Hi Zeke,
I set:
export FREESURFER_HOME=/usr/local/apps/freesurfer/5.1.0/
source $FREESURFER_HOME/SetUpFreeSurfer.sh
It says SUBJECTS_DIR /usr/local/apps/freesurfer/5.1.0/subjects
I then went into the directorycontaining 001ER and set environment with
following command:
setenv FREESURFER_HOME ${PWD}
I'm still getting errors running the command, so I must be setting this up
incorrectly.
Thanks,
Stefani
On Tue, May 19, 2015 at 8:41 PM, <freesurfer-requ...@nmr.mgh.harvard.edu>
wrote:
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. Re: bbregister error (Z K)
> 2. Longitudinal difference... (Gonzalo Rojas Costa)
> 3. Re: error in atlas creation (Anthony Dick)
> 4. Re: funcroi-table-sess error, \"set: variable name must begin
> with a letter\" (Joseph Andreano)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 19 May 2015 12:00:32 -0400
> From: Z K <zkauf...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] bbregister error
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <555b5e20.6000...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> It looks like the SUBJECTS_DIR environment variable is probably set
> incorrectly.
>
> Does /usr/local/apps/freesurfer/5.1.0/subject/001ER exist? What is
> SUBJECTS_DIR set to?
>
> SUBJECTS_DIR should be set to the directory containing "001ER".
>
> -Zeke
>
> On 05/19/2015 11:48 AM, Stefani O'Donoghue wrote:
> > Hi Freesurfer users,
> >
> > I'm trying to run the bbregister command on the brain.mgz file.
> >
> > Here is the command line and resulting error:
> >
> > [12239012@psych2 ~/001ER]$ bbregister --s 001ER --mov mri/brain.mgz
> > --reg register.dat
> > ERROR: cannot find 001ER in /usr/local/apps/freesurfer/5.1.0/subjects
> >
> > I need to co-register the Freesurfer ROIs to the skull-stripped
> > brain.mgz file. Is this an environment error or am I calling on the
> > subject file and volume file incorrectly?
> >
> > Any help would be greatly appreciated!
> >
> >
> > Thanks,
> >
> >
> > Stefani
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 19 May 2015 15:36:00 -0300
> From: Gonzalo Rojas Costa <gonzalo.rojas.co...@gmail.com>
> Subject: [Freesurfer] Longitudinal difference...
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <CAHPHMw6WPSrpKJp1+4jbPqV=XRGQz=
> d1r5v31q9s6c+84ac...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:
> We have GE 1.5T MRI fspgr volumetric acquisition of a MS patient (39 years
> old) and a Siemens 3T MRI mprage acquisition of the same patient three
> years after (42 years old)... we processed that images to got the volume of
> some structures that we need and compare... but, we found that multiple
> brain structures are bigger in the 42 year old images: right hypocampus
> (3187-3755), right cerebral white matter (151164-172448), right
> Cerebellum-White-Matter (12652-14902), right Cerebellum-Cortex
> (48812-51935), etc... And a similar situation occurs in left hemisphere...
> The Intracranial volumen in both cases is: 1348899,976 and
> 1332590,755197... Why is the difference in volumen in the structures in
> both studies ?... Why is always bigger at 42 years old than 39 years
> old?... Any technical problem ?... We got a similar difference
> by normalizing with ICV...
>
> Sincerely,
>
>
> Gonzalo Rojas Costa
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150519/14c3159d/attachment.html
>
> ------------------------------
>
> Message: 3
> Date: Tue, 19 May 2015 14:39:45 -0400
> From: Anthony Dick <ad...@fiu.edu>
> Subject: Re: [Freesurfer] error in atlas creation
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <555b8371.7020...@fiu.edu>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> Hello,
>
> I just wanted to give this message a bump. Thanks!
>
> Anthony
>
> On 5/15/15 9:49 AM, Anthony Dick wrote:
> > Hello,
> >
> > I have been stumped by this error I keep getting using the
> > rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas,
> > so I am wondering if the problem is with the brains we parcellated, or
> > with my installation etc. The brains consist of manually segmented
> > cerebellums from the original T1. The T1 is run through Freesurfer,
> > and the ROIs are made in Freeview. The edited file is called
> > seg_edited.mgz. Things run smoothly up until this error:
> >
> > using MR volume /<path>/subjects/4/mri/brain.mgz to mask input volume...
> > reading 23 input volumes...
> > logging results to talairach_one.log
> > reading 'subjects/average/RB_one_2015-05-14.gca'...
> > gcaAllocMax: node dims 32 32 32
> > gcaAllocMax: prior dims 128 128 128
> > gcaAllocMax: max_labels 0
> > average std = 8.4 using min determinant for regularization = 7.1
> > 0 singular and 119 ill-conditioned covariance matrices regularized
> > reading '/<path>/subjects/4/mri/nu.mgz'...
> > reading '/<path>/subjects/average/RB_one_2015-05-14.gca'...
> > gcaAllocMax: node dims 32 32 32
> > gcaAllocMax: prior dims 128 128 128
> > gcaAllocMax: max_labels 0
> > reading frame -1 of gca
> > MRIcopyFrame: src and dst must be same type
> > reading '/<path>/subjects/4/mri/transforms/talairach_one.lta'...
> > mri_read(): couldn't determine type of file
> > /<path>/subjects/4/mri/transforms/talairach_one.lta
> > mri_em_register: could not open input volume
> > /<path>/subjects/4/mri/transforms/talairach_one.lta.
> >
>
> --
> Anthony Steven Dick, Ph.D.
> Assistant Professor
> Director, Cognitive Neuroscience Program and Graduate Certificate in
> Cognitive Neuroscience
> Department of Psychology
> Florida International University Modesto A. Maidique Campus AHC4 454
> 11200 S.W. 8th Street
> Miami, FL 33199
> Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
> Email: ad...@fiu.edu
> Webpage: faculty.fiu.edu/~adick
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 19 May 2015 14:55:11 -0400 (EDT)
> From: "Joseph Andreano" <andre...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] funcroi-table-sess error, \"set: variable
> name must begin with a letter\"
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <4182.172.20.143.77.1432061711.squir...@mail.nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Doug,
>
> I'm following up on a thread from a few months back, where we were
> experiencing difficulty with funcroi-table-sess. (You can find the
> earlier thread here:
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg39326.html
> )
>
> I've attached the dng.log file you requested. Please let me know if you
> can figure out the problem.
>
> Thanks,
> Joe Andreano
>
>
> _________________________________
>
> Joseph M. Andreano, PhD
> Postdoctoral Researcher
> Interdisciplinary Affective
> Science Laboratory
> Massachusetts General Hospital
> _________________________________
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: dng.log
> Type: text/x-log
> Size: 7721185 bytes
> Desc: not available
> Url :
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150519/610d54fe/attachment.bin
>
> ------------------------------
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> End of Freesurfer Digest, Vol 135, Issue 28
> *******************************************
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
