Hi Anastasia:
I have run trac-all using the following command:
trac-all -prep -c /data/alanf/FreeSurfer_5.3/diffusion_recons/dmrirc-101309
However, I get an error message which is as follows:
INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3/diffusion_recons
INFO: Diffusion root is /data/alanf
n both
> dcmroot and dcmlist.
>
> a.y
>
>
> On Wed, 25 Feb 2015, Alan Francis wrote:
>
> Hi Anastasia:
>> I have run trac-all using the following command:
>>
>> trac-all -prep -c /data/alanf/FreeSurfer_5.3/
>> diffusion_recons/dmrirc-101309
&
Hi Anastasia:
Sorry to bother you again. I ran trac all on our cluster but it gave me an
error message. I have enclosed the text file. I used vim to see if I could
decipher the error but I am not entirely sure what the problem is
Please advice.
thanks,
Alan
trac-all.o103866
Description: Bina
aparc+aseg.mgz
> WARN: You will not be able to complete TRACULA processing without it
>
> You have to make sure your freesurfer recon is there, or define
> SUBJECTS_DIR appropriately if it's elsewhere.
>
> Hope this helps,
> a.y
>
>
> On Thu, 26 Feb 2015, Alan Franci
Dear Anastasia:
Hope all is well. I have done tracula analysis on 75 brains (HARDI) and I
am statistically analyzing the data. Do I need to use ICV as a covariate in
my statistical model?
thank you,
Alan
--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
*Alan N. Francis PhD*
N
Hi Marie:
I am trying to run the LGI post processing step on 60 ASD subjects. I am
using FreeSurfer 5.3. The recons went well and the processed brains look
great. However when I run the LGI step, I am getting the following error
which is as follows: Could you please help me?
[alanf@micc FreeSurfe
-s Asperger1 exited with ERRORS at Tue May 5 11:24:52 EDT 2015
For more details, see the log file
/data/alanf/FreeSurfer_5.3/Asperger1/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Thu, Apr 30, 2015 at 2:29 PM, Alan Francis
wrote:
>
Hi Marie:
I installed the Image Processing Toolbox on Matlab 2015a and proceeded with
the analysis of brain that underwent the recon- all processing. However, it
gave me another error message which is as follows. Could you please help me.
thank you,
Alan
Hi Marie:
I just had another problem wi
you're analyzing an anisotropy
> or diffusivity measure, you wouldn't expect those to be affected my how big
> the head is.
>
> Best,
> a.y
>
>
> On Sat, 25 Apr 2015, Alan Francis wrote:
>
>
>> Dear Anastasia:
>>
>> Hope all is well. I have
Hi Marie:
I am trying to run the LGI algorithm on 32 brains. As shown in the
archives, I set the environment (on tcsh) and provided the MATLAB pathway.
[afrancis-mac:~] afrancis% setenv MATLABPATH
/Applications/MATLAB_R2015a.app/
[afrancis-mac:~] afrancis% setenv PATH ${MATLABPATH}/bin:${PATH}
I
Hi Marie -
I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I
am unable to get FreeSurfer to recognize this (see below) , so I am getting
an error. Is there any way to overcome this?
Thanks,
Alan
afrancis-mac:~ afrancis$ export FREESURFER_HOME=/Applications/freesurfer
af
Thanks Bruce.
On Fri, Sep 16, 2016 at 2:02 PM, Bruce Fischl
wrote:
> Hi Alan
>
> make sure matlab is in your path. You can check by typing:
>
>
> which matlab
>
>
> cheers
> Bruce
>
> On Fri, 16 Sep 2016, Alan Francis wrote:
>
> Hi Marie -
>>
>
Hi Prasser:
Did you set the environment for MATLAB e.g.,
setenv MATLABPATH /Applications/MATLAB_versionsetenv PATH
${MATLABPATH}/bin:${PATH}
This is required for FS to source MATLAB.
best,
Alan
On Thu, Sep 29, 2016 at 6:46 PM, prasser wrote:
> Hi, Reposting. Thanks.
>
> On Tue, 27 Sep
Hi Eugenio -
Hope all is well with you at UCL. I have the run the subfields algorithm on
a set of subjects using Freesurfer 6.0. All the brains were processed
without much fuss. However, when I ran the following:
quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt
It yielded nothing.
Can yo
of any subject
> you’ve analyzed?
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> ERC Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 22 Nov 2016, at 16:48, Alan
gt; ERC Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 22 Nov 2016, at 18:00, Alan Francis wrote:
>
> Hi Eugenio -
>
> The command I used was :
>
> [afrancis-mac:/Applicat
Hi Bruce et al,
Is the parcellation of the cerebellar subdivisions in the works for the
next version of FS? Is there an ETA for this?
thanks so much,
Alan
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailm
Hi Krista:
You may want to update tcsh. You can do this by using SUDO and 'yum update'.
best,
Alan
On Thu, Nov 14, 2013 at 10:42 AM, krista kelly wrote:
> Hello,
>
> I'm running freesurfer's recon-all using Linux and the past few subjects
> I've run, recon-all has exited with errors. I've ran
Hi Bruce et al,
Is it possible to load just the Hippocampal mask/ROI from the ASEG onto a
brain in Freeview?
thanks,
Alan
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The info
rize to pull it out of the aseg.mgz. FYI: Once loaded
> into freeview you can also generate an isosurface for the hippocampus label
> in the 3D view.
> -Louis
>
>
> On Thu, 5 Dec 2013, Alan Francis wrote:
>
> Hi Bruce et al,
>>
>> Is it possible to load ju
Thanks Bruce.
On Fri, Dec 6, 2013 at 2:51 PM, Bruce Fischl wrote:
> Hi Alan
>
> yes, this one:
>
> https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf
>
> although it is based on the CMA manual definitions
>
> cheers
> Bruce
>
> On
Hi Eugenio:
I have HSF data on 60 Asperger brains. Is there a script that will allow me
to extract the volumes into a single location?
thanks so much,
Alan Francis
Martinos Center
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
> Cheers,
> /E
>
> On Mon, 2014-02-03 at 14:52 -0500, Alan Francis wrote:
> > Hi Eugenio:
> >
> >
> > I have HSF data on 60 Asperger brains. Is there a script that will
> > allow me to extract the volumes into a s
elsewhere?
thanks so much,
Alan Francis
Martinos Center
___
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
le_5_3/data
>
>
>
> On Fri, 2014-02-07 at 12:33 -0500, Alan Francis wrote:
> > Hi Eugenio;
> >
> >
> > I ran the kvl quantify script for 70 processed Asperger brains.
> > However, it was not able to save the output since the the nmr center
> > disallow
Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:
> Hi again, Alan,
> can you please send me the exact command you are running, as well as the
> value of SUBJECTS_DIR, FREESURFER_HOME, and so on?
> Cheers,
> /E
>
>
> On Fri, 2014-02-07 at 14:46 -0500, Alan
Hi Anastasia:
Hope all is well. I have DTI data for 65 brains. They are in nifti format.
However, they do not have the bvecs and bvals information. I searched the
web but they only have the conversion information for dicom files.
I opened the header on MRICRON but how does one convert these valu
fusion sequence?
>
> a.y
>
>
> On Fri, 14 Feb 2014, Alan Francis wrote:
>
> Hi Anastasia:
>> Hope all is well. I have DTI data for 65 brains. They are in nifti format.
>> However, they do not have the bvecs and bvals information. I searched the
>> web but they only ha
corresponding file from the
> directory above.
>
> Hope this helps,
> a.y
>
>
> On Mon, 17 Feb 2014, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> Yes I am using a standard MGH diffusion sequence.
>>
>> thanks,
>>
>> Alan
>>
>>
thod can only be
done on 3T. Is the 1.5T results valid? Please advice.
thanks,
Alan Francis
___
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
can only be
done on 3T. Is the 1.5T results valid?
Please advice.
thanks,
Alan Francis
___
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
out the matter. In general, I am quite
> optimistic about automated methods to segment the subfields.
>
> Joshua
>
>
>
> -
> Joshua K. Lee
> Doctoral Candidate
> Department of Psychology &
> Center for Mind and Brain
> University of California, Davis
>
'd be interested in
> hearing what other people think about the matter. In general, I am quite
> optimistic about automated methods to segment the subfields.
>
>
>
>
> Joshua
>
>
>
>
>
>
>
> -
>
> Joshua K. Lee
> Doctoral Candidate
>
> Department of Psycholog
Hi Anastasia:
I processed 42 brains on Tracula and it ran without problems. I am now
trying to run them individually on DTK to test another hypothesis. [I am
using the DTK for the first time]. I loaded the diffusion weighted image,
filled the parameters in the GUI and ran one single brain. However
d at the generated tracks, they looked weirdly
straight. I have a hunch that I am processing 'already processed' brains
and hence this anomaly.
Please advice.
Thanks,
Alan
On Thu, Nov 12, 2015 at 4:20 PM, Ruopeng Wang
wrote:
> Hi Alan,
>
> The tracks look weird
Hi Eugenio:
I am trying to run the HSF method on 42 subjects. The FS version on our
cluster is 5.3. However when I use the following command I get an error
message.
[alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields
ERROR: Flag -hippocampal-subfields unrecognized.
-s Smoke_d004
ould be pretty
> soon=.
> Cheers,
> Eugenio
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
>
Hi Eugenio:
Hope all is well. I have a question. I have run the HSF algorithm on 32
brains and they ran smoothly without problems. I used only T1 scans. I did
not have T2s. Now to extract the data, do I need to run the following:
*.FSspace.mgz*: the additional scan, rigidly registered to the
T1 d
ook into the mgz segmentation
> files.
> Cheers
> Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message
legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
> *From: *"Alan Francis"
> *To: *"Freesurfer support list" ,
> "eiglesias"
> *Sent: *Friday, December 11, 2015 6:36:42 PM
> *Subject: *HSF in 5.3
>
> Hi Eugenio:
> I am
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
> *From: *"Alan Francis"
> *To: *"Eugenio Iglesias"
> *Cc: *"Freesurfer support list"
> *Sent: *Thursday, January 28, 2016 9:18:46
gt; Let me know if it doesn't work!
>
> Cheers,
>
> /Eugenio
>
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
Hi Anastasia:
I am working on a set of DTI data that were obtained at the Martinos
center. The data is in a single nii.gz file. The BVECS and BVALS files are
also embedded in this. Could you please advice me how do I code this in the
DMRIRC file?
Should I convert the nii.gz file into Analyze to g
ou can pass those volumes to TRACULA, and pass the gradient table
> and b-value table as separate files.
>
> Run "mri_convert --help" to see all image file formats that we can handle.
>
> Hope this helps,
> a.y
>
>
> On Wed, 3 Feb 2016, Alan Francis wrote:
>
> H
Hello Achcha:
Detailed instructions on how to install FS on Windows via Virtual Box can
be found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage
best,
Alan
On Fri, Jan 22, 2016 at 3:28 PM, Ачча Чимагомедова wrote:
>
> Hello!
>
> My name is Achcha. I am a P
ient table and
>> b-value table as separate files.
>>
>> Run "mri_convert --help" to see all image file formats that we can
>> handle.
>>
>> Hope this helps,
>> a.y
>>
>> On Wed, 3 Feb 2016, Alan Francis
H
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Ema
> >> - Original Message -
> >> From: "Bruce Fischl"
> >> To: "Freesurfer support list"
> >> Sent: Wednesday, March 16, 2016 3:49:31 PM
> >> Subject: Re: [Freesurfer] FreeSurfer 6.0
> >>
> >> yes, although the
Hi Elizabeth:
I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
Beta is available for download. Here is the URL:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
best,
Alan
On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul <
elisabeth.p...@student.uva.nl> wrote:
> Dea
On Wed, 16 Mar 2016, Alan Francis wrote:
>
> Hi Elizabeth:
>>
>> I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
>> Beta is available for download. Here is the URL:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>
&
Hi Jasmin -
In your dmrirc file , the dcmlist refers to the dicom list. You have put
the BVEC/BVAL files there. That is not correct. You need to place the
actual pathway to your niftis in this position.
set subjlist = (40 39 36)
# Input diffusion DICOMs (file names relative to dcmroot)
# If orig
p $
>
> reading from Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz...
>
> Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
> Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>
> trac-preproc exited with ERRORS at Tue Apr 12 08:04:37 P
y Tracula
> cannot open it. Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz this is
> where the the dti file is.
>
>
> On Tue, Apr 12, 2016 at 11:45 AM, Alan Francis
> wrote:
>
>> Hi Jasmin -
>>
>> When replying please cc the FS group so that they may weigh
Hi Imagers -
I am looking at the Uncinate fasciculus in a Cannabis use disorder (CUD). I
found that CUD subjects have significantly shorter tract length and a
significant group x side interaction in comparison with controls. Have you
seen this before? What is the interpretation of this finding?
tion their utility (see Wang et al., 2012; doi:
> 10.1016/j.neuroimage.2011.12.062). However, tract volume at least makes
> more intuitive sense (for example, quantifying Wallerian degeneration in T1
> scans is essentially a volume measure). I thought Alan raised an important
> issue.
>
Hi Jonathan, FreeSurfer folks:
Did you have success in combining 4 echoes of MEMPRAGE images into one? I
went through the archives and it appears to me that you would use:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the
scan has been through the recon all process. My questi
he input to recon-all)
>
> cheers
> Bruce
>
>
>
> On Mon, 15 Jul 2013, Alan Francis wrote:
>
> Hi Jonathan, FreeSurfer folks:
>>
>> Did you have success in combining 4 echoes of MEMPRAGE images into one? I
>> went through the archives and it appears to me t
Hi Anastasia and others:
I have been trying to run Trac all on five brains. It keeps giving me the
error message:
ERROR: run list is longer than subject list
My run list is equal to the subject list: Here is the environment:
Thanks for your help,
Alan
Martinos Center for Biomedical Imaging
__
Hi All:
When I ran trac-preproc I got an error that read s as follows:
trac-preproc exited with ERRORS at Mon Aug 5 13:12:53 EDT 2013. I do have
a bvec.txt and bval file in each directory.
thanks for your help,
Alan
The following are the messages:
csh::alanf@cerebro[/autofs/space/dali_003/u
/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
> Data/diffusion_recons/bvecs.**txt': No such file or directory
>
> Does this file exist?
>
>
> On Mon, 5 Aug 2013, Alan Francis wrote:
>
> Hi All:
>>
>> When I ran trac-preproc I got an error that read s as follows:
&
ding the
> extension, if it has one.
>
> a.y
>
>
> On Mon, 5 Aug 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> Yes this file does exist but it did not have the *.txt suffix. Maybe I
>> will
>> change the suffix and run this again.
>>
>&g
Surfer_5.3_**
> Data//bin/dmri_train
>
> I can't tell exactly what's going on without looking at your trac-all.log
> in its entirety. Can you please send it?
>
>
> On Tue, 6 Aug 2013, Alan Francis wrote:
>
> Thank you. It worked. I have been running a few brains and
Hi Anastasia:
For one brain I got this error message :
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107
Too many ('s.
ERROR: must sp
wrote:
>
> Hi Alan - Try removing the "\" character from the end of the dcmlist
> definition. That's a change of line character.
>
>
> a.y
>
> On Wed, 7 Aug 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> Here is the trac-all log. Please f
#x27;t tell what's going on just by
> looking at the end of it.
>
>
> On Wed, 7 Aug 2013, Alan Francis wrote:
>
> Thank you Anastasia. Another brain had a different problem: Here is the
>> trac-all log:
>>
>> mri_concat --i
>> /autofs/space/dali_
Hi Anastasia:
Thanks to your advice most of the data have been processed using Tracula.
Two brains gave me error messages that are as follows:
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all -prep -c
/autofs/space/dali_003/users/BW_
#x27;m guessing the problem is in the b-value table. How many entries are
> there that correspond to low-b images?
>
> a.y
>
>
> On Tue, 13 Aug 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> Thanks to your advice most of the data have been processed using Tracu
end...@nmr.mgh.harvard.edu> wrote:
>
> Where did you get this command line? You should set the SUBJECTS_DIR to
> the location on disk where your freesurfer recons are.
>
>
>
> On Wed, 14 Aug 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> I fixed that problem - than
gt;
> a.y
>
>
> On Wed, 14 Aug 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> Sorry to bother you again. Another of my brains gave an error message. I
>> have enclosed the trac-all log as an attachment.
>>
>> Thanks ever so much for your help,
&
Hi Anastasia:
Sorry to bother you again. I am trying to extract trac stats from the FS
data. When I run the following script, it gives me an error message:
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: tractstats2table --load-pathstats-from
is there,
> because the error message suggested to me that a '/' was missing from a
> filename listed IN that text file. Check your original error message.
>
>
> On Thu, 15 Aug 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> I took off the '/' befor
?
>
>
> On Thu, 15 Aug 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> Yes the '/' is really there before the autofs. It is puzzling.
>>
>> thanks,
>>
>> Alan
>>
>>
>> On Thu, Aug 15, 2013 at 3:15 PM, Anastasia Yendiki
&g
Hi Anastasia:
I wish to echo David's sentiments. Thanks for this great software. I was
able to process and extract data for all brains without losing any of the
brains. Thanks so much.
best,
Alan
On Fri, Aug 16, 2013 at 12:14 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Ok
Hi Anastasia:
Just a quick question. When comparing FA, AD, RD etc between 2 groups, do
we need to use covariates like Intra Cranial volume or AGE?
If the answer is no, should I do an ANOVA or will T tests be sufficient?
thank you,
Alan
___
Freesurfer
t; for any group differences in motion before you proceed and make sure your
> groups are matched in terms of motion. If you do separate t-tests for each
> tract, you'll need to adjust for multiple comparisons (by the number of
> tracts).
>
>
> On Tue, 20 Aug 2013, Alan Francis
-lh.BA.stats
--subjectsfile=BA_LGI.txt
thanks so much,
Alan Francis
___
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
2013 at 11:08 AM, Douglas N Greve
wrote:
> Hi Alan, it would be a lot easier to help if you told us what the error
> msg is:). Please supply the full terminal output including error msg.
> thanks
> doug
>
>
> On 09/03/2013 10:52 AM, Alan Francis wrote:
> > Hi FreeSurfer f
lh.BA.stats files. I am using
FreeSurfer 5.0.
thanks so much,
Alan
On Tue, Sep 3, 2013 at 11:59 AM, Douglas N Greve
wrote:
>
>
> Your comamnd line is incorrect. Use --subjects instead of -s. Or just use
> only the --subjectsfile.
> doug
>
>
>
> On 09/03/2013 11:55 AM,
this,
thanks so much,
Alan
On Tue, Sep 3, 2013 at 12:24 PM, Alan Francis wrote:
> Thanks Doug. So I change the command line syntax to the following:
>
> csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] :
> aparcstats2table --hemi lh --subjects /HM0403 /HM0503 /HM
Hi Doug:
I solved the problem. The aparcstats2table script works. But I have
another. It appears that the script does not recognize "foldind" or
FoldInd, so how do I get LGI values of the Brodmann areas?
thank you,
Alan
On Tue, Sep 3, 2013 at 1:30 PM, Alan Francis wrote:
> Hi Do
Hi Marie et al,
I have run recon all on the data and calculated LGI for all the brains in
my dataset. How does one go about extracting LGI values for each region (eg
left Pars Triangularis). Is the Folding index given in the aparc stats
sheet the same as LGI?
thanks so much,
Alan
___
e thickness column, and that the volume in this
> same text file will not mean anything relevant anymore.
>
> Then you can go for:
>
> aparcstats2table --subjects ALL_YOUR_SUBJECTS --hemi ?h --meas thickness
> --parc aparc_lgi --tablefile aparc_lgi_?h.txt
>
>
> Let me k
ck one of those
> aparc_lgi.stats file to see whether they look similar to another
> aparc.stats file in term of structure (except that the values will be
> different)?
>
> Marie
>
> On Sep 4, 2013, at 8:54 AM, Alan Francis
> wrote:
>
>Hi Marie:
>
> Thanks so much.
Hi Marie:
I fixed it. It was a pathway error. Thanks again for your help,
best,
Alan
On Wed, Sep 4, 2013 at 2:36 PM, Alan Francis wrote:
> Hi Marie:
>
> It puzzles me too. I checked a few of the aparc_lgi.stats with a regular
> aparc.stats file and they all look exactly th
Hi Anastasia and FreeSurfers:
Is it possible to model Tracula data on Qdec? I have some interesting
findings in FA and AD between two groups that I am hoping to visually
represent on a single brain.
Any advice would be deeply appreciated.
thank you,
Alan
If it's not on the surface, freeview will more likely do
>> the trick rather than qdec.
>>
>> a.y
>>
>> On Fri, 13 Sep 2013, Alan Francis wrote:
>>
>> Hi Anastasia and FreeSurfers:
>>
>>
> Hi Alan - Glad to hear that you have an interesting finding! Can you
> describe what type of thing you want to visualize a bit more? If it's not
> on the surface, freeview will more likely do the trick rather than qdec.
>
> a.y
>
>
> On Fri, 13 Sep 2013, Ala
<
ayend...@nmr.mgh.harvard.edu> wrote:
>
> I see, then it's an ROI analysis, where the tract is the ROI. Isn't it
> sufficient for you to visualize the tracts in an example subject with the
> -tv option in freeview? What would you like to do beyond that?
>
>
> On
Thanks Anastasia.
On Fri, Sep 13, 2013 at 1:37 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Alan - Sorry, tracula doesn't do voxel-based analyses, only tract-based.
>
>
> a.y
>
> On Fri, 13 Sep 2013, Alan Francis wrote:
>
> Hi Ana
Hi Jennifer -
Ostensibly your pathways and environment variables look correct. I ran into
this problem once before, so I changed from BASH to the enhanced C shell
and it worked. You may want to try that. All you need to do is to exit out
of bash and set the environment in tcsh and it could work.
Hello Elisabetta -
The Corpus callosal volumes are included in the ASEG output and not in the
WM files. They are titled CC_Anterior, CC_Midbody etc.
Best,
Alan
On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta <
elisabetta_de...@hms.harvard.edu> wrote:
> Dear experts,
> Is the corpus callosu
he corpus?
>
> My understanding is that the volume of the corpus is included in the
> calculation of the volume of the cerebral white matter.
>
> Can you confirm?
>
> Thank you,
>
> Elisabetta
>
>
>
>
>
> --
> *From:* freesurfe
External Email - Use Caution
Hi Kody -
In my view, its best not to do group comparisons using data from scanners
of different field strengths. Even between scanners of same magnetic field
strength (e,g., 3T Siemens and 3T GE), there are large variations that need
to be covaried ou
Hi Marie & FreeSurfers:
I am running the LGI command on a group of brains and I am getting an error
message. MATLAB opens up and begins to run when this error appears:
< M A T L A B (R) >
Copyright 1984-2011 The MathWorks, Inc.
R20
t; Best,
>
> Marie
>
> On Jul 9, 2014, at 11:51 AM, Alan Francis
> wrote:
>
> Hi Marie & FreeSurfers:
>
> I am running the LGI command on a group of brains and I am getting an
> error message. MATLAB opens up and begins to run when t
:
http://www.icn.ucl.ac.uk/motorcontrol/imaging/suit.htm
best,
Alan Francis
On Tue, Jul 15, 2014 at 8:53 AM, Sarosh, Cyrus
wrote:
> We are interested in using the Cerebellar vermis for an analysis with
> our PET data. Is the cerebellar vermis segmented during the FreeSurfer
> pipeline
Hi Andreas:
Very kind of you to share your code. I am sure many of us will benefit from
this.
thanks,
Alan Francis
On Mon, Jul 21, 2014 at 9:12 AM, Andreas Berger <
n0642...@students.meduniwien.ac.at> wrote:
> Hello FreeSurfers,
>
> during the course of my diploma thesis
HI Melly:
I assume that you have run your brains through the FreeSurfer recons. Once
you have done this and made corrections to the surfaces, run your brains
through a post processing step as below:
recon-all -s -localGI
This will give you gyrification indices for all lobes across the brain.
C
Hi Knut:
Gryification and Surface Area are two completely different things. Surface
Area, as measured by FreeSurfer, gives you the area of the surface (roughly
length x breadth) of a given region of interest: e.g., Pars triangularis.
It is measured in millimeter squared.
Gyrfication index, by con
External Email - Use Caution
Hi Ben -
Although I have not worked on this myself, it is my belief that FS
quantifies the CP fairly accurately. The volumes of the CP are being used
in understanding etiology and pathogenesis of psychiatric disorders such as
Schizophrenia. The lab I
1 - 100 of 175 matches
Mail list logo
