; dir?
>
> cheers
> Bruce
> On Fri, 6 Oct 2017, Ali Radaideh wrote:
>
> Dear FreeSurfer Experts,
>>
>> I have just launched a new project and collected new T1 weighted images
>> (as my previous ones) and
>> started processing them using FreeSurfer. Un
Dear FreeSurfer Experts,
I have just launched a new project and collected new T1 weighted images (as
my previous ones) and started processing them using FreeSurfer.
Unfortunaely non of them works with FreeSurfer. When I run recon-all
-autorecon-all -s subjecname, I get the following error:
#@# Ta
Dear FS experts,
I have managed to run the *glm_fit* on the cortical thickness and area on a
group of MS patients. However, i am not sure how to do this on the cortical
volume. which file represents the cortical volume in subject's directory?
Many thanks,
--
*Ali M. Al-Radaideh. PhDHead
Dear Douglas,
Can I check with you if you have received my reply below to your question??
Thanks,
Ali
On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh wrote:
> Thanks alot.
>
> Below are the commands I used in order:
>
> mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsav
--surf
fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir
mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp
0.05 --2spaces
On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve
wrote:
> what is your mri_glmfit command?
>
> On 6/4/17 8:10 PM, Ali Radaideh wrote:
Dear FS experts,
I am trying to analyse the cortical thickness for a group of MS patients
and healthy controls. I have followed the instructions on how to perform
group analysis but I am still unable to achieve what I am looking for.
I am trying to produce a significance map to show the cortical
Dear FreeSurfer Experts,
We have two high resolution datasets (T1 and T2* images). T2* is
co-registered to the T1 volume. The T1 volume was processed in freesurfer
using the recon-all and we want to use the segmented cortex (by freesurfer)
as a mask to extract the cortex from the T2* volume.
Woul
?
Many thanks for your great help.
Ali
On Fri, Oct 2, 2015 at 8:25 PM, Douglas Greve
wrote:
> what about them?
>
> On 10/2/15 1:20 PM, Ali Radaideh wrote:
>
> Thanks Douglas,
>
> The second line worked fine, but can I show you the results attached to
> this email?
>
>
>
/
> complete or not?
> These are 46 segmentations although I am using 17 networks cortical
> parcellation, is this true?
> Can I add anything to make the output more informative?. Also can I get
> any surface area etc?
>
>
>
> Many thanks in advance.
> Ali
>
>
can use mri_segstats to get stats from it
> Bruce
> On Thu, 1 Oct 2015, Ali Radaideh wrote:
>
> Can we get any stats from this type of parcellation? I only can see two
>> annotation files after running the mri_surf2surf command and these can be
>> loaded tksurfer as an overlay.
the individual subject surface of
> Thomas Yeo's 17-network clustering. It won't do anything with the thickness
> though. What are you trying to do?
>
> On Tue, 29 Sep 2015, Ali Radaideh wrote:
>
> mri_surf2surf --srcsubject fsaverage --trgsubject scz10 --hemi rh
>>
>
wrote:
> what is your surf2surf command?
>
> On 9/28/15 5:11 PM, Ali Radaideh wrote:
>
> Dear Douglas,
>
> Thanks for your email. I meant to say that after running the recon-all, i
> ran the sur2surf command to get the cortical parcellation using Thomas Yeo
> Atlas.
>
works_N1000.annot]. We thought that
> > using Yeo Atlas will give slightly different cortical thickness, are
> > we correct?
> >
> > Thanks,
> > Ali
> >
> > On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wr
On Mon, Sep 28, 2015 at 8:27 PM, Douglas N Greve
wrote:
> does that file exist?
>
> On 09/28/2015 01:05 PM, Ali Radaideh wrote:
> > Dear FreeSurfer experts,
> > After finishing the recon-all, I am trying to extract the cortical
> > thickness for each subject and gr
Dear FreeSurfer experts,
After finishing the recon-all, I am trying to extract the cortical
thickness for each subject and group them into one table but unfortunately
i keep getting the following error:
rh.aparc.DKTatlas40.stats is not found or is too small to be a valid
statsfile
Use --skip flag
hould work with the old processed data.
>>
>> --Thomas
>>
>> On Sun, Sep 20, 2015 at 12:00 AM, Ali Radaideh
>> wrote:
>> > Dear Thomas,
>> >
>> > Many thanks for your detailed explanation. I will try it and let you
>> know.
>> >
;
> On Sun, Sep 20, 2015 at 12:00 AM, Ali Radaideh
> wrote:
> > Dear Thomas,
> >
> > Many thanks for your detailed explanation. I will try it and let you
> know.
> >
> > One more question please, last year, I processed another set of subjects
> > using a
is only for the left hemisphere. You can replace
> all the "lh" with "rh" to transform the right hemisphere instead.
>
> Note that the above is for the 7 networks. You can replace all the "7"
> with "17" to transform the 17-network atlas instea
lh.Yeo2011_7Networks_N1000.annot
>
> # use "sval" option to transfer confidence map.
> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
> --tval $SUBJECTS_DIR/$s/label/lh.
ransfer confidence map.
> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>
> Cheers,
> Thoma
Dear FreeSurfer experts,
I have finished processing a group of brains MR images collected at 7T
scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine).
However, we need to get the cortical parcellation based on functional
network connectivity. So I have downloaded the Atlas data
(Yeo_JNeurophysi
ill take a look:
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>
> Let me know once you have uploaded the file.
>
> -Zeke
>
>
>
>
> On 09/01/2015 01:04 AM, Ali Radaideh wrote:
> > Thanks Bruce,
> >
> > Could you please suggest something
Ali
>
> it's not that I know that the quality is fine. It might be (or not), but
> this seems to be a perl error that doesn't have to do with quality
> Bruce
> On Mon, 31 Aug 2015, Ali Radaideh wrote:
>
> Dear Bruce and Jürgen,
>>
>> Now I see somethin
)
>>
>>
>> This e-mail (and any attachment/s) contains confidential
>>
>> and/or privileged information. If you are not the intended
>>
>> recipient (or have received this e-mail in error) please notify
>>
>> the sender immediately and destroy
a.
>
>
> I have no other solution
>
>
> Cheers
>
> Jürgen
>
>
>
> Von: on behalf of Ali Radaideh <
> ali.radai...@hu.edu.jo>
> Antworten an: Freesurfer Mailinglist
> Datum: Samstag, 29. August 2015 13:41
> An: Freesurfer Mailinglist
> Betreff: [Fr
Dear FreeSurfer experts,
I have sent email 10 days ago asking for a help with processing 8 out of 55
subjects who failed to pass the Talairach phase and gave me the following
error:
tmpdir is transforms/tmp.talairach.5272
/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/
Thanks a lot
> Pınar Karadayı
>
> iPhone'umdan gönderildi
>
> 23 Ağu 2015 tarihinde 19:42 saatinde, Ali Radaideh
> şunları yazdı:
>
> Dear Freesurfer Experts,
>
> I have finished the recon-all for 30 subjects successfully. However, I
> started to get the foll
Dear Freesurfer Experts,
I have finished the recon-all for 30 subjects successfully. However, I
started to get the following error for the remaining subjects (8 subjects)
mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg
-protocol icbm transforms/tmp.
> >
> > chmod -R a+x freesurfer/bin
> >
> > -Zeke
> >
> > On 10/28/2014 01:19 AM, Ali Radaideh wrote:
> > > Dear Douglas
> > >
> > > Thanks for your reply. unfortunatey I still get the same error.
> &g
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K wrote:
> I beleive it should have a lower case X, as in:
>
> chmod -R a+x freesurfer/bin
>
> -Zeke
>
> On 10/28/2014 01:19 AM, Ali Radaideh wrote:
> > Dear Douglas
> >
> > Than
fer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~>
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
wrote:
>
> Try chmod -R a+X freesurfer/bin
>
>
> On 10/26/14 1:57 PM, Ali Radaideh wrote:
>
> Dear FreeSurfer users,
>
> I am using freesurfer on 16 PCs
Dear FreeSurfer users,
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has
the latest version of freesurfer 5.3.0 while the others have the version
5.0.0. The PC that is installed with the latest version freesurfer 5.3.0
does not allow me to run any command and everytime I tr
Dear FreeSurfer experts,
I have a problem running any command in the terminal (Ubuntu 12.04). For
example when I run the following command
tkmedit bert orig.mgz
I get the following error
ERROR: A segfault has occurred. This is not your fault, : but is most
likely an unrecoverable error and has
> (412)521-4431 Cell/Text
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Ali Radaideh
> *Sent:* Tuesday, August 19, 2014 8:06 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] tkmedit
>
>
>
opy/paste of the terminal output when you type:
>
> $> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz
>
> -Zeke
>
>
>
>
> On 08/12/2014 06:48 AM, Ali Radaideh wrote:
> > Dear Zeke,
> >
> > Thanks for your email. For some reasons your email went to
eeSurfer and what version of ubuntu? What graphics cards do you have?
>
> cheers
> Bruce
>
>
> On Tue, 5 Aug 2014, Ali Radaideh wrote:
>
> Dear FreeSurfer experts,
>>
>> I have installed FreeSurfer on multiple machines in our image processing
>> lab
>&
> $> freeview
>
> -Zeke
>
>
> On 08/05/2014 04:32 PM, Ali Radaideh wrote:
> > Dear FreeSurfer experts,
> >
> > I have installed FreeSurfer on multiple machines in our image processing
> > lab (15 PC, Linux Ubuntu) and made sure that the setting are fine.
>
Dear FreeSurfer experts,
I have installed FreeSurfer on multiple machines in our image processing
lab (15 PC, Linux Ubuntu) and made sure that the setting are fine. However,
I have tried to test if freesurfer works or not by typing the following:
tkmedit bert orig.mgz
Unfortunately, I have got
:22 AM
To: Ali Radaideh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] control points
you need to visualize it in tkmedit. As for the control points, we
haven't seen that happen. Can you try saving a couple and seeing if the
file changes?
cheers
Bruce
On Tue, 7 Sep 2010
07, 2010 1:30 AM
To: Ali Radaideh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] control points
Hi Ali,
that means that there are 0 control points stored in the file. For the
2nd
error have you checked the talairach.xfm?
cheers
Bruce
On Tue, 7 Sep
2010, Ali Radaideh wrote:
> Hi
ischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 06, 2010 3:30 PM
To: Ali Radaideh
Subject: RE: [Freesurfer] control points
Hi Ali,
can you post your responses to the list? Try catting that file to see
what's in it. Also, what version are you running?
cheers
Bruce
On
Dear Freesurfer experts,
One more question for today please. I have edited the wm in tkmedit and
saved the control points then ran
Recon-all -autorecon2-cp -autorecon3 -s mySubjectName
But unfortunately I got the following message after 5min of running. I
tried to use a different subjec
Hello,
After the success of running the freesurfer on the 7T human data a while
ago, I am trying now to extract the cortical volume. However, if I use
asegstats2table command to get the segmented volume then I get the
following values
Rt_cerebral_cortex = 236732
Lt_cerebral cortex = 242649
Dear FreeSurfer experts,
I have two question for you please,
First, I started recently to get the following message when I try to
load the tkmedit
GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by
display: IP address
And sometimes
tkmedit.bin: xcb_io.c:452: _XRead: Ass
Dear Freesurfer experts,
I was running freesurfer in a normal way as usual but unfortunately I
got the following error. This is the first time I see this error. Any
ideas, please?
Many thanks in advance
Ali
Reporting on 48 segmentations
#
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