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 Depar
arameter for it)
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
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HI Marie,
What is the minimum radius that you would suggest to use, and still produce
reliable results
JOn
- Original Message -
From: "Marie Schaer"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Friday, October 11, 2013 9:04:27 PM
Subject: Re: [Freesurfer] LGI
t 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"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Monday, October 21, 2013 12:46:09 PM
Sub
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 i727137.M
elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )
Jon
- Original Message -
From: "Anastasia Yendiki"
To: "Jon Wieser"
Cc: "freesurfer" , "ebelleau"
Sent: Tuesday, October 22, 2013 12:24:22 PM
Subject: Re: [Freesurfe
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
/BrainLabDocs/Studies
Message -
From: "Z K"
To: "Skyler Gabriel Shollenbarger"
Cc: "Anastasia Yendiki" ,
freesurfer@nmr.mgh.harvard.edu, "Jon Wieser"
Sent: Wednesday, December 4, 2013 2:29:43 PM
Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
According t
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"
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
0: Tue Jun 7
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-Milwauk
fit, 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 sele
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"
To: "Jon Wieser"
Cc: "fr
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"
To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 10, 2013 1:42:37 PM
Subject: Re: [Freesurfer
ans that you
will have to run mri_glmfit-sim yourself, something like
mri_glmfit-sim --glmdir glmdir --cache 1.3 abs
doug
On 12/10/2013 02:53 PM, Jon Wieser wrote:
> i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the
> qdec output directory
> Jon
>
>
>
yes, that is what we want, but the files contain only 1-3 columns
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Tuesday, December 10, 2013 3:44:50 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
From: "Douglas N Greve"
To: "Jon Wieser" , 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? The va
".
it shows me the graph of the thickness for each cluster, with thickness values
for all subjects. is it possible to output the data values used to make the
graph?
Jon
- Original Message -
From: "Jon Wieser"
To: "Douglas N Greve"
Cc: "freesurfer&qu
oh, so it's showing the thickness values for one vertex in the cluster, not
the average of all veretices in the cluster. we are interested in the average
of the cluster
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer
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"
To: "Jon Wieser"
Cc: "freesurfer&quo
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
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-sim didn't rec
Hi Doug
I ran :
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9
I have attached three of the output summary files
Can you please confirm how to assess the cluster-wise p-value?
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wiese
-
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
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 wrote:
> Hi Doug
>
> I ran
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"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Tuesday, December 17, 2013 10:46:36 AM
Subject: Re: [Freesurfer] qdec analysis w
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
ava
the dmri_train command is giving a segmentation fault. how can I fix this?
Jon
- Original Message -
From: "Jon Wieser"
To: "freesurfer"
Sent: Wednesday, January 8, 2014 2:23:34 PM
Subject: [Freesurfer] Fwd: trac-all -prep error
Hello
I'm getting the followin
dmri_paths is producing a segmentation fault. How can I fix this?
thanks
JOn
- Original Message -
From: "Jon Wieser"
To: "freesurfer"
Sent: Wednesday, January 8, 2014 11:54:55 AM
Subject: [Freesurfer] Fwd: trac-all -path error
Dear freesurfer experts
I'm ge
Hi Anastasia,
I din't see anything missing from the brainmask or aparc+seg. I sent you the
brainmask and aparc+seg files
did you find anything wrong. if not, what else could cause the segmentatino
fault?
Thanks
- Original Message -
From: "Anastasia Yendiki"
To: &
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"
To: "Jon Wieser"
Cc: "freesurfer"
S
Hi Anastasia,
I didn't see anything missing from the brainmask or aparc+seg. I sent you the
brainmask and aparc+seg files
did you find anything wrong. if not, what else could cause the segmentatino
fault?
Thanks
- Original Message -
From: "Anastasia Yendiki"
To: &
- Forwarded Message -
From: "Jon Wieser"
To: "Anastasia Yendiki"
Cc: "freesurfer"
Sent: Wednesday, January 22, 2014 10:10:19 AM
Subject: Re: [Freesurfer] Fwd: trac-all -prep error
Hi Anastasia,
I didn't see anything blatently wrong with the apar+as
: "Anastasia Yendiki"
To: "Jon Wieser"
Cc: "freesurfer"
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) registration. Did you use flirt or
aking this realignment difficult
thanks again!
JOn
- Original Message -
From: "Anastasia Yendiki"
To: "Jon Wieser"
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 gene
:33:36 PDT 2011; 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
Fa
line 9, in
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
i fixed the problem
- Original Message -
From: "Jon Wieser"
To: "freesurfer"
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
error
tract
or 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 Specialist
UW-Milwaukee
Psychology Depart
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 W
attached is the dmrirc config file
- Original Message -
From: "Jon Wieser"
To: "freesurfer"
Sent: Wednesday, March 27, 2013 3:33:03 PM
Subject: [Freesurfer] error during trac-all -prep
i ran
trac-all -prep -c dmrirc_single_subject
and got the error :
fslmaths
/
txt" (attached)
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 Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
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n, 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 lowe
nifti file from the merged afni brik. i will try running
tracula on the merged nifti file.
Jon
- Original Message -
From: "Douglas Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Thursday, April 11, 2013 9:56:53 AM
Subject: Re: [Freesurfer] merging dti d
Hi Doug
I can motion correct the briks with 3dvolreg
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Thursday, April 11, 2013 11:22:13 AM
Subject: Re: [Freesurfer] merging dti data
That might work. I think "mot
Hi Doug
we got good results with the dit of the merged brik's
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Thursday, April 11, 2013 11:22:13 AM
Subject: Re: [Freesurfer] merging dti data
That might work. I
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
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
artners.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.
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 5
the brain)
i have set X11forwarding to yes in the /etc/sshd_config file
so xeyes works ok remotely
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: 41
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"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Thursday, May 30, 2013 12:16:55 PM
Subject: R
yes,
I have ForwardX11Trusted yes in ssh_config
and I do ssh -Y
Jon
- Original Message -
From: "R Edgar"
To: "Jon Wieser"
Cc: "Z K" , "freesurfer"
Sent: Thursday, May 30, 2013 3:26:05 PM
Subject: Re: [Freesurfer] tkmedit on ssh remote machin
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
Description: Binary data
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Freesurfer mailing list
Freesur
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
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https://mail.nmr.mgh.harvard.edu/mailma
-
From: "Anastasia Yendiki"
To: "Jon Wieser"
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 ,-a
hello
i ran a trac-all -prep -c ./dmrirc_single_subject and got the following error:
flirt -in
/BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat.nii.gz
-ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/BrainLabDocs/Studies/Alcohol_Study/Alc
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
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Freesurfer mailing list
Freesur
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 p
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
00733-1008.long.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 Ea
-rate,
long.pial_lgi-pc1, long.pial_lgi-spc ) measure regarding the LGI ?
Jon
- Forwarded Message -
From: "Jon Wieser"
To: "freesurfer"
Sent: Monday, May 19, 2014 2:53:43 PM
Subject: [Freesurfer] LGI qdec analysis on longitiudinal data
Hi freesurfer experts
I am trying to
th 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 lines t
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
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