input volume and seg
input 256 256 192
seg 256 256 256
can you tell me how to fix this?
thanks
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh
but not in the following directories
100674_base/surf
100712_base/surf
100724_base/surf
100733_base/surf
How can I fix this?
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
,
long.pial_lgi-pc1, long.pial_lgi-spc ) measure regarding the LGI ?
Jon
- Forwarded Message -
From: Jon Wieser wie...@uwm.edu
To: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Monday, May 19, 2014 2:53:43 PM
Subject: [Freesurfer] LGI qdec analysis on longitiudinal data
Hi freesurfer experts
: the percent change with respect to the first time point
spc: symmetrized percent change (rate with respect to the average)
if any of this is meaningful for LGI, I don't know, you were the one
trying to do this analysis ;-).
Best, Martin
On 05/19/2014 04:20 PM, Jon Wieser wrote:
I added the following
this realignment difficult
thanks again!
JOn
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, February 6, 2014 3:16:16 PM
Subject: Re: [Freesurfer] Fwd: trac-all -path error
We've
: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, February 6, 2014 11:00:25 AM
Subject: Re: [Freesurfer] Fwd: trac-all -path error
So there's your culprit. You need to fix the intra-subject
(diffusion-to-T1
...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Friday, January 10, 2014 6:15:23 PM
Subject: Re: [Freesurfer] Fwd: trac-all -path error
Hi Jon - Have you checked the brain mask and aparc+aseg for this subject?
Anything missing there that might affect
- Forwarded Message -
From: Jon Wieser wie...@uwm.edu
To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, January 22, 2014 10:10:19 AM
Subject: Re: [Freesurfer] Fwd: trac-all -prep error
Hi Anastasia,
I didn't see anything
...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Friday, January 10, 2014 6:15:23 PM
Subject: Re: [Freesurfer] Fwd: trac-all -path error
Hi Jon - Have you checked the brain mask and aparc+aseg for this subject?
Anything missing there that might affect the left
Hi Anastasia,
I didn't see anything blatently wrong with the apar+aseg or the DWI's. Can
you be more specific as to what I should be looking for
Thanks!
Jon
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer
the dmri_train command is giving a segmentation fault. how can I fix this?
Jon
- Original Message -
From: Jon Wieser wie...@uwm.edu
To: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, January 8, 2014 2:23:34 PM
Subject: [Freesurfer] Fwd: trac-all -prep error
Hello
I'm
dmri_paths is producing a segmentation fault. How can I fix this?
thanks
JOn
- Original Message -
From: Jon Wieser wie...@uwm.edu
To: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, January 8, 2014 11:54:55 AM
Subject: [Freesurfer] Fwd: trac-all -path error
Dear freesurfer
POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION;
UNIVERSITY OF WISCONSIN-MILWAUKEE. Sponsor: Krista Lisdahl, Ph.D.
A Postdoctoral Fellow position at the University of Wisconsin-Milwaukee (UWM),
Psychology Department (http://www4.uwm.edu/letsci/psychology/) will be
-
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Monday, December 16, 2013 4:28:30 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
look at the CWP column
doug
On 12/16/2013 05:14 PM, Jon Wieser
and contrast
MTA_ADHD_MJ2/tmp.mri_glmfit-sim-9440/lh-Avg-thickness-Age-Cor.mtx X has 4
cols, C has 8 cols
What does this mean and how to fix it?
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414
I would think that a p-value of 0.8013 is very insignificant. Am I missing
somthing?
Jon
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 17, 2013 10:46:36 AM
Subject
Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu
Sent: Friday, December 13, 2013 12:12:01 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I would have thought that it would have gotten all of them. You can try
something like --cwp .9
On 12/13/2013 01:03 PM, Jon Wieser wrote
HI Doug
MRI_glmfit-sim didn't recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99
ERROR: Flag --cwd unrecognized.
--glmdir MTA_ADHD_MJ --cwd .99
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer
: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Friday, December 13, 2013 11:18:49 AM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
HI Doug
MRI_glmfit
i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the
qdec output directory
Jon
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 10, 2013 1:42:37 PM
Subject
...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 10, 2013 2:30:31 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
OK, sorry, I thought qdec was running a script called mri_glmfit-sim but
it appears to be running
yes, that is what we want, but the files contain only 1-3 columns
Jon
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 10, 2013 3:44:50 PM
Subject: Re: [Freesurfer
: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu, Freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 10, 2013 4:20:30 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
which contrast are you looking at in QDEC? Also, what is the voxel-wise
threshold in QDEC
, mri_glmfit, mri_glmfit-sim)
doug
On 12/05/2013 02:57 PM, Jon Wieser wrote:
HI freesurfer experts
I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage)
and 2 covariates(age and gender) to study the effect of these factors on
cortical thickness. I can only select
I found data for the average thickness all subjects for each cluster, but I
haven't found the individual subject's thickness for each cluster. can you
direct me to that data?
Jon
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc
16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have reinstalled Xquartz and rebooted, but I still get the same error.
what else can I do?
system info:
mac pro 6-core intel Xeon
MAc OS 10.6.8 snowleopard
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology
Hi Zeke,
thanks for the info. we had installed the 64 bit lion version of freesurfer.
perhaps the trac-all was engaged from the wrong (older) directory. I am nuking
the old versions. and will try it again
Jon
- Original Message -
From: Z K zkauf...@nmr.mgh.harvard.edu
To: Jon Wieser
?
Thanks
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
Message -
From: Z K zkauf...@nmr.mgh.harvard.edu
To: Skyler Gabriel Shollenbarger sholl...@uwm.edu
Cc: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu,
freesurfer@nmr.mgh.harvard.edu, Jon Wieser wie...@uwm.edu
Sent: Wednesday, December 4, 2013 2:29:43 PM
Subject: Re: [Freesurfer] DTI - tracula
we install freesurfer 5.3
when we run trac-all -prep -c dmrirc
the process ends with the error:
tkreg2FSL: mov det = -64, ref det = 1
INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det,
applying LR flip to registration matrix.
Tue Dec 3 13:32:26 CST 2013
Hi anastasia,
I work with Emily. the wild card she used i*.MRDC.1 specifies only the
first dicom image. the dicoms are in the format:
i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 i727092.MRDC.37
i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 i727128.MRDC.73
/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )
Jon
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu, ebelleau ebell...@uwm.edu
Sent: Tuesday, October 22, 2013 12:24
the recon-all? I think I should restart at
-normalization2, since that that,s the next step after the aseg.mgz is created
JOn
- Original Message -
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Monday, October 21
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
Hio
We want to compute the LGI index, using our local computing cluster. the
cluster does not have matlab or it's image processing toolbox on the computing
nodes. Which matlab .m files does the LGI computation use?
Thanks
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department
both machines have Mac OS X 10.6.8
the tkmedit works fine when not logged in remotely
there is no error and the brain image is there
Jon
- Original Message -
From: Z K zkauf...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Thursday
yes,
I have ForwardX11Trusted yes in ssh_config
and I do ssh -Y
Jon
- Original Message -
From: R Edgar freesurfer@gmail.com
To: Jon Wieser wie...@uwm.edu
Cc: Z K zkauf...@nmr.mgh.harvard.edu, freesurfer
freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, May 30, 2013 3:26:05 PM
Subject
to a specific ROI. how do i do this?
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
dear FS experts
I have some PAR/REc format anatomical file from a Phillips scanner. I want to
convert the to nifti or MGZ format for freesurfer. how do I do this conversion
what program do I use?
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
Hi Doug
we got good results with the dit of the merged brik's
Jon
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, April 11, 2013 11:22:13 AM
Subject: Re: [Freesurfer] merging
data
Hi Jon, I don't know how to make this work, but I'm sure that those
commands will not do it. Sorry:(
doug
On 4/10/13 1:13 PM, Jon Wieser wrote:
we captured some dti data. there were 2 runs. we acquired in the axial plane,
2mm slice thickness the first run captured the lower half
file from the merged afni brik. i will try running
tracula on the merged nifti file.
Jon
- Original Message -
From: Douglas Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, April 11, 2013 9:56:53 AM
Subject: Re
Hi Doug
I can motion correct the briks with 3dvolreg
Jon
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, April 11, 2013 11:22:13 AM
Subject: Re: [Freesurfer] merging dti data
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman
)
in the output table all the values for the variables are the same for the 7
rows.
the values are from last file in the list
DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt
why is this? input files have different values for the various variable
Jon
--
Jon Wieser
Research
are the same for the 7
rows.
the values are from last file in the list
DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt
why is this? input files have different values for the various variable
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
if i do the 7 subjects individually, 1 by 1 with the tractstats2table for each
subject, the data in the table are ok,
it's just when I process them all with 1 tractsstat2table command, that the
data is the same in each row of the output
Jon
- Original Message -
From: Jon Wieser wie
from fsutils import TractOverallStatsParser, TractByvoxelStatsParser,
BadFileError, tractlogger
ImportError: cannot import name TractOverallStatsParser
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone
i fixed the problem
- Original Message -
From: Jon Wieser wie...@uwm.edu
To: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, March 26, 2013 4:21:35 PM
Subject: [Freesurfer] trackstats2table error
I am trying to convert my dti tracts stats to a table and got the following
; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Fri Mar 22 11:41:39 CDT 2013
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
JOn
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
___
Freesurfer
Hi Nicole,
It looks like recon-all -autorecon2 had trouble segmenting the gray/white
matter. you can try using 3duniformize to make the gray,white matter more
uniform, before doing the freesurfes recon-all. you can also try
skullstrippong in afni with 3dskullstrip first, before freesurfer
hello,
we have acquired dti scans on a subject during a FMRI experiment. is it
possible to process both dti's with tracule to get an average of the 2 dti's?
If so, how do I setup the config file for this?
Thanks
Jon
___
Freesurfer mailing list
: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Sent: Thursday, February 14, 2013 1:22:02 PM
Subject: Re: [Freesurfer] trac-all problem
Great!
On Thu, 14 Feb 2013, Jon Wieser wrote:
Hi Anastasia,
update on my processing.
I finished recon-all -autorecon1 ,-autorecon2
Hi,
I am runnning fressurfer on a Mac with 23.06 Ghz 6-core intel Xeon
processors. is it possible to run recon-all and trac-all on multiple cores.
Jon
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun
7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013
can you tell me how to fix this?
Thanks
Jon Wieser
UW-Milwaukee
dmrirc_single_subject
56 matches
Mail list logo
