ersity College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Jasmin
> Alves
> *Reply-To: *Freesurfer support list
> *Date: *Wednesday, 11 July 2018 at 17:16
> *To: *Freesurfer support list
>
segmentSubjectT1_autoEstimateAlveusML
works with this version of OS X. You may need to reinstall the application.
Be sure to install any available updates for the application and OS X.
Thanks,
Jasmin
On Wed, Jul 11, 2018 at 9:15 AM, Jasmin Alves wrote:
> Hello Eugenio,
>
> Thank you for the reply. T
gt; like pwd and dirname. Are these in your path?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
o no avail.
Version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
OS: X V 10.9.5
Thanks!
Jasmin
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Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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t; prematurely? I see no reason in the log that it wouldn't have finished
>
>
> Bruce
>
>
> On Thu, 1 Jun 2017, Jasmin Alves wrote:
>
> Hi Bruce,
>> So it does not matter that the recon-all.done script never appeared in the
>> script folder? Or that the isrunning
it to finish ok. I doubt
> you can get realiable thickness estimates off this kind of data, but you
> should be able to do e.g. fMRI analysis.
>
> There were a bunch of big defects so the topology fixing took a lot longer
> than usual, but it did complete
>
> cheers
> Bruce
&g
upload it
>
> On Wed, 31 May 2017, Jasmin Alves wrote:
>
> Hi Bruce,
>> Thanks for the reply, below is a couple of sentences from the
>> recon-all.log
>>
>> reading initial pial vertex positions from white.preaparc...
>>
>> mean border=65.6, 300 (300)
e? Or does FS6.0
possibly take longer to complete for some brains?
Thanks,
Jasmin
--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Freesurfer@nmr.mgh.harvard
to our file drop (URL) below?
>
> On 08/12/2016 12:00 PM, Jasmin Alves wrote:
> > Dear Freesurfer
> >
> > I encountered an error on the aseg mask for a participant, both
> > hemispheres for the aseg appear on one hemisphere of the brain mask.
> >
> &
--
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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The information
iness, V.S., Jr.
> (1994). The young adult human brain: an MRI-based morphometric analysis.
> Cereb. Cortex 4, 344–360
>
> You can find the refs in our Neuron paper on whole-brain segmentation
>
> cheers
> Bruce
>
>
> On Mon, 8 Aug 2016, Jasmin Alves wrote:
>
>
includes as
regional boundaries for the hippocampus.
Thank you,
Jasmin
--
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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https
sity volume. We
> typically check the aseg.mgz display *over* the norm.mgz to see if the
> labels make sense w.r.t. the intensities.
>
> cheers
> Bruce
> On Sat, 2 Jul 2016, Jasmin Alves wrote:
>
> Dear Freesurfer support,
>> I noticed in previous threads, people ha
will have to
edit almost every voxel. Your suggestions would be greatly appreciated.
Thanks,
Jasmin
--
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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is being mapped onto
one hemisphere. This is the case with two different mprage files.
I have attached a screenshot.
I am not quite sure how to fix this. Is it something I should fix using
TKMEDIT?
Thank you,
Jasmin
--
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University
check if you are indeed typing a
> plain "-c".
>
> Best,
> a.y
>
>
> On Wed, 25 May 2016, Jasmin Alves wrote:
>
> Hi Anastasia,
>> I am still receiving the following error message when I run a different
>> participant doing, trac-all -path –c
>> dm
, May 22, 2016 at 9:07 PM, Jasmin Alves <jal...@usc.edu> wrote:
> Correct.
>
>
> On Sunday, May 22, 2016, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>
> wrote:
>
>>
>> No idea, sorry. You used the -c option with the previous steps of
>> trac-all and
Correct.
On Sunday, May 22, 2016, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>
wrote:
>
> No idea, sorry. You used the -c option with the previous steps of trac-all
> and didn't see this error, correct?
>
> On Sun, 22 May 2016, Jasmin Alves wrote:
>
> Hi Anastas
previous mailing lists, and found no match to
this problem.
Thank you,
Jasmin
On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Ok, then you can ignore the error that you see when you run the bedpost
> step.
>
>
> `On Sun, 22 May
yqa6rNRHLug=7c1gaW5UpDUs-Df4uqLGaiN1YKi8WpD7PUUFUH_Yh_8=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA=
> What's in the dmri.bedpostX/ directory?
>
> On Sun, 22 May 2016, Jasmin Alves wrote:
>
> Output files are being generated, ie.
>> 1. dtifit_FA.nii.gz - Fractional Anisotropy
>> 2. dtifit_MD.nii.g
gt;
>
> On Sun, 22 May 2016, Jasmin Alves wrote:
>
> Hi Anastasia,
>> Thank you for the reply, when I do just let it run, I get the following
>> error when I try to do trac-all -path –c dmrirc1_sim.txt
>>
>> I get the following error:
>>
>> ERROR: f
<
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Jasmin - Check if things are running despite that error. Are output
> files being generated?
>
> a.y
>
> On Sat, 21 May 2016, Jasmin Alves wrote:
>
>
>> Dear Freesurfer,
>>
>> While doin
Dear Freesurfer,
While doing the bedpost step for TRAC-all ( trac-all -bedp -c
dmrirc1_sim.txt) I received the following error:
/Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No
such process
Any ideas?
Thank you,
Jasmin
Jasmin Alves
Predoctoral Student
Medical Biology
;
> Tracula is not able to open your DTI.nii.gz
>
> Please check this file or pathway.
>
> best,
>
> Alan
>
>
>
> On Tue, Apr 12, 2016 at 11:17 AM, Jasmin Alves <jal...@usc.edu
> <javascript:_e(%7B%7D,'cvml','jal...@usc.edu');>> wrote:
>
>> Hi Al
are in nifti format, could this possibly be the cause of this
error? I have attached my configuration file for reference.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.5.0 x86_64
Thanks so much!
Jasmin
Jasmin Alves
Predoctoral
want to know what that text is. You can run the following
> command and send me the dng.log file
>
> dt_recon --debug --i DTI.nii.gz --s 40 --o
> /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log
>
>
>
>
>
> On 03/16/2016 11:35 AM, Jasmin Alves
> On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Can you send the full terminal output from when you run dt_recon with
>> the nifti as input?
>>
>> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
>> > How was
, 2016 at 12:34 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:
> Can you send the full terminal output from when you run dt_recon with
> the nifti as input?
>
> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> > How was DTI.nii.gz created? DTI.nii.gz was converted from the
d.edu
> wrote:
>
> How was DTI.nii.gz created? What happens if you run
> mri_info DTI.nii.gz
>
> If the DICOM is a siemens dicom but has been stripped of special siemens
> info, then we cannot unpack it
>
>
> On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> >
> >
en running with nifti?
>
>
> On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> >
> > Dear Freesurfer experts,
> >
> > FREESURFER_HOME: /Applications/freesurfer
> >
> > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> >
> > Kernel info: Darwin 14.5.0 x8
that occurs, but
the files I have were directly exported from our siemens scanner via
Osirix. I also tried running dt_recon using nifti format but that resulted
in an error as well. Is there anything else I can do?
Thanks,
Jasmin
--
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
as white matter, is it necessary
to use the voxel edit to remove where the skull is considered part of the
white matter mask?
Thank you,
Jasmin
--
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
>
> On Wed, Feb 10, 2016 at 5:30 PM, Jasmin Alves <jal...@usc.edu> wrote:
> > Hello freesurfer,
> >
> > I received this odd inflated surface image. I am not sure if this is
> > something that can be fixed via a registration step or should be fixed in
>
dir doesn't exist within $SUBJECTS_DIR), you still need to specify the
> input volume with -i T1_original_joya.nii
>
> cheers
> Bruce
>
>
> On Tue, 26 Jan 2016, Jasmin Alves wrote:
>
> Bruce,
>> Sorry to be a pain, but for some reason, I cannot still get recon-all to
dn't exist. Create it first with
>
> mkdir /Desktop/Brain_Child_subs
>
> then try rerunning.
> Bruce
>
>
>
> On Wed, 27 Jan 2016, Jasmin Alves wrote:
>
> Hi Bruce,
>> Could you elaborate on what you mean I need to specify the input volume?
>>
>>
ii -subject \
> joya -all &
>
> cheers
> Bruce
>
>
> On Mon, 25 Jan 2016, Jasmin Alves wrote:
>
> Hi Bruce,
>> Thanks for the reply, I attempted to direct Subjects_dir to the folder
>> with
>> my data but I received the following error.
>>
>
read-only) location. You can do this on the command line of recon-all via:
>
> recon-all -sd ...
>
> cheers
> Bruce
>
>
>
> On Sun, 24 Jan 2016, Jasmin Alves wrote:
>
> Hello Freesurfer,
>>
>> I am trying to learn freesurfer and ran into the fol
.nii -subject
joya -a
Thank you,
Jasmin
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh
--out lh.gender_age.thickness.10.mgh &
[2] 5633
Jasmins-MacBook-Pro:glm jasminalves$ ERROR: cannot find
/buckner_data/tutorial_subjs/group_analysis_tutorial
Thanks!
Jasmin
--
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
U
mgh.harvard.edu>
wrote:
> What happens if you try to run mri_convert ?
>
> On 01/14/2016 05:10 PM, Jasmin Alves wrote:
> >
> > Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l
> > $FREESURFER_HOME/bin/tksurfer
> >
> > -rwxr-xr-x 1 root wheel 103 May 14 20
ks,
Jasmin
--
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Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/
/QuickInstall
> which links to this mac specific page.
> https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall
>
> ?
>
> hth
> d
>
> On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves <jal...@usc.edu> wrote:
> > Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l
--
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Predoctoral Student
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University of Southern California
jal...@usc.edu
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be very useful.
Thank you,
Jasmin
--
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Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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nds? What is the
> result of
> ls -l $FREESURFER_HOME/bin/tksurfer
>
>
>
> On 01/14/2016 04:16 PM, Jasmin Alves wrote:
> > Hello,
> >
> > I recently downloaded freesurfer on my mac with a Yosemite operating
> > system. The application itself appears to work, however
Here is the output to the ls command
On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves <jal...@usc.edu> wrote:
> Hi Dr. Greve,
>
> I am still receiving the same message that I am denied access to freeview.
> Is there anything I can do?
>
> Thanks,
> Jasmin
>
>
Jan 14, 2016 at 2:04 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> Jasmin, can you just cut and paste it into the email?
>
> On 01/14/2016 04:59 PM, Jasmin Alves wrote:
> > Here is the output to the ls command
> >
> > On Thu, Jan 14, 2016 at 1
jal...@usc.edu
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Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Hello,
Are there possibly any travel grants available to attend the Freesurfer
workshop in April? It would greatly benefit my PhD studies to attend this
workshop to learn more about structural techniques, however my PI does not
have sufficient funds to send me.
Thanks,
Jasmin
--
Jasmin Alves
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