Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30

Good morning Bruce, And many thanks again. Yes, bert inflated looks OK on the other computer. I will try to update the video card driver and see if this will fix the problem. In the mean time I have one more question: while running the recon-all on a new computer hhttps://kidmail.sickkids.

Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 30

Here is my results after running mri_info on the file NPI001.nii.gz (I can run recon-all for the same file on a different computer without getting this multiple frames error): niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm Volume information for NPI001.nii.gz type: nii dimensions: 18

[Freesurfer] Error with multiple frames

Hi Bruce, Sorry for making you confused. The true is I have 3 computers in my office. On two of them (LNX2 and LNX3) I installed by myself the new version of the FS. LNX2 is the one on which the bert infalted surface is looking weird. LNX3 is working perfect ( I cross my fingers and hope noth

[Freesurfer] Multiple frames error

Good morning Bruce, 1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer where I got the multiple frames error is a Linux, Ker

[Freesurfer] Fw: Multiple frames error

HiBruce, I 1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer where I got the multiple frames error is a Linux, Kernel Li

Re: [Freesurfer] Corrections with white matter

the two volumes. Will be this OK? Many thanks, Antonella From: Bruce Fischl To: Antonella Kis Sent: Wed, July 13, 2011 4:36:21 PM Subject: Re: Corrections with white matter Hi Antonella, you can't tell whether it is correct from overlaying it on the w

Re: [Freesurfer] Corrections with white matter

t. It looks like part of the cerebellum had been removed. Should I adjust the watershed threshold by passing the -wsthresh flag to recon-all? Thank you very much for your help. Antonella From: Bruce Fischl To: Antonella Kis Cc: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Saving all the edits

Hi Bruce, I promise this is my last question for today. I finished all the wm edits and I understood from the tutorial that I have to save this work. I understood that by default tkmedit will edit on the main volume loaded, if the wm volume is loaded as your aux volume (which is my case), I also

[Freesurfer] Running autorecon2-wm

Hi Bruce, Based on your last suggestion, after running the recon-all on my NPI001 subject: recon-all -s NPI001 -i /usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz -qcache -all and editing the wm, I saved all my edits (using the tool box menu as Save Volume As) under wm_edits_befor

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