[Freesurfer] dev -FLAIRpial bug?

Hi FS Devs, We're running some reconstructions of 7T MPRAGEs with the -FLAIRpial flag turned on using the Martinos install of the dev version. Recently we encountered the error in the attached recon-all log in which it appears that recon-all is trying to use the aseg.mgz before it has been

Re: [Freesurfer] 7T recon

d. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary. On Wed, Jun 7, 2017 at 3:39 PM, Hibert, Matthew Louis <mhib...@mgh.harvard.edu<mailto:mhib...@mgh.harvard.edu>> wrote: Hi Bruce, I edite

Re: [Freesurfer] 7T recon

: [Freesurfer] 7T recon Hi Matt we keep track of edits by setting erased voxels to 1, not 0. If you do the editing within freeview using the "recon edit" tool, this will happen automatically cheers Bruce On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote: > Hi Bruce, > Thanks again for your he

Re: [Freesurfer] 7T recon

f of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, May 26, 2017 1:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote: > Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run

Re: [Freesurfer] 7T recon

as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it will show you the regions of the surface that are defective. You will then need to edit the wm.mgz to remove the handle/hole that is the defect. cheers Bruce On Fri, 26 May 2017, Hiber

Re: [Freesurfer] FS6 recon-all hangs at mris_fix_topology

correct the wm.mgz to remove the non-brain tissue cheers Bruce On Tue, 24 Jan 2017, Hibert, Matthew Louis wrote: > Hi Freesurfer Devs, > I'm trying to re-process a subject who had a right temporal lobectomy using > FS6 but the recon hangs at the mris_fix_topology step, saying "XL def

Re: [Freesurfer] T2 vs. T2-FLAIR update

In my experience, if the only goal is to improve the pial surface reconstruction, it is better to use a T2-SPACE-FLAIR than a T2-SPACE. Whenever possible, we acquire a bandwidth matched T2-SPACE-FLAIR at approximately the same resolution as our T1 and use this with our Freesurfer

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error Check the contents of /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname It may have the subjectname repeated 3 times On 07/18/2016 05:45 PM, Hibert, Matthew L

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

nd send me dng.log? register-sess -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update |& tee dng.log On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote: > Hi All, > I'm running into an error analyzing some fM

[Freesurfer] FS-FAST "If: Expression Syntax" Error

Hi All, I'm running into an error analyzing some fMRI data with FS-FAST in Freesurfer version 5.3. The analysis runs fine until it gets to the register-sess part, which quits before actually starting to do any registration. The last line of the log file, attached, is "if: Expression syntax",

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 9 Jun 2016, at 21:51, Hibert, Matthew Louis <mhib...@mgh.harvard.edu<mailto:mhib...@mgh.harvard.edu>> wrote: Hi Eugenio, Would it also be possible to use the -hires flag in the initi

Re: [Freesurfer] Hippocampal subfields error

: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [mhib...@mgh.harvard.edu] Sent: Thursday, June 16, 2016 11:10 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields error I've also gotten this error

Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 hippocampal segmentations. It looks like the files exist at /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf exist, they just don't have the ".ctf" file extension. Matt

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Eugenio, Would it also be possible to use the -hires flag in the initial recon-all command to prevent the T1 from being downsampled and maintain the voxel size that the T1 was acquired at, and use that resulting recon for the hippocampal subfield segmentation? I've tested this with MEMPRAGE

Re: [Freesurfer] mri_convert doubling file size

Hi Afsana, I think adding "-odt int" or "-odt short" to your mri_convert command will set the data type of the output Nifti to int16, but I'm not sure if it conflicts with the -tr flag. You can also convert to .nii.gz instead of just .nii which will help keep the file size down. Hope that

Re: [Freesurfer] registering 2 scans

? You could use the longitudinal tools depending on what you are up to cheers Bruce On Fri, 14 Aug 2015, Hibert, Matthew Louis wrote: Hi Freesurfers, I've scanned the same subject with 2 different head coils and reconstructed the memprage's from each coil with freesurfer. I'd now like

[Freesurfer] registering 2 scans

Hi Freesurfers, I've scanned the same subject with 2 different head coils and reconstructed the memprage's from each coil with freesurfer. I'd now like to register these two reconstructions to each other, both the volumes and the surfaces. I've generated an lta registration matrix using