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 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
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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
<
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
> 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
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 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
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
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.
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
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
___
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
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
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,
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
--subjectsfile=BA_LGI.txt
thanks so much,
Alan Francis
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The information in this e-mail is intended only for the person to whom
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
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
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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
?
>
>
> 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
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
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
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,
&
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
#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
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;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_
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
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
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
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
/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:
&
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
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
__
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 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
Hi Imagers:
Is there a command that will allow you to extract the volumes of the
EC from the Entorhinal Ex vivo label ? I need to extract this in 77
brain scans.
thanks ~
Alan
BIDMC/ Boston
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ht
Hi Ruopeng:
Is there a command that will allow you to extract the volumes of the
EC from the Entorhinal Ex vivo label ? I need to extract this in 77
brain scans.
thanks ~
Alan
BIDMC/ Boston
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ht
Hi Joshua:
What version of FS 4 did you use?
best,
Alan
On Tue, Apr 17, 2012 at 2:56 PM, Joshua Lee wrote:
> Hi All,
>
> I thought I'd share my recent experiences with the newest Freesurfer v.
> 5.10 and subcortical segmentation.
>
> I ran a large sample of brains using the default stream of
t; UCSF | Memory and Aging Center
> 350 Parnassus Avenue, Suite 905
> San Francisco CA 94143-1207
> wir...@memory.ucsf.edu | memory.ucsf.edu
> p: 415.476.1680 | f: 415.476.1816
>
> ** **
>
> ** **
>
> ** **
>
> *From:* Alan Francis [mailto:alandar
Hi Jeff:
We too have found Wacom tablets are great for editing and also these are
easy on the back and eyes.
best,
Alan
On Wed, Apr 4, 2012 at 6:46 PM, Emily Rogalski wrote:
> We have found Wacom tablets are excellent for editing.
> On Apr 4, 2012 4:40 PM, "Jeff Stout" wrote:
>
>> Hi All,
>
Hi Martijn:
In our lab, we basically add a greater density of control points - almost 1
CP for every 2 voxels. This way the corrected pial looks closer to what's
expected.
best,
Alan
BIDMC
On Mon, Mar 12, 2012 at 5:38 AM, Martijn Steenwijk <
martijnsteenw...@gmail.com> wrote:
> Dear all,
>
>
Hi Ayaz:
Both packages are equally good. The main difference, is that DTI studio
runs on Windows while FreeSurfer is Linux/ Unix based. So it depends on
your platform. It also depends on your research question/s.
best,
Alan
BIDMC/ Boston
On Thu, Mar 8, 2012 at 7:29 PM, Bruce Fischl wrote:
> H
d you run from scratch each
> time on the original inputs? (Or did you run it on top of the previously
> processed version?)
>
> cheers,
> -MH
>
> On Tue, 2012-02-21 at 11:04 -0500, Alan Francis wrote:
> > Dear Bruce:
> >
> > I ran 3 brains twice and checked the
Dear Bruce:
I ran 3 brains twice and checked the ASEG and APARC values for each of
these. It turns out that the ASEG values are exactly the same - both
times, while the APARC values differ. Could you please explain why
this happens.
thanks so much ~
Alan
Beth Israel Deaconess Medical Center
__
Hi Bruce et al,
Thanks for the stimulating discussion on the Hippocampal subfields. I have
a question. How exactly does FS segment and parcellate the Corpus Callosum
volume ?
thanks again,
Alan
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pute the total volume of the hippocampus, you'll
> need to add the volume of this part, though..
>
> Hope this helps,
>
> Koen
>
>
> On Wed, Nov 16, 2011 at 2:10 PM, Alan Francis
> wrote:
> > Thanks Shashwath.
> >
> > On Wed, Nov 16, 2011 at 2:0
ery meaningful info.
>
> Sent from my iPhone
>
> On Nov 16, 2011, at 1:01 PM, Alan Francis
> wrote:
>
> > Hi Koen and FreeSurfers:
> >
> > I have a 3T dataset that has undergone processing using 5.1. I have also
> run the Hippo sub fields comman
these are "subfields" of the Hippocampus, should
not the sum of all subregions be equal the volume of the Right Hippocampus?
Thanks so much!
Alan Francis
Beth Israel Deaconess Medical Center, BOSTON
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Hi FreeSurfer folk:
I have a question that is in the same vein as Marie's. Should not the sum
of the Hippocampal subregional volumes be = total hemispheric Hippocampal
volume?
thanks,
Alan
On Wed, Nov 16, 2011 at 2:52 AM, Marie Schaer wrote:
>
> Hi all,
>
> I just ran the hippo-subfield segme
Hello Bruce et al,
I have a dataset processed in 5.0. Can I use the Hippocampal Sub-Field
Segmentation tools of 5.1 to process these?
thanks so much,
Alan
BIDMC/ Psychiatry
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Hi Bruce, Nick & Doug:
How does Folding index differ from Gyrification index?
thanks,
Alan
BIDMC
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The information in this e-mail i
Hi Anderson:
Your explanation is very well put. I have a question. Suppose one is looking
at High Risk datasets (for example Schizophrenia) where the
brain morphological alterations are subtle but spread across the brain,
which covariate would you use?
thanks,
Alan
[Beth Israel Deaconess Medica
irach xform using Randy
>> Buckner's method (see his paper on this topic). It includes everything
>> inside the skull implicitly.
>>
>> I'll leave Supratentorial for someone else, as I don't remember.
>>
>> cheers
>> Bruce
>>
>>
&
Hi Bruce:
Following up on Carolina's question, if I understand correctly,
Is ICV = GM+WM+Ventricular Volume ?
and
Supratentorial Volume = GM+WM ?
thanks,
Alan
On Tue, Aug 16, 2011 at 10:03 AM, Bruce Fischl
wrote:
> it includes all of those
>
> cheers
> Bruce
> On Tue, 16 Aug 2011, carolina
Hi Marie:
I have the same problem. I am doing LGI on a group of Genetic High Risk (for
Schizophrenia) subjects (n=77).
Here is what I got for one brain:
*
WARNING -- Problem for vertex iV = 57001, lGI value is aberrantly high
(lGI=47.4609)...
...lGI computation will be stopped. This may be caused
Hi Shashwath:
The QDEC model in FS will allow you to do this. The website has all the
details.
best,
Alan
On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda wrote:
> Hello Freesurfers - I just finished up with some group ROI analyses on
> thickness and surface area measures derived from Freesurfe
Hi Tracy:
You may be able to do manual tracing of the CP using FSL or 3D slicer.
best,
Alan
On Wed, Jun 8, 2011 at 3:45 PM, Tracy Butler wrote:
> Is there a good method to segment choroid plexus and calculate volume? I
> know it’s an aseg label.
>
> Thanks,
>
> Tracy
>
>
manipulating the
*aparcstats2table but
it only generates volumes from the lh.aparc files.*
thanks so much,
Alan Francis
Beth Israel Deaconess medical Center
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Hi Nick and Bruce:
Congratulations and thanks for releasing FS 5.1. We have a longitudinal
study of First Episode Schizophrenia that was awaiting this release.
best,
Alan Francis
Beth Israel Deaconess Medical Center
On Tue, May 24, 2011 at 4:28 PM, Nick Schmansky
wrote:
> FreeSurfer Us
Hi Leo:
I have faced this problem before. Philips scanner's default output format is
the PAR/REC format - but it also outputs in Dicom format. What I believe is
the problem is that the images are oriented wrongly. Take a look at this in
MRICRO and see how the images are oriented. You may need to r
Hi Bruce, Nick & Doug:
Any chance of FS 5.1 coming out in the near future? We have 2 longitudinal
data sets that we are holding back till we have this installed.
Thanks so much,
Alan
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https://ma
ta to look
for inconsistencies between scanners.
thanks,
Alan
On Mon, Jan 31, 2011 at 1:07 PM, Bruce Fischl wrote:
> Hi Alan
>
> what kind of phantom? And what would you want to do with it?
>
> Bruce
>
> On Mon, 31 Jan 2011, Alan Francis wrote:
>
> Hi Bruce, Nick, Doug
Hi Bruce, Nick, Doug and others:
I have Phantom data from around 900 scans collected across 5 sites in the
US. Does FS have a way of processing Phantom data.
Thanks much,
Alan
Alan Francis
Beth Israel Deaconess Medical Center
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Bevil:
Please take the FreeSurfer list out of your personal email list. How is your
personal agenda of any relevance to the entire FreeSurfer group?
Alan
On Wed, Jan 12, 2011 at 10:48 AM, Bevil R. Conway wrote:
> I will be out of the country from Jan. 10 - Jan 18, 2011, and will not
> have acc
Hi FSL and FreeSurfer folk:
Does anyone know how to convert *.raw files to analyze, nifti or mgz format?
thanks much,
Alan
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The inf
Thank you
On Sat, Nov 6, 2010 at 1:32 AM, Martin Reuter
wrote:
> Hi,
>
> as mentioned before, target for 5.1 is still end of November.
>
> Best, Martin
>
> On Thu, 2010-11-04 at 19:40 -0400, Bruce Fischl wrote:
> > Martin is the one to ask
> > Bruce
> >
Hi Bruce, Doug:
I am planning to process scans in a longitudinal study on First break SZ. I
heard that FS 5.1 will have features that will be better than 5.0. Any idea
on when 5.1 will be released?
thanks much,
Alan
BIDMC
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F
Hi All:
This is for the FSL VBM experts out there. I have finished all the pre
processing steps for a dataset using FSL VBM and I am trying to design a
matrix for statistical analysis. I am having difficulty with the *design.mat
* file and the* design.con* files. Do any of you know an easy of crea
Hi Nick:
I processed around 183 brains using 4.0.3 a few years ago. I have numbers on
the CC volume, thickness SA and Curvature. Are these not valid anymore?
thanks,
Alan
On Mon, Sep 13, 2010 at 10:27 AM, Nick Schmansky
wrote:
> corpuscallosum was removed from the parc stats because it is not
Hi:
Are you using FS 4.0.3? This problem has been rectified in the later
versions. I believe a '0' has been placed at the slot of the missing sulci
in FS 4.3.0 and upwards.
best,
Alan
On Tue, Aug 31, 2010 at 10:13 AM, Daniel Goldberg wrote:
> Hi,
>
> I have processed about 50 subjects using fr
Hi Ali:
Q 1: I believe this has to do with your NVIDIA driver/ X windows. If you are
using Linux, open a terminal and type 'glxgears'. If you see a window pop-up
with 3 colored gears running, then your graphics driver is working within X
windows. If you do not see this, then you need to goto the i
Fischl wrote:
> Hi Alan,
>
> which curvature index do you mean?
>
> Bruce
>
> On Mon, 16 Aug 2010, Alan Francis wrote:
>
> Hi All:
>>
>> Does a lower score on the curvature index of the CC (as done by
>> FreeSurfer)
>> imply that the Corpus Callosum
Hi All:
Does a lower score on the curvature index of the CC (as done by FreeSurfer)
imply that the Corpus Callosum is more curved (smaller radius) or is it the
other way around?
thank you,
Alan
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan Francis
Brain Spectroscopy and Neuroimaging
Hi All:
Does a lower score on the curvature of the CC (as done by FreeSurfer) imply
that the Corpus Callosum is more curved or is it the other way around?
If I am not making any sense in my previous statement, a simpler question
would be : What do the scores on the curvature index mean for the sh
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