Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

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

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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

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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

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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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FS 6.0 Freeview
by Daniel Carey 23 Feb '17

23 Feb '17

Dear All, I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable to load volumes in Freeview. When selecting 'File > Load volume', the dialog box appears, but when I select any T1.mgz and click Ok, Freeview immediately crashes. Has anyone encountered this same issue? Best wishes, Dan --- Dr. Daniel Carey Post-Doctoral Research Fellow - Statistician The Irish LongituDinal Study on Ageing (TILDA) Trinity College Dublin Dublin 2, Ireland. Email: careyda(a)tcd.ie

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Re-running after Base Image Edits
by Corrina Fonseca 22 Feb '17

22 Feb '17

Hi there, We are attempting edits on base images and a couple of questions came up when re-running through the pipeline: 1. After cp, wm, or pial edits on the base image, is it okay to simply start at ‘-autorecon2’ or must the specific starting points be used? (ie. “-autorecon2-cp”, “-autorecon2-wm”, “-autorecon2-pial”). 2. When re-running a base, after edits, starting at autorecon2, is it necessary to include all the timepoints in the command like (ie. “-tp subj1 –tp subj2”)? It’d make things simpler if that wasn’t necessary and our reading of the longitudinal processing protocol seems to suggest all the “tp” related stuff happens in autorecon1 when the norm image and transformations are generated. After that, the doc suggests that it simply processes that averaged image per-usual. Thanks in advance for any help! *Corrina Fonseca* Staff Research Associate II Senior Imaging Technician *Center for Imaging of Neurodegenerative Diseases* *San Francisco VA Medical Center* *4150 Clement Street (114M)* *San Francisco, CA 94121* *http://www.radiology.ucsf.edu/cind <http://www.radiology.ucsf.edu/cind>* *(415) 221-4810 x23088*

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gzip: stdin: unexpected end of file
by Kambiz Tavabi 22 Feb '17

22 Feb '17

After downloading CentOS 6 x86_64 (64b) stable v6.0.0 unzipping on Ubunt 16.04 (64b) machine with tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz Returns an error: gzip: stdin: unexpected end of file tar: Child returned status 1 tar: Error is not recoverable: exiting now Is there a way around this? ------------------------------------------------------------ Kambiz Tavabi PhD Institute for Learning & Brain Sciences 1715 Columbia Road N Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 Tel: 206-685-6173 ------------------------------------------------------------ *Confidentiality Notice: Because email is not secure, please be aware that we cannot guarantee the confidentiality of information sent by email. If you are not the intended recipient of this email, please notify the sender by reply email, and then destroy all copies of the message and any attachments.*

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No FTP Access
by Rockers, Elijah D. 22 Feb '17

22 Feb '17

Is there by any chance another way to download Freesurfer? My institution does not allow FTP connections (HIPPA...) Same goes for the tutorial data, but obviously Freesurfer is the priority here... thanks. - Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Accessing Freesurfer
by Ly, Kien-Ninh Ina,M.D. 22 Feb '17

22 Feb '17

Hi, I’m trying to access Freesurfer on my Mac but have been unable to do so. It appears that I’m sourcing Freesurfer through nmr-stable6-env but an error message keeps showing up when I type in “freeview”. I’ve also tried doing the Freesurfer tutorials online but the same error message appears. Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable6 FSFAST_HOME /usr/local/freesurfer/stable6/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /space/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable6/mni FSL_DIR /usr/pubsw/packages/fsl/current [scheherazade:~] (nmr-stable6-env) freeview X Error: BadValue (integer parameter out of range for operation) 2 Extension: 149 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 Abort (core dumped) Any thoughts on how to fix this? Many thanks, Ina

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mri_nu_correct.mni error after manual talairach alignment
by teodora petrova 22 Feb '17

22 Feb '17

Hello Freesurfer Developers, I have tried a manual Talairach alignment, according to this tutorial: http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview . But when I run the command recon-all -all -subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 , the run stops at the following step: #-------------------------------------------- #@# Talairach tor 16 feb 2017 11:09:05 CET /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux siv 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at tor 16 feb 2017 11:09:08 CET I have searched in the support archives, but I did not find a complete solution of the problem in none of the threads. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuntu MATE 16.04 3) see recon-all.log attached Thank you for your help. Best,Teodora

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Freesurfer February 2017