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Hi Doug:
I used the following command:
[airhunger:Structural_for_7T] (nmr-stable6-env) aparcstats2table --subjects
100610 --hemi rh --meas thickness --tablefile aparc_stats.txt
However, I got an error message:
File "/usr/local/freesurfer/stable6/b
need to use the gradients extracted from the data by FSL (or
> freesurfer).
>
> Ruopeng
>
> On May 23, 2019, at 5:02 PM, Alan Francis
> wrote:
>
> External Email - Use Caution
>
> Hi Ruopeng -
>
> I used Diffusion Toolkit to recon DTI data that was preprocesse
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
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 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
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
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 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
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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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
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
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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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
__
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
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
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 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,
>
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 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
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 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
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Dear Anastasia -
I tried running tracula preproc. However, it gave me an error message.
Could you please shed some light on this?
Thank you,
Alan
[airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc
INFO: SUBJECTS_DIR is /autofs/c
ber of volumes in your DWI data. I think it's
> expecting to find a b=0 volume as the 64th volume, but your DWI nifti has
> only 63 volumes.
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.har
External Email - Use Caution
Hi Eugenio -
Hope you are well. I am trying to extract the HSF from a group of processed
brains. Previously I used the command:
quantifyHippocampalSubfields.sh 195950 HSF_Cannabis
Has this changed? If so what is the new command?
Thanks,
Alan
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*
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Hi Anastasia -
Is it possible to run Tracula on a stand alone Linux machine (Ubuntu) which
has 64 GB RAM and hyper threading? At Martinos, I used to run this on the
cluster.
Thanks,
Alan
--
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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Hi Doug et al,
I know that this question may have been asked before, but does the latest
version of FS segment/ parcellate the volume of the periaqueductal gray
(PAG?
Thank you,
Alan
--
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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
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
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 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
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 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 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 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
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 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
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 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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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:
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
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 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
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 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
>
>
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 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
External Email - Use Caution
Good evening all:
I am trying to coregister T1 and T2 images and run the recons. However, the
T2's are giving me an error message. Please see below:
Thanks,
Alan
[DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/
fs-check-v
External Email - Use Caution
Good evening Doug et all:
I am trying to coregister T1 and T2 images and run the recons. However, the
T2's are giving me an error message. Please see below: I opened the T2
image on Freeview. It looks normal. I tried running a second brain. Same
probl
l register them together. Or do
> you just want to register them outside of recon-all?
>
> On 8/14/2023 2:46 PM, Alan Francis wrote:
>
> External Email - Use Caution
> Good evening Doug et all:
>
> I am trying to coregister T1 and T2 images and run the recons. How
the --flair flag is slotted?
thanks,
Alan
On Tue, Aug 22, 2023 at 9:08 AM Douglas N. Greve
wrote:
> External Email - Use Caution
>
> Sorry, you need to pass it to recon-all with --flair or --T2
>
> On 8/21/2023 1:19 PM, Alan Francis wrote:
>
> External Ema
the new surfaces. For example:
>
>
>
> recon-all -s subjectname -T2 /path/to/T2_volume -T2pial -autorecon3
>
> “
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.
External Email - Use Caution
Hello Lauren:
Open the sR0391178-0002-1-000208-01.nii.gz file using freeview and see
if the whole 3D brain is in place. This should give you a clue as to why
this occurred.
best,
Alan
On Wed, Sep 13, 2023 at 1:02 PM Lauren Stephens
wrote:
>
External Email - Use Caution
Hi All :
I just bought a 2023 MAC PRO with an M2 Ultra Chip for my lab. It's running
macOS Ventura. I have installed MATLAB on it but it refuses to run in a
terminal or from the Applications folder.
MATLAB runs perfectly fine on my other Linux machine
External Email - Use Caution
Hi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file
based on your recommendations. However it is giving me an error message
when I run it. The error is : Unmatched ' " "
I have attached the RC file. Could you please
-
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Thursday, August 4, 2022 12:23 PM
> *To:* Freesurfer
> *Subject:* [Freesurfer] Tracula Config file
g the example
> names and they're not going to work. You want your RC file to have the
> minimum necessary for your analysis.
>
> Best,
> Anastasia.
>
>
> ------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nm
than 3 paths in the pathlist and only 3 numbers in ncpts.
>
> Best,
>
> King-Wai
>
>
>
>
> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis
> wrote:
>
>> External Email - Use Caution
>>
>> Good morning Anastasia -
>>
>> I made the
) don't match.
> You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
>
> Best,
>
> King-Wai
>
>
>
>
> On Fri, Aug 5, 2022 at 10:53 AM Alan Francis
> wrote:
>
>> External Email - Use Caution
>>
>> Good morning Anast
Chu wrote:
> External Email - Use Caution
>
> Hi Alan,
>
> They still don't match.
> See attached excel file.
>
> Best,
>
> King-Wai
>
> On Fri, Aug 5, 2022 at 2:35 PM Alan Francis
> wrote:
>
>> External Email - Use Caution
ot; in your file.
> Change ac to acomm and you should be good to go.
>
> Best,
>
> King-Wai
>
> On Fri, Aug 5, 2022 at 4:23 PM Alan Francis
> wrote:
>
> External Email - Use Caution
>
> Hi King-Wai -
>
> First of all, thank you so much for taking the
External Email - Use Caution
Hi Anastasia, King Wei:
I did as you suggested with the config file and the preprocessing ran for a
bit but then an error occurred. I have attached the run script. It says BET
not found. Is this the Brain Extraction tool?
Could you please shed some li
7;s from FSL. It's needs to be in $FSLDIR.
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Thursday, August 11, 2022
u don't get all these, your FSL is not installed correctly.
>
> Best,
>
> King-Wai
>
> On Fri, Aug 12, 2022 at 12:34 PM Alan Francis
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Anastasia and King wei -
>>
>> I checked
for registration, you have to have ANTs installed
> and set ANTSPATH to its location.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
>
aging/ANTs
>
> On Fri, Aug 12, 2022 at 5:54 PM Alan Francis
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Anastasia :
>>
>> I installed ANTS and tried this
>>
>> set ANTSPATH = /home/afrancis/Imaging/ANTs
>>
>> but it did
, 2022 at 10:13 AM Alan Francis
wrote:
> Thank you so much King Wai,
>
> On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu
> wrote:
>
>> External Email - Use Caution
>>
>> For bash shell
>> ANTSPATH=/home/afrancis/Imaging/ANTs
>>
>> For
Use Caution
>
> Hi Alan,
>
> Do you have the latest version of ANTs?
> It should be 2.1.0
> Older version don't have all the binaries and scripts required by trac-all.
>
> Best,
>
> King-Wai
>
> On Mon, Aug 15, 2022 at 11:49 AM Alan Francis
> wrote:
>
&
> # cd ANTs
> # git checkout v2.3.1
> # cd -
>
> # If you want to build a particular release, do so here
> cd ANTs
> git checkout v2.3.1
> cd -
>
> you can also try v2.3.5 or v2.4.0.
>
> I don't know if it will work or not because I don't write this scr
External Email - Use Caution
Hi Eugenio -
Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime
2014b. However when I run the thalamic segmentation routine I get this
error. Please help.
Thanks,
Alan
copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770
Set
-web.cisco.com/1-F2deM4oNalZVW-blsG0oWLgbKUPi9lklFoUJexQqa87w6TBW80F65uV3keXC_JNnhNLjdgs5T3DVG3xGEMIgcb7cMHk2Q_ALBFO9Oi6RrXZyCulsv9K8E_IWAPqNCnI1vFAlkCEf71E98zI0kcYlNH6bHeV9q3ASpBGrbdZM55ULbrYFlerLR3edJIPeSOZkReV7GSq0OlTnO8h6R0G38zKEZdDh-2r98CGtXw-xmmNTNyKlT9K-tpnOb9wFWu5viucqTNIlnzPhcp5yWDmDwUuQyb8g50ui9YFgpCNoMSrr0WMSkbg9zqr7LxhdyS4/http%3A%2F%2Fwww.jeiglesias.com
>
>
> On Oct 18, 2022, at 2:37 PM, Alan Francis
&g
to
> install the Matlab runtime environment,
>
> $ cd $FREESURFER_HOME/bin
> $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2014b
>
> - R.
>
> On Oct 19, 2022, at 16:41, Alan Francis wrote:
>
> External Email - Use Caution
>
> Hi Eugenio -
>
External Email - Use Caution
Hi King-Wai:
I have been running Tracula on 7T images and it keeps giving me an error.
The error is as follows:
copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2
Unmatched '"'.
I have attached my config file. Can you please let me know w
ome/alanfrancis/IMAGING/DTI/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz
>
> Best,
>
> King-Wai
>
> On Tue, Jul 18, 2023 at 12:59 PM Alan Francis
> wrote:
>
>> Hi King-Wai:
>>
>> I have been running Tracula on 7T images and it keeps giving me an error.
>> The error i
to correct for b0 inhomogeneity distortions you need to
> provide the PE direction of your volumes.
>
> Best,
>
> Chiara
>
>
> > On Jul 18, 2023, at 1:01 PM, Alan Francis
> wrote:
> >
> > External Email - Use Caution
> >
> >
> > Hi K
External Email - Use Caution
Hi Doug et al,
I recently moved from Linux to MAC OS running Ventura. When I run the
recon-all, it gives me this message:
“mri_compute_overlap” cannot be opened because the developer cannot be
verified.
The help given at the FS website is for previou
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