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HI Vivek,
you probably need 2 steps, first registration, second recon-all. Something
like:
...
do
recon-all -i $SUBJECTS_DIR/$i/ -s $i
recon-all -all -subjid $i
I didn't check if the scrips runs. That's the general structure.
Best,
Alex
Le l
10/30/2014 03:08 PM, Alex Hanganu wrote:
> Hi Martin,
>
> could you please confirm whether the glm analysis was correctly
> performed ?
>
> the command line is:
> /mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh
> //--label lh.fsaverage.cortex.label //--fsgd
On 10/30/2014 03:08 PM, Alex Hanganu wrote:
Hi Martin,
could you please confirm whether the glm analysis was correctly performed ?
the command line is: mri_glmfit --glmdir DIR --y
lh.thickness-pc1.stack.fwhm15.mgh --label lh.fsaverage.cortex.label --fsgd
FSGD_FILE --C Contrast-010..0
l on the wiki, which describes
the process.
Best, Martin
On 10/23/2014 02:40 PM, Alex Hanganu wrote:
Hi Martin,
thanks for confirming. I duplicated the parameter and got good results in
qdec.
I also tried to repeat the analysis with mri_glmfit but I can't manage to
ot what you want.
Otherwise I think it is the correct approach.
Best, Martin
On 10/21/2014 04:31 PM, Alex Hanganu wrote:
Dear Martin,
thank you very much for your answer ! and thanks for all the details ! - yes,
we have exactly 2 time points in all subjects and the parameter is a si
Dear Martin,
thank you very much for your answer ! and thanks for all the details !- yes, we
have exactly 2 time points in all subjects and the parameter is a single number.
In qdec - it seems that qdec table has to include the parameter 'A' both at
time 1 and at time 2 in order for "long_qdec_ta
Hi
Du A.T. Brain 2007 ”Different regional patterns of cortical thinning in
AD" - used the smoothing level of 10-mm. This article can be added as
reference.
Additionally "higher smoothing levels, for ex. at 20 mm, would bring
partially inflated patterns due to excessive smoothing and due to
fa
istance in time is also important.
And maybe you want to cite our longitudinal paper 2012 neuroimage
within subject template ...
Good luck with your paper.
Best Martin
Sent via the Samsung Galaxy S^(TM) III, an AT&T 4G LTE smartphone
Original message ----
From: Alex Han
Dear Martin,
we used the longitudinal two stage model for our analysis and we are
writing the manuscript. In the discussions we want to add the
limitations of this procedure, asdescribed in the wiki.
We want to say that this model "does not account for different certainty
of within subject s
Hi,
I run FS without FSL and recon-all finishes without error.
Alex.
Le 13/8 11:20, Alexopoulos, Dimitrios a écrit :
A quick question. Do all versions of FS (even the older 4.4 version)
require a full FSL install to run recon-all -all.
Would the command run "without error" even if you don't
Hello everyone,
isthere a method to verify which was the last version of FreeSurfer that
was used to perform the recon-all ?
For. ex. in /subjects/subject_name/scripts/build-stamp.txt/I can see
that this subject was registered the first time with FS version 5.0but
after that, an additional r
Thank you Doug !
Le 7/8 11:44, Douglas N Greve a écrit :
> Hi Alex, use the eTIV from the longitudinal subject. In theory, the size
> of the skull is not changing, and the longitudinal analysis gives you
> the best estimate of this unchanging number.
> doug
>
> On 08/06/2
Hello,
I am measuring the changes of subcortical volumes in a longitudinal
study, so I took the volumes from longitudinal subjects
(/name.long.base/). Now we need to perform the correction using the eTIV
parameter, but the eTIV for longitudinal subjects for all time points is
the same (/i//.e
,fstats.sgn,lhcor//tex,0.05,0);//
/
only takes a few seconds to finish. Please check if /Y, Beta2,
fstats.pval/,/fstats.sgn,/ /sided_pval
/
all have the same number of columns.
Best
-Jorge
*De:* Alex Hanganu
*Para
Hi Jorge,
I got an error in the correction, and I can't find a way out.
this is the cmd I use:
-
/[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
Qdec = fReadQdec('.../LME.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
ni = [2 2... 2
st is given by the sum of the
previous coefficient and the coefficient of the interaction term:
CM.C = [0 1 0 1]
Best
-Jorge
*De:* Alex Hanganu
*Para:* FS Mailing List ; Jorge L.
Bernal-Rusiel
*En
Dear Jorge,
For the statistical analysis of longitudinal data we used the "Two Stage
Model" (TSM) and the "Linear Mixed Effects".
Our intergroup LME results (2 groups, 2 time points) had many
similarities with TSM results. Then with TSM we analysed the intragroup
changes (one group, and 2 ti
Hi Paul,
I also had such problems previously. My initial analyses were performed
on mac. Though it might seem strange, some analyses resolved after I
just restarted the computer. Other ones I analysed on centos. Now I am
doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, pau
ist and not directly to me. thanks!
>
>
> On 12/14/2012 02:17 PM, Alex Hanganu wrote:
>> Dear Douglas,
>>
>> I am using tksurfer for analysing the results.
>>
>> Can you please tell me - what flag should I use in order to limit the
>> minimal threshold of
I think Emily is talking about this one:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/
a.
Le 14/12/2012 12:59 PM, Jonathan Holt a écrit :
Emily,
This is good news, can I find or download this revised version somewhere?
jon
On Dec 14, 2012, at 11:37 AM, Emily Rogals
Dear FreeSurfer List,
How can I visualise the beta maps ?
previously there is a mail about this:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02048.html
The "/average7/" subject is missing in FreeSurfer 5.1, so I guess using
"/fsaverage/" is the same, but that command shows
eep most of the spatial resolution of
the data).
Best
-Jorge
*De:* Alex Hanganu
*Para:* Jorge Luis
*Enviado:* Viernes 7 de diciembre de 2012 23:59
*Asunto:* Re: Re: [Freesurfer] Longitudinal anal
,ni] = sortData(M,1,Y,sID);/
//
and use /ni /instead of 144 everywhere. Note that /ni/ must be a
vector of the same size as the number of subjects in your study (36),
not a single numeric value.
Best
-Jorge
*De:* Alex Hanganu
*Para:* Martin Reuter
*CC:* FS Mailing List ; Jorge Luis
apply the lme tools. But the gain in flexibility for building your
design matrix and analysis is significant. As you see, the relatively
difficult part is how to get from the Qdec variable to your design
matrix X. It requires some study-specific Matlab code. Sorry, but this
is what he h
Can you please help with this ?
Thanks in advance !
best,
Alex.
Le 05/12/2012 6:12 PM, Alex Hanganu a écrit :
Hi Jorge,
On the page presenting the "../fswiki/LinearMixedEffectsModels", I
think there is a misunderstanding -
You show the command:
"mris_preproc --qdec &qu
Hi Jorge,
On the page presenting the "../fswiki/LinearMixedEffectsModels", I think
there is a misunderstanding -
You show the command:
"mris_preproc --qdec "
but "--qdec" is not recognized, and in the help menu of "mris_preproc" I
don't see this flag. So I guess you meant the "--fsgd" fl
, especially for those studies with more than
three repeated measures.
Just write to me any doubt you have and I will answer you ASAP.
Best
-Jorge
*De:* Alex Hanganu
*Para:* Martin Reuter
*CC:* FS Mailing List
*Enviado:* Martes 4 de diciembre de 2012 19:19
*Asunto:* Re:
tly on the differences (or slopes). Basically you get a
> thickness_yearly_change (or pct change) in each base directory and can
> then see if that correlates with any covariate or group membership etc.
>
> Qdec just makes is easier to use.
>
> Best, Martin
>
> On Tue, 2012-
h temporal and spacial correlation of measures. This model is
> especially useful if you have differently many time points and time
> distances per subject.
>
> Best, Martin
>
>
> On Tue, 2012-12-04 at 18:26 -0500, Alex Hanganu wrote:
>> Dear Freesurfer Experts,
>>
&
Dear Freesurfer Experts,
We are analysing longitudinal data - the difference between 2 groups (P
and M) [19 and 17 subjects] with 2 time points for each group (A, B).
We are using the example of "Repeated Measures Anova"
(http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova)
For our
d it works for me. When you setup
> the subjectsdir and have the file in $SUBJECT_DIR/qdec/.Qdecrc then
> after starting qdec you should be able to select e.g.
> long.thickness-rate under 'Measure' in the 'Design' tab.
>
> Best, Martin
>
> On Tue, 2012-11-13 at 13
; qdec --table ./qdec/cross.qdec.table.datBest, Martin- Original
> Message -
> From: "Alex Hanganu"
> To: "Martin Reuter"
> Cc: "FS Mailing List"
> Sent: Friday, November 09, 2012 9:47 PM
> Subject: Re: [Freesurfer] Qdec - longitudinal. File missin
n
>
> On Fri, 2012-11-09 at 17:13 -0500, Alex Hanganu wrote:
>> Dear FreeSurfer Experts,
>>
>> we performed the long_mris_slopes cmd and finished without error.
>> According to the "Longitudinal Processing Tutorial", we created after
>> that the
Dear FreeSurfer Experts,
we performed the long_mris_slopes cmd and finished without error.
According to the "Longitudinal Processing Tutorial", we created after
that the cross sectional form of the qdec table, and then the
qdec/.Qdecrc file.
When running the qdec analyses, we receive an error:
Hello Martin,
everything works fine with the newer versions of files.
Thanks for the help!
Have a wonderful day !
Alex.
Le 04/10/2012 8:04 PM, Martin Reuter a écrit :
You need a newer version of glmfit. This is not the 5.1 I think.
Best Martin
Alex Hanganu wrote:
Hello Martin
/
Best Martin
Alex Hanganu wrote:
Dear Freesurfer Experts,
>
>While performing the long_mris_slopes cmd, we receive an error:
>
>>
>
>SUBJECT pls_pd_base00 Running Within-Subject GLM
>
>Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-lon
Thank you Doug !
regards,
alex.
--- En date de : Lun 14.3.11, Douglas N Greve a
écrit :
Hi Alex, you can compute the difference in those slopes using an appropriate
contrast matrix passed to mri_glmfit. QDEC should do so autotmatically (this
would be an interaction between group and age).
Dear Freesurfer Experts,
We have
two groups at similar ages and the thickness-age correlation shows
many cluster of significant values. Pointing to this maximum the
plots present similar regressions coefficients for both groups. Actually
it would be intresting to have the regions were the thic
eesurfer] Qdec - ROI - different thickness results
À: "Alex Hanganu"
Cc: "FS Mailing List"
Date: Dimanche 27 février 2011, 0h28
the easiest way to determine X from Y and blue from red (ie, which group
is getting thicker or thinner) is to Ctrl-right click on a vertex within
t
hat>
mris_anatomical_stats -l (ROIx-lh.label address) -b SUBJECT_NAME lh
the results are the same,
qdec: X>Y
mris: X a
écrit :
De: Douglas N Greve
Objet: Re: [Freesurfer] Qdec - ROI - different thickness results
À: "Alex Hanganu"
Cc: "FS Mailing List"
Date: Vendredi 25 février
e a
écrit :
De: Douglas N Greve
Objet: Re: [Freesurfer] Qdec - ROI - different thickness results
À: "Alex Hanganu"
Cc: "FS Mailing List"
Date: Vendredi 25 février 2011, 16h52
blue means that X>Y. So that sounds like it is compatible with your ROI
results, yes?
doug
Ale
Dear Freesurfer Experts,
In qdec for question:
"Does the average thickness differ between X and Y"
we received blue colored regions, meaning that thickness for group Y is lower
then X ?
We created ROIs for each region, and extracted cortical thickness for each ROI
for each subject using mris_an
écrit :
De: Chris Hyatt
Objet: Re: [Freesurfer] aparcstats2table error
À: "FS Mailing List" , "Alex Hanganu"
Date: Jeudi 24 février 2011,
18h48
You have /stat/ rather than /stats/ in the address. Have you checked that?
>>> Alex Hanganu 2/24/2011 12:22 PM >>&g
Dear Chris, Doug,
We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness.
The cmd used:
aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label --meas
thickness --t ROI.txt
ERROR: cannot find
.../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR
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