Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

help error RB_ALL_2008-03-26
by Flavia Arduini 24 Feb '17

24 Feb '17

Hi, I try tu run this code: recon-all -s CAROFILO -i /home/matlab/Scrivania/SEGMENTAZIONE/CAROFILO/T2/Phase2/c2scCAROFILO.nii -autorecon2-wm but compare this error ERROR: cannot find /usr/local/freesurfer/average/RB_all_2008-03-26.gca How can I fix this problem? Thanks Flavia Arduini

2 1

Virtualbox for FS v6.0 ?
by Randolph Andrews 24 Feb '17

24 Feb '17

In past releases of FreeSurfer, there had been a version of the software suite contained in a VirtualBox (alongside the MacOS and Linux versions). Currently, I only see Mac & Linux. Is there a plan to release a VirtualBox edition of 6.0 ?

2 1

mri_binarize --gm
by Jinsong Tang 24 Feb '17

24 Feb '17

Dear all, I am trying to run a mri_binarize command on FS 5.3 mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz I obtain this: ERROR: Option –gm unknown I found there was a previous post suggest to use the new mri_binarize from https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize I download this one, and replace the old one with this new one. however, I obtian this: mri_binarize : command not found. How to fix this? Thanks and best, Jinsong

2 2

Re: [Freesurfer] LGI data for each region?
by Antonin Skoch 24 Feb '17

24 Feb '17

Dear Shane, use this command: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats Look at the info on FreeSurfer wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI Antonin Skoch Hi Freesurfer, How can I get the LGI measurements for each brain region in Desikan atlas? Instead of getting thickness with aparcstats2table, I want the gyrification instead.Thank you. Cheers, Shane

1 0

LGI data for each region?
by Shane Schofield 24 Feb '17

24 Feb '17

Hi Freesurfer, How can I get the LGI measurements for each brain region in Desikan atlas? Instead of getting thickness with aparcstats2table, I want the gyrification instead. Thank you. Cheers, Shane -- Shane Schofield

1 0

Freeview 3D brush
by Chris Adamson 24 Feb '17

24 Feb '17

Freesurfer devs, I attempted a modification of freeview to insert a 3D brush. I have got it working. If you want to review it to put it in the main version it is there a way to submit the diff with the changes? Cheers, Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au<http://www.mcri.edu.au/> E chris.adamson(a)mcri.edu.au T 03 9936 6780 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

1 0

Make_average_subject
by Limachia, Gaurang (NIH/NINDS) [F] 23 Feb '17

23 Feb '17

Dear Freesurfer Experts, I received this error while running the make_avg_subject script. I would greatly appreciate it if you can point me in the right direction. Also, I do not know how the aparc.annot file is supposed to be created. not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject CON_201 (1 of 98) reading spherical surface /raids/hmcsraid3/silvina/PMD_FATCAT2015/CON_201/surf/lh.sphere.reg... could not read annot file /raids/hmcsraid3/silvina/PMD_FATCAT2015/CON_201/surf/../label/lh.aparc.annot No such file or directory mris_make_template: could not read annot file aparc No such file or directory ERROR: make_average_surface Thanks, Gaurang Shyam Limachia

1 0

hippocampal subfields - T1
by Rizvi, Batool 23 Feb '17

23 Feb '17

Hi, I was wondering if the hippocampal subfields analysis can still run on a lower resolution T1 scan than 1mm? One of our datasets has T1 scans with these dimensions: .93 x .93 x 1.3 . Would it still run on this dataset, if it's not the standard 1mm to begin with? Thanks! Batool

2 2

Fwd: a question about freeview
by Yen, Yi-Fen 23 Feb '17

23 Feb '17

Hello! I have problems running freeview but it used to work for me. Apparently, I am not the only user troubled by this. Please see my message to Sam below for details. Was there anything changed in freeview or in the Freesufer package in the past 12 months or so that may have caused this problem? Thanks. Yi-Fen Begin forwarded message: From: Help Desk -- Sam Mehl <help(a)nmr.mgh.harvard.edu<mailto:help@nmr.mgh.harvard.edu>> Subject: Re: a question about freeview Date: February 23, 2017 at 10:58:23 AM EST To: "Yen, Yi-Fen" <YYEN1(a)mgh.harvard.edu<mailto:YYEN1@mgh.harvard.edu>> Multiple users have reported this us in the past few days. Please email freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> about it. -- Sam Mehl (http://help.nmr.mgh.harvard.edu<http://help.nmr.mgh.harvard.edu/>) On Thu, 23 Feb 2017 3:55pm, Yen, Yi-Fen wrote: Hi Sam, I used to be able to run freeview from my mac by logging into getafix. But I now get an error message as follows. getafix:yifen[83] freeview X Error: BadValue (integer parameter out of range for operation) 2 Extension: 150 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 Abort (core dumped) This seems to be related to X terminal but why it worked before but not now? Do you think if something changed in the Freesufer software that may have caused this? Thanks. Yi-Fen

1 0

deformation fields
by Worker, Amanda 23 Feb '17

23 Feb '17

Hi All, I am trying to use the subcortical segmentation of regions from the longitudinal template to propogate to each time point using deformation fields. Does anyone know how if this is possible and if so, how can I do it? Thanks in advance, Amanda

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