[Freesurfer] dt_recon error: MatrixReadTxt: could not scan value [1][1]

Hello FreeSurfer Developers, I'm trying to pre-process some diffusion data based on the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 I am getting the following warning followed by the program hanging -- Creating output directory

[Freesurfer] convert nii to nii.gz

Hi Freesurfer Expert, I am very new to Freesurfer and have a very basic question. How to convert .nii files to nii.gz? I have tried the mri_convert subject_name.nii to subject_name.nii.gz directly. It gives me an error information that mri_convert: command not found. Thanks for your help!

Re: [Freesurfer] corRead(): can't open file /home/andraderenew/COR-.info

Hi Rene you typically need to specify a file explicitly. If you give it a directory, it will assume that it has our ages old COR format and try to read that out of it and fail (which is what it is telling you). If andraderene is the name of your SUBJECTS_DIR and bert is the name of your

[Freesurfer] Hippocampus Subfield analysis error

Hi Freesurfer experts, I tried to do hippocampus subfield analysis but failed. I got this error message: #@# Hippocampal Subfields processing (T1 only) left Fri Jan 19 15:27:36 PST 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found.

[Freesurfer] corRead(): can't open file /home/andraderenew/COR-.info

> Begin forwarded message: > > From: Renew Andrade > Subject: corRead(): can't open file /home/andraderenew/COR-.info > Date: 18 January 2018 at 12:15:49 CET > To: freesurfer@nmr.mgh.harvard.edu > > Hello: > I run the command to open freeview -v…(the installation guide

Re: [Freesurfer] Hippocampal segmentation flips on the left side

Hi Lauri, This error is occurring because the libstdc++.so.6 library included with the linked matlab is older than the version shipped with centos7. While I think about the best way to resolve this, setting the following environment variable before running recon-all should clear everything up

[Freesurfer] Incorrect display of control points when image geometries differ

Dear experts, I encountered a pitfall with displaying control points in freeView. When the T1 and T2 geometry differs (which can occur for example in hires stream where data are not conformed to 1mm3), it depends on which volume is active when control.dat is loaded. For example, when

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Hi Mohamed how are you visualizing the MT or PC ROIs. Did you sample them into the volume? If so, can you tell me where the file ROIs are in the data you sent me? cheers Bruce On Fri, 19 Jan 2018, m.ba...@uliege.be wrote: Dear Bruce, Many thanks for your kind help! I put the subject data

Re: [Freesurfer] recon-all exited with error

You can send it to either my email (ahoo...@mgh.harvard.edu) or Bruce’s best, Andrew On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much > wrote: thanks Andrew. I had seen that

Re: [Freesurfer] recon-all exited with error

thanks Andrew. I had seen that and will give it a go - just wanted to make sure that my recipient email would be the FreeSurfer support list. Trisanna On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew wrote: > Hi Trisanna, > > Okay - if your file is less than 2GiB, I

Re: [Freesurfer] recon-all exited with error

Hi Trisanna, Okay - if your file is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange). best Andrew On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much

Re: [Freesurfer] freesurfer segmentation: perirhinal Roi

Dear Bruce, Many thanks for your kind help! I put the subject data on your ftp site (s8201.tar). Best regards, Mohamed - Mail original - De: "Bruce Fischl" À: "Freesurfer support list" Envoyé: Jeudi 18 Janvier 2018

Re: [Freesurfer] Accounting for WMHs in PETSURFER PVC?

Yes, just add --keep-hypo On 1/19/18 7:06 AM, Elijah Mak wrote: > Hi Doug, > > Could we tweak the PETSURFER pipeline in order to account for inhomogeneous > PET activity in WM due to WMHs? > > Will running gtmseg with the command --keep-hypo be useful in this context? > > Thanks for any inputs.

[Freesurfer] Accounting for WMHs in PETSURFER PVC?

Hi Doug, Could we tweak the PETSURFER pipeline in order to account for inhomogeneous PET activity in WM due to WMHs? Will running gtmseg with the command --keep-hypo be useful in this context? Thanks for any inputs. Best Wishes, Elijah ___