Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

recon-all error
by 小麦 05 Jun '13

05 Jun '13

Hi experts, When I run recon-all,I met an error,the details are as follows. 1) the subject name is cwlzxm4 2) the entire command-line is recon-all -s cwlzxm4 -i /home/virtualuser/Desktop/raw/001.mgz -all 3)the recon-all.log is attached Thank you in advance, Best wishes, Wily

2 1

error while running autorecon1 and autorecon2 in fs-v5.3
by Mehul Sampat 04 Jun '13

04 Jun '13

Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it almost runs through but toward the end, when mri_segstats is called I get the error message: .../mri/ribbon.mgz, -1): could not open file any ideas why this could be occurring ? Thanks Mehul

4 10

longer run time on 5.3 versus 5.2 ?
by Mehul Sampat 04 Jun '13

04 Jun '13

In some cases, we are seeing that, for the same subject, the run time is slower for 5.3 versus 5.2; A quick check on recon-all-status.log shows that the CA Reg Inv step is taking longer with 5.3. recon-all-status.log from data processed with 5.2: #@# CA Reg Thu Jan 17 16:03:53 PST 2013 #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013 recon-all-status.log from data processed with 5.3 #@# CA Reg Mon Jun 3 19:46:37 PDT 2013 #@# CA Reg Inv Tue Jun 4 04:52:57 PDT 2013 Is this expected ? Or in your own testing are the recon-all processing times similar for 5.2 versus 5.3 ? The recon-all.log file for both cases are attached; Thanks Mehul

3 4

mri_nu_correct.mni
by Cristian Paz 04 Jun '13

04 Jun '13

Dear FreeSurfers! I want to do bias correction on some T1 and T2 images. I have heard that you can do this by using mri_nu_correct.mni how should I use this command? I could not understand this (I am a beginner in FS) : https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni would it be something like : mri_nu_correct.mni -i <path-to-input-file> -o <path-to-where-output-file-should-be written + filename>? Thank you very much! Kind regards, Cris

1 0

Freesurfer error..recon-all fails
by Manish Dalwani 04 Jun '13

04 Jun '13

Hello Freesurfer's I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine. I have checked the permissions to various and folders and they look ok to me. When I run the following command: recon-all -i MR1000200001.dcm -s test2 I get the following error server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am attaching the log file as well, and would appreciate if people can help with this issue. Best Regards, Manish Dalwani

2 4

v 5.3 pial- FLAIR vs T2
by octavian lie 04 Jun '13

04 Jun '13

Dear All, Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably used as auxiliary for pial definition? Does Freesurfer take care of coregistration between these and the MPRAGE? What would be the command line (Linux Ubuntu) if I want to use SPM generated nifti DICOM concatenations for the T2 or FLAIR, instead of native DICOMs? Thank you, Octavian

2 1

<no>motioncor
by Gabriel Obregon 04 Jun '13

04 Jun '13

Hi, Could someone please help me with the following concerns: A. If I have multiple source volumes in mri/orig/ and run recon-all using the -nomotioncor option, how are these inputs processed compared to the case in which motion correction is employed, and what should I expect as my output? B. If I want to process only one of the multiple source volumes, i.e., the "best", how should I proceed? C. I've been encountering displaying issues of the raw volumes using tkmedit. What other interfaces are readily available for browsing through the source volumes in order to assess their quality? D. Finally, if in one of my studies I could afford running only two MPRAGE sessions per subject, is motion correction advisable for segmenting the surfaces? Thanks! Gabriel

3 5

Recon-all difficulties off-site
by Nitenson, Adam 04 Jun '13

04 Jun '13

Hello users, I am trying to get Freesurfer (5.2) working properly off-site and am encountering errors I did not have while working at the Martinos center. We use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data is similar to work with. I have been using dcmunpack since unpacksdcmdir is not identifying the DICOM files properly. I have successfully unpacked the structural and bold scans using the command (entered from the raw scan data folder: dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2 MPRAGE nii struct (I also tried using mgz instead of nii, and also changed struct to other things as it appears to be a naming argument) dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii (path) just being an abbreviate piece of the relevant pathway These generate the MPRAGE and bold folders in the subject folder as expected. I have difficulties with the next commands (environment has been set). I try: recon-all -i <path to structural data> -s <subject name> -force recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3 (I got an error about using -force so I omitted that from my command) and get the following Error ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. Yet when I omit -i and just use "recon-all -s unpack3", I get "ERROR: nothing to do" I tried a different tactic and used "recon-all -s unpack3 -autorecon1" as well as "recon-all -autorecon-all -s unpack3" which both created the various folders (bem, label, mri, surf, etc) but failed with "ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri. Make sure to have a volume called 001.mgz in (path)/FreesurferPractice/unpack3/mri/orig. If you have a second run of data call it 002.mgz, etc." I have tried these commands in both bash and tcsh shells with the same effect. So the problem, it seems, is that my "mri" file is blank, and this was not a problem I had running these commands at Martinos. Any idea what the issue might be? Best, Adam Nitenson Neuroscience Graduate Program Laboratory of Affective Neuroscience Brown University

2 3

mri_convert mgz to nifti
by Ray, Siddharth 04 Jun '13

04 Jun '13

Hi all, I just want to convert .mgz files to .nifti using mri_convert, do I have to flip my image when I do that using RAS ? or I should simply use: Mri_convert input_file_name.mgz output_file_name.nii Thanks in advance, Siddharth

3 3

Fwd: [All] freesurfer and centos6 updates!
by Emily Boeke 04 Jun '13

04 Jun '13

Hi all, I would like to save copy of the CentOS5 release of Freesurfer in my group's work space as described in the email below. The link in the email that is supposed to explain this doesn't work; could someone please let me know how to do this or point me to another webpage that explains it? Thanks! Emily Begin forwarded message: > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: [All] freesurfer and centos6 updates! > Date: December 10, 2012 4:08:30 PM EST > To: all(a)nmr.mgh.harvard.edu > Cc: Martinos-tech <martinos-tech(a)yahoogroups.com>, Help <help(a)nmr.mgh.harvard.edu> > > > WARNING! The default Freesurfer version that runs on CentOS6 machines is > going to change next Monday the 17th to a new CentOS6 specific version. > > Right now at the Martinos Center we have a mix of CentOS4, CentOS5 and > CentOS6 machines at the center. All these currently use a version of > freesurfer built on CentOS4 for maximum compatibility. However, this > means those users with CentOS6 systems are using a version that is > slower than they could be using if properly optimized. > > It is time for users of CentOS6 system to no longer be held back by the > older systems. So on next Monday the 17th, the default Freesufer on all > CentOS6 systems (which includes launchpad, tensor, and the icepuffs) > will be updated to a new CentOS6-specific build. > > The mixed environment this results in can result in confusion for groups > with a mix of CentOS versions among their workstations. To avoid this > your group should do one of the following: > > (1) contact the Martinos IT Help Desk to upgrade your old CentOS4 > and CentOS5 systems to CentOS6. Sometime in the near > future we will drop support all together for the old systems. > > (2) make a copy of the current CentOS4 release for your study into > your group's work area and point your users' environments to > use that copy. This is what is recommended for study > consistancy anyway and instructions can be found on the wiki at > > http://surfer.nmr.mgh.harvard.edu/fswiki/MakingPrivateCopiesOfDistributions > > NOTES: > > (1) to tell what CentOS version your workstation is running, run > on it: > > cat /etc/redhat-release > > (2) you are using the default freesurfer release if your PATH has > in it directories that start with /usr/local/freesurfer. > This is a symlink that currently points to the CentOS4 release > on all Linux machines at the center but will change to point at > the CentOS6 release on all CentOS6 machines next Monday, the > 17th. > > Feel free to email me with questions. > > Nick Schmansky > > > > > > > _______________________________________________ > All mailing list > All(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all > >

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer