chance that your graphics card is broken. Unfortunately we are not able to diagnose that for you. Sorry. Best, Ruopeng > On Jun 28, 2016, at 4:17 PM, Ramtilak Gattu wrote: > > Attached is the screen

Re: [Freesurfer] freeview display problem

The color should be red, blue and green. It is your graphics card or graphics driver issue. Best, Ruopeng > On Jun 28, 2016, at 3:46 PM, Ramtilak Gattu wrote: > > glxgears shows up a screen with three gear wheels in blue, pink and green and > frame information rate being

Re: [Freesurfer] checking freesurfer output

Hi Gabor, it depends on what you are doing. What you describe is sufficient for maps/structure volumes, but for example if you wanted to measure thickness within parcels you would have to check the accuracy of the cortical parcellation cheers Bruce On Tue, 28 Jun 2016, Gabor Perlaki

Re: [Freesurfer] Question about FreeSurfer

Thank you! When I recon-all my files, I get the following error: files are not found to be different and cannot be sorted Do you have any suggestions? Thank you Dorsa On Tue, Jun 28, 2016 at 12:57 PM, Bruce Fischl wrote: > just give recon-all a single slice from

Re: [Freesurfer] freeview display problem

This sounds very likely a video card/driver issue. Would it be possible for you any other program that uses OpenGL/vtk, such as 3D slicer, Paraview? How does glxgears command show? > On Jun 28, 2016, at 2:55 PM, Ramtilak Gattu wrote: > > Nope they dont look normal they

[Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not

Re: [Freesurfer] freeview display problem

Nope they dont look normal they are being displayed in some other colors like heat is showing up as blue , jet as green etc. Even when the surfaces are loaded up the color of the surfaces doesnt look right. when the surface yellow is chosen are red it is being displayed as blue. Thanks

Re: [Freesurfer] Can't locate a good link to 5.3-dev builds (Linux/Ubuntu or Neuro-debian)

The Martinos Center is currently experiencing a system wide hardware failure on our network file servers and hope to have the issues resolved in a soon, but it might be a day or more depending on the exact nature of the problem. Thanks for you patience. -Zeke On 06/28/2016 02:41 PM, Shannon

[Freesurfer] Can't locate a good link to 5.3-dev builds (Linux/Ubuntu or Neuro-debian)

Hiya, I'm trying to download a copy of your latest dev build for Freesurfer 5.3 - I'm interested in getting the latest build for Freeview for Linux/Ubuntu or Neuro-Debian - but I seem to keep getting an "unreachable site" message?

Re: [Freesurfer] freeview display problem

Do other colormaps (heat scale, jets, etc) look normal? > On Jun 28, 2016, at 2:01 PM, Ramtilak Gattu wrote: > > Hey Ruopeng, > > I still couldnt figure out whats going on the freeview display. I updated the > Nvidia drivers but still its not displaying in gray scale. >

Re: [Freesurfer] freeview display problem

Hey Ruopeng, I still couldnt figure out whats going on the freeview display. I updated the Nvidia drivers but still its not displaying in gray scale. please help. thanks Regards Tilak From: Ramtilak Gattu Sent: Friday, June 24, 2016 12:25:50 PM To:

Re: [Freesurfer] tutorial_data

The Martinos Center is currently experiencing a system wide hardware failure on our network file servers and hope to have the issues resolved in a soon. Thanks for you patience. On 06/28/2016 01:32 PM, bruno fraccini pastorello wrote: > Dear freesurfer support, > I'm trying to download the

[Freesurfer] Applying the lta transformation to PET image | mri_coreg | mri_segstats

Hello All, I am trying to extract the SUV values a PET image mri_segstats --seg wmparc.mgz --sum petsuv.segstats.dat --i rPET --ctab-default since rPET is supposed to be coregistered to MRI, I did the following mri_coreg --s MRI --mov PET --lta mri_coreg.lta which did not generate the

[Freesurfer] tutorial_data

Dear freesurfer support,I'm trying to download the freesurfer data to learn freesurfer, but i can't it. Do you know why? Could you help me? I tried use this link  ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I obtain this error: Safari cant open the page

Re: [Freesurfer] Question about FreeSurfer

just give recon-all a single slice from the series with -i . It will figure out the rest of them On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote: > Hi, > I am a little confused about how should I save my files to execute recon-all > on > them. I have 240 slices of dicom format and I put them

Re: [Freesurfer] Question about FreeSurfer

Hi, I am a little confused about how should I save my files to execute recon-all on them. I have 240 slices of dicom format and I put them in a folder in my subjects_dir. but I get errors when using recon-all on the folder containing the MRIs. Can you help me with that? I really appreciate your

[Freesurfer] Research position, UCSF Department of Radiology and Biomedical Imaging

posted on behalf of Dr. Rahul Desikan: = The UCSF Department of Radiology and Biomedical Imaging is looking for a researcher with strong interests in neuroimaging interested in a Specialist position at UCSF. We are a neurodevelopment and neuroimaging lab.

Re: [Freesurfer] QSM Hippocampal Segementation

Hi Jessica if we have T1/PD maps we typically run them through mri_synthesize to create a strongly T1-weighted image that is then passed to recon-all. Can you tell us more about what data you have? cheers Bruce On Tue, 28 Jun 2016, Jessica Sevick wrote: Hello,  I was wondering if it

[Freesurfer] QSM Hippocampal Segementation

Hello, I was wondering if it was possible to use the hippocampal subfield segmentation function (for FreeSurfer V 6.0) on QSM images? We are working on quantitative stratification of the hippocampus. If you could let me know any thoughts/suggestions that would be great. Thanks, Jessica

[Freesurfer] Longitudinal Stream: Recon-all and Base template

Hello All, I am planning to run the longitudinal stream on my data set and I have a few questions: 1) When I run the data cross sectionally using "recon-all -all" should I specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or can I run each of my subject's T1 volumes

Re: [Freesurfer] Download FreeSurfer

Unfortunately their is no alternate location. We are experiencing a system wide hardware failure on our network file servers and hope to have the issues resolved in a day or so. Thanks for you patience. -Zeke On 06/28/2016 05:02 AM, Damien Marie wrote: > *This message contained a link to a

Re: [Freesurfer] updated mri_convert file

Hi Olivia and others we are having major disk problems at Martinos and many of the links may not work for a few days sorry Bruce On Tue, 28 Jun 2016, Olivia Cheung wrote: Hi Freesurfer team, I would like to download a copy of the updated mri_convert but the link on the Release Notes

[Freesurfer] recon-all sudden stop during Talairach

Dear Freesurfer Developers, I'm attempting to process high resolution images on a new system and following https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I at first try to run downsampled (1x1x1 mm) images. recon-all suddenly stops during #@# Talairach with no error codes except for the