[Freesurfer] syntax error near unexpected token 'newline'

External Email - Use Caution Dear All during freesurfer installation, I type export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh and I have this error syntax error near unexpected token 'newline' can you help me? thanks Mike

[Freesurfer] T2 flair as additional scan in hippocampal subfields segmentation

External Email - Use Caution Hello I’d like to know if there is any advantage in having a T2 FLAIR as additional scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal subfield segmentation tool. We do not have T2 nor PD available. Thanks for you help

[Freesurfer] PETsurf kinetic modeling with MRTM

External Email - Use Caution Hello, I'd like to perform MRTM2 approach in ADNI3 tau PET data for partial volume correction (PVC). So, I've tried to do a command line as below. mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz The

[Freesurfer] Substancia-Nigra ROI

External Email - Use CautionHi there,   I would like to make a ROI for a left Substanci Nigra. It is possible to make the ROIs for thalamus, putamen, caudate, etc. But, it is not possible to make the left Substanci Nigra  ROI as follows: mri_binarize --i

Re: [Freesurfer] Corresponding structures to an ROI

I think I'm confused about what the inputs and outputs of the bbregister command are. Should the input volume --mov be my FLAIR? I thought that would register the FLAIR to the T1--or is there no difference between registering FLAIR to T1 and T1 to FLAIR? Best, Lily

[Freesurfer] R: syntax error near unexpected token 'newline'

External Email - Use Caution Hi Bruce find attached the file. Sorry, do I have to install bash? I'm using Mojave. thank you Mike Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Bruce Fischl Inviato: venerdì 30 agosto 2019 15:15

[Freesurfer] recon_all cuda 9.1

External Email - Use Caution Dear all, Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make it work for CUDA 9.1. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] syntax error near unexpected token 'newline'

Hi Mike can you send us the full command line and screen output? And are you running bash? What operating system? thanks Bruce On Fri, 30 Aug 2019, michele rizzi wrote: External Email - Use Caution Dear All during freesurfer installation, I type export

Re: [Freesurfer] R: syntax error near unexpected token 'newline'

You have to give it an actual path (eg, /App/freesurfer/subjeccts). When you see it means that you need to supply the something On 8/30/2019 9:42 AM, michele rizzi wrote: External Email - Use Caution Hi Bruce find attached the file. Sorry, do I have to install bash? I'm using

Re: [Freesurfer] Corresponding structures to an ROI

In the end, the direction does not make a difference because the transform can just be inverted On 8/30/2019 9:35 AM, Wang, Lily wrote: I think I'm confused about what the inputs and outputs of the bbregister command are. Should the input volume --mov be my FLAIR? I thought that would

Re: [Freesurfer] I have a question for subthalamic nucleus ROI.

Hi Gwang-Won sorry, the STN is high on our to-do list, but we don't have anything distributable yet. cheers Bruce On Fri, 30 Aug 2019, Gwang-Won Kim wrote: External Email - Use Caution   Hi there,   I would like to make a ROI for subthalamic nucleus. But, there is not

Re: [Freesurfer] Substancia-Nigra ROI

sorry, Substancia Nigra is also on our list of next structures to be released, but it is not ready yet cheers Bruce On Sat, 31 Aug 2019, Gwang-Won Kim wrote: External Email - Use Caution Hi there,   I would like to make a ROI for a left Substanci Nigra. It is possible

Re: [Freesurfer] PETsurf kinetic modeling with MRTM

This is the time at which each frame was acquired. It is just a list of times in seconds in a text file. You will have to go to the person who collected the data On 8/30/2019 10:25 AM, Chanmi Kim wrote: External Email - Use Caution Hello, I'd like to perform MRTM2 approach in ADNI3

Re: [Freesurfer] R: R: syntax error near unexpected token 'newline'

oh, the export command is failing? You mentioned you weren't running bash (which is the shell that knows what to do with an export command). Can you install bash? If not, you can use setenv instead of export and the .csh file instead of the .sh On Fri, 30 Aug 2019, michele rizzi wrote:  

Re: [Freesurfer] R: R: syntax error near unexpected token 'newline'

External Email - Use Caution Hi, I think you are just mistyping it, if the subjects dir is in " /Applications/freesurfer/subjects/ " the command should be: export SUBJECTS_DIR=/Applications/freesurfer/subjects/ ( instead of export SUBJECTS_DIR=) Viv On Fri, Aug 30, 2019

Re: [Freesurfer] R: R: syntax error near unexpected token 'newline'

External Email - Use Caution Yes, as Viviana said, you need to specify the path to the Applications folder by using a leading slash “/“ character. You can test that path /Applications/freesurfer/subjects is OK by opening the terminal application and then typing at the dollar

[Freesurfer] R: R: syntax error near unexpected token 'newline'

External Email - Use Caution I put export SUBJECTS_DIR= but again I get -bash: syntax error near unexpected token `newline' ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu