? Is there
anything else you suggest?
Best regards,
Amirhossein Manzouri
On Mon, Jan 30, 2023 at 7:59 PM amirhossein manzouri
wrote:
> Thanks Martin. I assume in GLM approach I should calculate change for
> session 1 and 2 and then 3 and 4 and then run difference of difference
or sub-optimal).
>
> Best, Martin
>
>
>
> On 30. Jan 2023, at 16:40, amirhossein manzouri
> wrote:
>
>
>
> Thanks a lot Martin for the information.
> We have actually 2 sessions of placebo for each subject. How do you
> suggest to do the analysis including th
5AN_y-1pI39bu3w95rTUrH9BhH2ic1xtlG1hASibJjoDsnj87lYMrp6h4urWndK0g1UHCj-Scz0voeCsI6nuyoAYkEJEZLjFog8g/http%3A%2F%2Fwww.ajnr.org%2Fcontent%2F36%2F12%2F2277.long>
>
>
> Best, Martin
>
>
>
> On 30. Jan 2023, at 15:18, amirhossein manzouri
> wrote:
>
>
>
> Hi,
are the same) and wonder if I need to only run the
model with one random effect like
lhTh0_1RF = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3);
And what would be the next steps to get the stats and sig.mgh
Best regards,
Amirhossein Manzouri
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file
No such file or directory
mri_surfcluster: could not read surface
/storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white
No such file or directory
I wonder if you found the reason and solution?
Best regards,
Amirhossein Manzouri
On Thu, Dec 6, 2018 at 6:57 PM Greve, Douglas N
I see , so volumes are also surface based.
On Tue, 20 Feb 2018 at 23:16, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> so this is thickness data? Hippocampus is a volume-based structure and
> so not represented on the surface
>
>
> On 02/20/2018 05:13 PM, amirh
volume-rate.fwhm10_LHipp
> > Loading y from
> >
> /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh
> > ... done reading.
> > Saving design matrix to lh.testretest.volume-rate.fwhm10_LHipp/Xg.dat
> > Computing normalized matrix
> > Norma
: dimension mismatch 1 between y and mask
Best regards,
Amirhossein Manzouri
On Thu, Feb 15, 2018 at 7:49 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> Can you send your glmfit command line and terminal output?
>
>
>
>
> On 02/15/2018 07:21 AM, amirhossein
n analysis in subcortical volumes?
2) Is it possible to run mri_glmfit on the whole brain not lh and rh
separately ?
Best regards,
Amirhossein Manzouri
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with DODS, right?
Best regards,
Amirhossein Manzouri
On Fri, Feb 19, 2016 at 4:28 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> I think so. Just make sure you don't try to draw conclusions from the ROI
> or area around it.
>
>
> On 2/19/16 2:02 AM, amirhossein manzo
I just wanted to clarify a bit more to see if makes more sense now ?
On Thursday, 18 February 2016, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> Hi Amirhossein, I can't tell from below if you have a question or not
>
> On 02/18/2016 05:32 PM, amirhossein manzouri
will test whether the
> slopes change between "groups", where a "group" is the given time point.
> This analysis does not make sense to me, but that is how to do it.
> doug
>
> On 02/18/2016 12:16 PM, amirhossein manzouri wrote:
>
>> Hi,
>>
our measure and CTH differs from time point one to
time point 2. So the question will does the thickness and measure1
correlation differs between time point1 and tp2?
Best regards,
Amirhossein Manzouri
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Hi Doug,
I solved the problem by using:
bbregister --s subject --mov func_denoised/vol.nii --bold --init-spm
--reg register.dat
mri_label2vol --label mask.label --reg register.dat --temp
func_denoised/vol.nii --o mask.nii
Best regards,
Amirhossein Manzouri
On Mon, Jul 27, 2015 at 7
Hi Doug,
As you can see in the image I attached the average area is different for
the same set by two different editor. I wonder if there is any reason for
this?
Best regards,
Amirhossein Manzouri
On Mon, Jul 27, 2015 at 9:16 PM, amirhossein manzouri
a.h.manzo...@gmail.com wrote:
Hi Doug
wrote:
sorry, I'm not sure I understand. Can you elaborate what you did? Same set
of subjects edited independtly by two editors? Then you look for a
difference within the subjects and you don't find it with editor 1 but you
do find it with editor 2?
On 07/27/2015 07:24 AM, amirhossein manzouri
lh.transversetemp_1001.nii
Best regard
s
Amirhossein Manzouri
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The information in this e-mail is intended only for the person
? OR Do I need to reformat the
images before running recon-all and then use in the Qdec? If so, which
program do you recommend to use?
Best regards,
Amirhossein Manzouri
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https
# TableCol 10 Units unitless
# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv
GausCurv FoldInd CurvInd
lh.transversetemporal.label 1759 1138 3029 2.424 0.552
0.101 0.026 11 2.0
Best regards,
Amirhossein Manzouri
On Thu, May 28, 2015
FoldInd CurvInd
lh.transversetemporal.label 1759 1138 3029 2.424 0.552
0.101 0.026 11 2.0
Best regards,
Amirhossein Manzouri
On Wed, May 27, 2015 at 10:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Use mri_label2label. Run it with --help to get
to longitudinal template space?
Best regards,
Amirhossein Manzouri
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Hi Jorge,
Which direction does this contrast show? con pat is redis or vice versa?
I mean how can one interpret the result?
Best regards,
Amirhossein Manzouri
On Sat, Mar 28, 2015 at 3:46 PM, jorge luis jbernal0...@yahoo.es wrote:
Hi Amirhossein
You need another column in your design
);
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95);
The second step lasts forever without any response from Matlab, should it
take long time? or can I change some parameters or should I stick to your
method?
Best regards,
Amirhossein Manzouri
On Sat, Mar 28, 2015 at 3:46
Dear Freesurfer Experts,
I wonder if there is anyway in FS to measure the brain torque or if you
have any experience with other tools regarding this?
Best regards,
Amirhossein Manzouri
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'); *
*Would you please let me know if the approach is correct ? and if I want to
add the patient group should I do the same just change the contrast ?*
*Best regards,*
Best regards,
Amirhossein Manzouri
On Fri, Mar 13, 2015 at 5:52 PM, Jon Alan Wieser wie...@uwm.edu wrote
with
2 to 3 years difference between tp1 and tp2.
Best regards,
Amirhossein Manzouri
On Mon, Feb 23, 2015 at 5:25 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi,
yes, the first is to stack all the data into a single file (on your study
average, usually that is fsaverage). The second
Hi and thanks Martin for your help,
I am trying to do mixed effect analysis, should I use the registered to
template data for this ( sub1-t1.long.tempsub1 and sub1-t2.long.tempsub1)
and how should the aded.table.dat look like? Do I need to run :
mris_preproc --qdec-long qdec.table.dat --target
Hi FreeSurfer,
What would be the best way to compare the patient group before and after
treatment with a control group? Should one use the tp1 and tp2 registered
to the template from longitudinal analysis and compare those with the
control group?
Best regards,
Amirhossein Manzouri
registered
to the template from longitudinal analysis and compare those with the
control group?
Best regards,
Amirhossein Manzouri
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Dear experts,
I have created a label from Qdec and used mri_label2label to apply it to
all subjects. Now I need to extract the pc1 measure from longitudinal
analysis in my label. Would you please advise how to do this since
kris_anatomical_stats doesn't work here?
Best regards,
Amirhossein
Dear Bruce,
I meant cingulate cortex, the cuneus and precuneus !
Best regards,
Amirhossein Manzouri
On Mon, Aug 11, 2014 at 12:53 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Amirhossein
which structures do you mean? Like the ventricles? We usually mask those
regions out
Dear All,
I wonder if you have experienced or there is any report on cortical
segmentation reliability in the mid-line structures of the brain, so one
should take them into consideration in running group differences with Qdec?
Best regards,
Amirhossein Manzouri
(fits the same slope to both
groups), or (b) stay with DODS and demean the ages. This is the same as
what you are doing already, but it tests for the difference at the mean
of your group instead of at 0.
Best regards,
Amirhossein Manzouri
On Tue, Aug 5, 2014 at 12:53 AM, Sarah Whittle swhit
Hi,
I am looking at group differences between patients(20) and controls(n=20).
I get significant results when I use Age, while I get no significance using
Demeaned age both with DODS, also the pattern of significance is different.
Would you please explain why?
Best regards,
Amirhossein Manzouri
Thanks Doug,
I used the first link and works perfectly now!
Best regards,
Amirhossein Manzouri
On Tue, May 20, 2014 at 5:03 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
I just ran it, and it works fine. It may be that I need to give you more
libraries.
Start with this one
ftp
Dear Doug,
Kindly find attached a sample of my lh.aparc.stats file!
Best regards,
Amirhossein Manzouri
On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Can you send me your lh.aparc.stats file?
doug
On 05/14/2014 01:41 PM, amirhossein manzouri wrote
Yes!
On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Is the mean thickness in the ?h.aparc.stats file? Something like
# Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm
On 05/13/2014 05:18 PM, amirhossein manzouri wrote:
Hi,
The same result! the last
Hi,
The same result! the last is insula !
Best regards,
Amirhossein Manzouri
On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
greve/aparcstats2table
On 05/12/2014 03:41 AM
Hi again,
I think I missed my question, How can I get the Mean Thickness of each
hemisphere for several subjects using the aparcstats2table command?
On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com
wrote:
Dear Doug,
I have read this post(
https://www.mail
lh.Cth.bert.txt
Best regards,
Amirhossein Manzouri
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Tanks doug,
Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3 neg ?
Best regards,
Amirhossein Manzouri
On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
you will have to run the correction for multiple comparisons with
mri_glmfit-sim
Thanks.
Best regards,
Amirhossein Manzouri
On Mon, Mar 17, 2014 at 5:55 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Yes, GM volume.
doug
On 03/12/2014 09:58 AM, amirhossein manzouri wrote:
Hi All,
Would please let me know about the origin of volume in the measures menu
Can I also use mri_surfcluster as it is in qdec since I want to compare the
whole brain and masked brain results?
Best regards,
Amirhossein Manzouri
On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
you are doing it the right way. There is no difference
with Monte Carlo (threshold 1.3) command based?
Best regards,
Amirhossein Manzouri
On Mon, Mar 17, 2014 at 6:52 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
I don't know what you mean. Can you elaborate?
doug
On 03/17/2014 01:19 PM, amirhossein manzouri wrote:
Can I also use
( no difference in significance! ). I expected to see a different pattern
of significance by limiting the region. Would you please advise if I am
doing this in a right way?
Best regards,
Amirhossein Manzouri
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Hi All,
Would please let me know about the origin of volume in the measures menu of
Qdec, so I can interpret the results from group comparisons. Is it Gray
Matter volume?
Best regards,
Amirhossein Manzouri
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intensity they can be effective. I wonder if there is a way to correct
this, or if they may affect the qdec analysis between group afterwards a
lot.(since they are present in one or few slices and create thick GM in
those slices!)
Best regards,
Amirhossein Manzouri
Thanks Bruce for the prompt reply. Would you please explain how can I
control mris_make_surfaces parameters, is this a part of recon-all process?
Best regards,
Amirhossein Manzouri
On Mon, Feb 17, 2014 at 3:35 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Amirhossein
it's hard
Thanks a lot.
Best regards,
Amirhossein Manzouri
On Mon, Feb 17, 2014 at 4:54 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
they are automatically detected, but sometimes they can be too permissive
(or restrictive) in some regions in some acquisitions. If you look through
the recon
,
Amirhossein Manzouri
On Thu, Jan 30, 2014 at 10:31 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi,
with one group you want to check if atrophy is significantly different
from zero? That is probably the case for any group (e.g. aging), so it
won't tell you anything really. Also
Hi,
Would you please advise if it is possible to do longitudinal statistical
analysis within a group with two time points in Qdec. And if it is not
possible in Qdec how I suppose to do it?
Best regards,
Amirhossein Manzouri
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or …?
Thanks in advance,
Best regards,
Amirhossein Manzouri
On Mon, Jan 13, 2014 at 5:10 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
If there is no interaction, then either DODS or DOSS is appropriate.
DOSS will be more powerful and a little more interpretable
Thanks Doug and how can check if the slopes are different?
On Jan 12, 2014 12:33 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
Use DODS to test whether the slopes differ between the three groups. If
they do not, then use DOSS.
doug
On 1/11/14 5:03 PM, amirhossein manzouri wrote
subjects in each.
My question is which results design matrix type is more reliable for such a
study? And also what if I include a covariate of interest in my comparison?
Thanks in advance,
Best regards,
Amirhossein Manzouri
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41, 39, and 24
subjects in each.
My question is which results design matrix type is more reliable for such
a study? And also what if I include a covariate of interest in my
comparison?
Thanks in advance,
Best regards,
Amirhossein Manzouri
The information in this e-mail is intended only
.
In the QDEC output folder, you will see a glm folder. In that there will
be folders for each contrast. In the contrast folder, you will see an F.mgh
file which will be the F-values. You can convert this to a t =
sign(gamma.mgh)*sqrt(F)
doug
On 10/28/2013 07:27 AM, amirhossein manzouri wrote:
Hi
need more information in detail regarding calculating
the power !
--
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Amirhossein Manzouri
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The information in this e
the DOSS model. Search
for fsgd on our wiki to get examples
doug
On 10/16/2013 03:19 AM, amirhossein manzouri wrote:
Dear Experts,
Hi,
I have already done my data analysis having group as fixed factor and age
as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would
you please
--
Best regards,
Amirhossein Manzouri
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again.
--
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again.
--
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On Mon, 23 Sep 2013, amirhossein manzouri wrote:
Hi,
In the attached Slice image of a processed brain, there is a yellow line
which defines the WM and red line for the cortex but in segmentation some
WM
have been segmented as cortex and some part of cortex have not been
segmented ! Would you
are encountering a memory
error? If so, why?
-Zeke
On 07/24/2013 11:28 AM, amirhossein manzouri wrote:
Kindly find attached the recon-all.log
On Wed, Jul 24, 2013 at 4:50 PM, Z K zkauf...@nmr.mgh.harvard.edu
mailto:zkauf...@nmr.mgh.**harvard.edu zkauf...@nmr.mgh.harvard.edu
wrote:
Hello Amir
?
-Zeke
On 07/22/2013 04:23 PM, amirhossein manzouri wrote:
Hi,
Yes I am getting the memory error with version 5.3, exactly the one that
is reported in this link:
https://mail.nmr.mgh.harvard.**edu/pipermail//freesurfer/**
2011-July/019392.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail
to the link?
On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri
a.h.manzo...@gmail.com wrote:
The format of my bval file was wrong so I edited your file and tried and
it worked, also bvec should be in three columns as you have mentioned
before.
On Wed, Jul 17, 2013 at 5:11 PM, Anastasia
- That fix applied only to the 5.1 version. I'd recommend
using the 5.3 version for tracula. Are you getting a memory error, and if
so with which version?
Thanks,
a.y
On Mon, 22 Jul 2013, amirhossein manzouri wrote:
Dear Anastasia,
I am trying to download the dmri_5.1_snow_leopard.tar.**gz
Thanks Anastasia,
IT HELPED!
On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Amirhossein - I'm attaching sample files.
a.y
On Tue, 16 Jul 2013, amirhossein manzouri wrote:
Hi Anastasia,
I have tried both , 3-row and 3-column format and still
- Are your original bvecs/bvals in 3-row format instead of
3-column format? http://surfer.nmr.mgh.harvard.**
edu/fswiki/FsTutorial/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Thanks,
a.y
On Mon, 15 Jul 2013, amirhossein manzouri wrote:
Dear Experts,
I am running trac-all
the structure is tentorium of the cerebellum) and improve
segmentation?
On Fri, Jul 12, 2013 at 6:54 PM, amirhossein manzouri
a.h.manzo...@gmail.com wrote:
Thanks a lot!
On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
Hi Amir
I'm not sure I understand
Dear Experts,
I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I
get the attached bval and bvec file which the bvec one is wrong so the
process exits with error in dtifit. I have also attached original bvec and
bval.
--
Best regards,
Amirhossein Manzouri
bvals
N Greve
gr...@nmr.mgh.harvard.eduwrote:
The first command loads the left hemisphere overlay onto the right
hemisphere. Why do you want to do this?
doug
On 07/11/2013 11:13 AM, amirhossein manzouri wrote:
As I mentioned before in my second question :
tksurfer fsaverage_sym rh inflated
://www.partners.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.
--
Best regards,
Amirhossein Manzouri
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can use on his website if you want
guidance on parameters and such.
cheers
Bruce
On Fri, 12 Jul 2013, amirhossein manzouri wrote:
Dear Bruce,
Would you please explain how and where to acquire FLAIR or T2 images to
solve the problem?
BR/Amir
On Thu, Jul 11, 2013 at 9:47 PM, ye tian
/2013 02:37 AM, amirhossein manzouri wrote:
Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack
of voxel-wise cortical thickness difference between left and right
hemisphere of each subject? I need to see the difference map of left and
right (lh-rh) overlaid on both
Thanks Doug,
When I overlay the results on L R , I see different patterns on each
hemisphere. Is it something that I don't understand correctly?
BR
On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
On 07/10/2013 01:26 AM, amirhossein manzouri wrote:
Dear Doug
...@nmr.mgh.harvard.eduwrote:
I don't know what you mean by overlaying the results on L R. What is
your command line?
On 7/11/13 3:34 AM, amirhossein manzouri wrote:
Thanks Doug,
When I overlay the results on L R , I see different patterns on each
hemisphere. Is it something that I don't understand
glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh)
4) Is there any way to look at the results through the brain per slice and
also the whole brain?
--
Best regards,
Amirhossein Manzouri
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https
the
procedure with Xhemi.
BR-Amir
On Wed, Jun 19, 2013 at 9:18 AM, amirhossein manzouri
a.h.manzo...@gmail.com wrote:
I use curl to download in MAC with the links you mentioned and it is not
there!
amir% curl -O
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg
% Total
SpentLeft
Speed
0 00 00 0 0 0 --:--:-- 0:00:01 --:--:--
0
curl: (78) RETR response: 550
On Wed, Jun 19, 2013 at 8:42 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
try now
On 6/18/13 9:37 PM, amirhossein manzouri wrote:
I have version 5.1 so
Dear Doug,
I can not download the files needed for Xhemi in mentioned link. Would you
please advise how to download them?
--
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Amir
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