Dear Doug,
It is a mac. I made the meditation.levels file using emacs.
emacs meditation.levels -- type Normal (level1) -- hit enter -- type
TM (level2) -- save file
Thank you very much!
Sincerely,
Ye
On Thu, Aug 8, 2013 at 4:22 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
How did
Hello,
I have another newbie question. I'm running qdec, trying to compare cortical
thickness in children with and without ADHD. However, I'm seeing a discrepancy
between the clusters that are significant according to the terminal (after
applying the Monte-Carlo simulation with default
Hi Maria, can you tar up the qdec output folder and send it to our file
drop? I'm traveling now, so it might be the 1st week of august before I
can take a look. You can also go into the qdec output folder and run
tksurfer to show you the results.
doug
On 7/26/13 1:37 PM, Maria Kharitonova
Hello,
I have a question regarding the interpretation qdec's output for the custom
ROI's thickness estimates. I ran an analysis comparing cortical thickness in
children with and without ADHD (categorical variable), controlling for age and
demeaned ICV, using 5.0. After controlling for multiple
Dear all,
I am using qdec to do a shape analysis with 16 control variables. I was
wondering if there is a limit on how many covariates can be used in qdec?
Because it seems that I cannot select all my covariates in nuisance
factors.
Thanks and regards,
Jiyang
Dear
Freesurfer experts,
is it already possible to define more than two possible factors for discrete
variables
in the latest qdec version or is that option still limited to 2 possible
variables?
Thanks for your help!
Best regards
Peter
Hi Peter, no it is not. You will have to use mri_glmfit.
doug
On 7/9/13 9:29 AM, Peter Bohn wrote:
Dear Freesurfer experts,
is it already possible to define more than two possible factors for
discrete variables in the latest qdec version or is that option still
limited to 2 possible
you can have two discrete variables (two levels each) and two continuous
variables. If you want more than that, you will need to run mri_glmfit
instead.
doug
On 07/09/2013 02:30 AM, Jiang Jiyang wrote:
Dear all,
I am using qdec to do a shape analysis with 16 control variables. I
was
Hello,
Is this running in Ubuntu? If so, it should be solved by running the
following command:
$ sudo apt-get install libjpeg62
-Zeke
Dear All,
When I tried to running qdec, I'm getting the following error.
qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
shared
Dear All,
When I tried to running qdec, I'm getting the following error.
qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
shared object file: No such file or directory
What is the solution for this.?
Any help will be greatly appreciated.
Hello Anupa,
Did you try to open the files in their directory?
Ye
On Mon, Jul 1, 2013 at 12:23 AM, Anupa AV av.an...@yahoo.com wrote:
Dear All,
When I tried to running qdec, I'm getting the following error.
qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
Hi Maria, can you elaborate on exactly what you have done? Is the data
the same and you are only changing the version of QDEC? What is the
nature of the difference? Can you send pics or stats?
doug
On 6/18/13 6:06 AM, Maria Kharitonova wrote:
Hi,
I'm learning how to use QDEC and was
Hi,
I'm learning how to use QDEC and was comparing results that it produces under
FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS or DOSS
method of producing a design matrix, while the 5.3 only has DODS. This suggests
that results should be identical (or at least similar)
Hi list,
how can I use qdec to investigate the difference among groups regarding the
measures contained in .stats file (for example thalamic volume)?
Thanks,
Stefano ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
you can't. qdec only computes stats on surfaceoverlays.
On 05/23/2013 01:49 PM, std...@virgilio.it wrote:
Hi list,
how can I use qdec to investigate the difference among groups
regarding the measures contained in .stats file (for example thalamic
volume)?
Thanks,
Stefano
Hi Marcos,
the hippocampal subfield volumes are single values for each subject and
hemisphere, so you cannot display them on the brain surface.
Cheers,
/Eugenio
On Thu, May 16, 2013 6:22 pm, Marcos Martins da Silva wrote:
Hi, Doug
Thank you for your answer.
Well I guess that after I read your
Hi, Eugenio
Thank you for your answer.
Em Sex, 2013-05-17 às 07:49 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
the hippocampal subfield volumes are single values for each subject and
hemisphere, so you cannot display them on the brain surface.
Cheers,
/Eugenio
On Thu, May 16, 2013
Hi Marcos,
On 05/15/2013 08:32 PM, Marcos Martins da Silva wrote:
Hi, freesurfers
I have two questions:
1- Is there a way to use QDEC to analyze data from hippocampal
subfields created by recon-all -s subj -hippo-subfields? That is, I
know I can manually put data from posterior* files
Hi, Doug
Thank you for your answer.
Well I guess that after I read your both tutorials for group analysis
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis )
I mistook the concepts of qdec.table.dat and
Hi, freesurfers
I have two questions:
1- Is there a way to use QDEC to analyze data from hippocampal subfields
created by recon-all -s subj -hippo-subfields? That is, I know I can
manually put data from posterior* files when making the FSGD file but it
would be great if I could import it like I do
Dear all,
I am trying to run statistical analysis on cortical thickness data using
Qdec. I have one group of control subjects that are split into three
genotype groups. I want to investigate if cortical thickness significantly
between the three genotype groups. Is it possible to look at
Hi Sinead, you cannot use QDEC for this design since it has one factor
with 3 levels (only 2 levels possible now). You can create an FSGD file,
follow the example here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V
doug
On 05/09/2013 06:42 AM, Sinead Kelly wrote:
Dear all,
I am
Hello,
I'm new to Freesurfer and I was wondering whether anybody could tell me
what steps I need to do in Freesurfer in order to conduct the following
analysis?
I would like to know which sex differences in cortical thickness (subjects
12-18 years old) are present in the 12 year olds already.
I am interested ing doing a group surfaces analysis like that specified in:
ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis, or
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28cortical%29%7C%28thickness%29
but I want to limit the analysis to a
Apologies for my previous long email; if anyone gets a chance to look over
the questions I'd be really grateful!
Many thanks indeed,
Tudor
On 16 April 2013 19:40, Tudor Popescu tud...@gmail.com wrote:
Thanks Nick, (and thanks Doug too for the answer to question 2.)
It must indeed have been a
Here's part 1. I'll write until I have to catch my shuttle, answer the
rest tomorrow ...
On 04/18/2013 05:27 PM, Tudor Popescu wrote:
Apologies for my previous long email; if anyone gets a chance to look
over the questions I'd be really grateful!
Many thanks indeed,
Tudor
On 16 April
For #2, it is hard to say without seeing the design. I would not say
that covariates should not change the results (otherwise one would not
add them), especially age. If you have a balanced design, then one would
hope that adding age would reduce the residual noise and show more of an
effect.
Thanks Nick, (and thanks Doug too for the answer to question 2.)
It must indeed have been a disk-space issue, as running the -qcache again,
after clearing up some space, produced all the expected .mgh files
If I can follow up on two of my previous questions:
3) Not sure I understand your
Tudor,
In the recon-all.log, it has this line:
ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
correctly, so this indicates to me that it might have run out of disk
space. is that the case?
to answer the others:
2.
Hi Harry,
I assume you ran the 2-stage-model , i.e. long_mris_slopes script (else
you would not have the long.thickness-avg, rate ,... files.
As described here:
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel
and
Hi,
I'm new to freesurfer and I'm trying to use qdec to run a 2-way anova (sex,
age, sex*age). How do I set up the design to get results for the
interaction? Do I do that withing the qdec design tab? Or how else do I do
it? (e.g. do I need to create a FSGD file? But where in qdec would I upload
Hi Klara, in QDEC, this contrast will automatically be computed. It
should read something like Is there a difference of thickness/age
slopes between males and females. If you do it from the command line
(mri_glmfit), search our wiki for the term FSGD and go to the examples
page.
doug
On
Hi,
I'm currently doing a long analysis of a data set that contains two groups
(training and control) and 3 timepoints (baseline -BL, follow up1- FU1 follow
up2-FU2)
I've put it through qdec. But for the analysis qdec only gives me one measure
for long.thickness-avg, rate, pc1 and spc. How do
Hi list,I'm performing qdec. This my file.dat1 diagnosis discrete 21
Pathology2 Controls2 Thickness_lh continuous 03 Thickness_rh
continuous 04 NPStest continuous 0Continuous Factors:
Mean: StdDev:--- -
Hi,
I'm performing qdec. This my file.dat
1 diagnosis discrete 21 Pathology2 Controls2 Thickness_lh
continuous 03 Thickness_rh continuous 04 NPStest continuous 0
Continuous Factors: Mean: StdDev:
--- -
Hi list,
I'm performing qdec. This my file.dat
1 diagnosis discrete 21 Pathology2 Controls2 Thickness_lh
continuous 03 Thickness_rh continuous 04 NPStest continuous 0
Continuous Factors: Mean: StdDev:
---
Hi Tudor,
On 03/22/2013 05:19 PM, Tudor Popescu wrote:
Hello everyone,
I created a qdec.table.dat for my design (a simple group analysis,
with gender as categorical factor and age as continuous factor), and
created a gender.levels file containing the values that are found in
I think the right way to do it is to use the symmetric template
(fsaverage_sym) as the target (instead of fsaverage). You will need to
run the symmetric registration. See
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi (if you have 5.2, you do
not need to download anything). You can map
Hello!
I am running qdec group analysis on my patient data and have one very
important question. I am studying the differences between two Epilepsy
subtypes. Each one of my patients has a hemisphere of onset, either Left or
Right, that I would like to use in looking for differences between
Hello!
I am running qdec group analysis on my patient data and have one very
important question. I am studying the differences between two Epilepsy
subtypes. Each one of my patients has a hemisphere of onset, either Left or
Right, that I would like to use in looking for differences between
Hi list,
I'm performing cortical thickness on three group of subject. I have also three
covariates (age, gender and educational level).
I'm doing:
1-built a .fsgd file2-mris_preproc3-mri_surf2surf4-mri_glmfit5-Bonferroni
correction
Are those processes correct?
Alternatively should I use qdec
That is correct (though you might not want to use Bonferroni as it is a
little harsh). QDEC will do the same thing. It provides a GUI but is
less flexible.
doug
On 03/05/2013 07:59 AM, std...@virgilio.it wrote:
Hi list,
I'm performing cortical thickness on three group of subject. I have
Thank you Doug!
This is a great suggestion and will prevent me from getting lost in the
different analyses. And it will also offer the opportunity to analyze
subjects from the two different cohorts together without coping the data
in one SUBJECTS_DIR.
Thanks again!
Best regards, Katharina
Hi chikku. Yes all steps are necessary (see the description on the wiki).
First all time points need to be processed cross sectionally.
Best Martin
Varghese Chikku chik...@tcd.ie wrote:
Martin,
Forgive my ignorance and sorry to pester you. From what you said in
the
mail,
*The base is like an
Hi Katharina, is there really a problem with the output going into the
SUBJECTS_DIR? If so, you can create a separate SUBJECTS_DIR for each
project. Inside of each SUBJECTS_DIR you can then create a symbolic link
back to the original SUBJECTS_DIR, linking only the subjects you want in
that
Dear FreeSurfer users,
we started to analyze structural MRI data from two large cohorts (one
with over 2100 and the other with over 1100 subjects).
Preprocessing is completely done for all datasets and I've worked myself
through this Qdec tutorial
Dear all,
I am bit confused with the Qdec process.
I finished recon all for 2 time points and want to create
longitudinal data.From FS tutorial I learned to create
within-subject templates for processing,which is running now with
recon-all -base templateID -tp tp1id -tp tp2id ... -all.
Hi Chikku,
the -qcache command is for cross sectional processing. It is not done in
the base and does not need to be done there.
The base is like an additional time point so it does run from the start
and even contains some extra steps. 12hrs are not unlikely.
You will need to also run the
Hi Sophie, can you cut and paste the actual command line that you are
using? I don't know what all the symbols mean.
doug
On 02/04/2013 08:15 AM, Sophie Maingault wrote:
Hello everyone !
I want to use qdec so I tried to smooth the subjects with the
following command: recon-all -s t0001 …
Objet : Re: [Freesurfer] qdec and file -qcache
Hi Sophie, can you cut and paste the actual command line that you are
using? I don't know what all the symbols mean.
doug
On 02/04/2013 08:15 AM, Sophie Maingault wrote:
Hello everyone !
I want to use qdec so I tried to smooth the subjects
I never received a reply, so I am reposting my message below. Any help
would be greatly appreciated.
Thanks in advance,
Crystal
On 2/4/13 10:35 AM, Franklin, Crystal G frankl...@uthscsa.edu wrote:
So I ran mri_surf2vol --help and I am still a little confused on what to
run. Where do I
something like
mri_surf2vol --surfval sig.mgh --hemi lh --identity fsaverage --o
sig.lh.vol.nii.gz
doug
On 02/06/2013 09:50 AM, Franklin, Crystal G wrote:
I never received a reply, so I am reposting my message below. Any help
would be greatly appreciated.
Thanks in advance,
Crystal
On
Hello everyone !
I want to use qdec so I tried to smooth the subjects with the following
command: recon-all -s t0001 . t0742 -qcache (. = all my subjects !). The
tutorial said that it takes about an hour but immediately a file was created
: -qcache (2.95 Ko). Is it normal ? Does the process
So I ran mri_surf2vol --help and I am still a little confused on what to
run. Where do I actually give the sig.mgh file? All the options seem to
ask for an individual subjects file.
Thanks,
Crystal
On 2/1/13 5:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
You can run it with --help
Freesurfer,
I ran a group comparison using qdec and got my results showing the differences
in the thickness between the groups. I want to take these results I see in the
viewer and convert them to nifti format so I can use them in another software
called MANGO. Which files do I need to
You can run it with --help to get more info, let me know if you have
questions after that
On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
Which options should I use when running mri_surf2vol?
Crystal
On 2/1/13 1:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
QDEC will create an
You have either too many effects that you are trying to fit or you don't
have enough subjects. Decrease one or increase the other!
doug
On 01/28/2013 01:00 PM, Pablo Emanuel wrote:
Hi,
My name is Pablo. I am using the freesurfer in my analyses, but when I
try use the QDEC to statistical
Hi,
I am considering using qdec, however due to our large dataset (and
different individuals having been in charge at different times) I just
realized that the folders fsaverage etc are missing. As these are
necessary for the qdec use, is there anything else I can do? Eg a
command line to
Hi Catherine, fsaverage is part of the FS distribution. You can just:
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage .
This will create a symbolic link to fsaverage in your $SUBJECTS_DIR
doug
On 01/22/2013 09:17 AM, Catherine Bois wrote:
Hi,
I am considering using qdec, however due
Maria,
In qdec there is not a built-in mechanism to restrict analysis to a
particular region. By design it runs a whole-cortex analysis, masking
just the medial (non-cortical) region, and then i suppose if your lucky
(if your ROI is significant compared to everything else) your region will
Hi Maria, you can do it with the commandline tools (mri_glmfit) by
specifying --mask or --label. This is a common thing to do, but you will
need to run simulations for multiple comparisons correction.
doug
On 01/04/2013 06:35 AM, Nick Schmansky wrote:
Maria,
In qdec there is not a
Dear Freesurfer users,
I have a question regarding qdec and I would like your help. When
conducting qdec analyses, is it possible to restrict the analyses to
specific brain regions? I would like to limit my qdec analyses to brain
regions typically associated with social cognition and have
Hanganu al.hang...@yahoo.ca
To: Martin Reuter mreu...@nmr.mgh.harvard.edu
Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu
Sent: Friday, November 09, 2012 9:47 PM
Subject: Re: [Freesurfer] Qdec - longitudinal. File missing
Hello Martin, thanks for your answer,
I used the --qcache. The cmd
...@nmr.mgh.harvard.edu
Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu
Sent: Friday, November 09, 2012 9:47 PM
Subject: Re: [Freesurfer] Qdec - longitudinal. File missing
Hello Martin, thanks for your answer,
I used the --qcache. The cmd was:
long_mris_slopes --qdec qdecfile --meas thickness
, November 09, 2012 9:47 PM
Subject: Re: [Freesurfer] Qdec - longitudinal. File missing
Hello Martin, thanks for your answer,
I used the --qcache. The cmd was:
long_mris_slopes --qdec qdecfile --meas thickness --hemi
lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time
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:
Hi Alex,
check the bases of other subjects. Are there any fwhmfsaverage
files?
Did you run with the --qcache flag? Then these should have been created.
Maybe you passed a specific fwhm value different from 10?
Best, Martin
On Fri, 2012-11-09 at 17:13 -0500, Alex Hanganu wrote:
Dear
Hello Martin, thanks for your answer,
I used the --qcache. The cmd was:
long_mris_slopes --qdec qdecfile --meas thickness --hemi lh --do-avg
--do-rate --do-pc1 --do-spc --do-stack --do-label --time months --fwhm
10 --qcache fsaverage --sd SUBJECTS_DIR
All the bases subjects have the specific
Hi Darren, yes, you'll need to put an FSGD file together. This design
has two discrete factors, one with two levels and one with three. It's
the three level that breaks QDEC.
doug
On 9/23/12 12:34 AM, Darren Gitelman wrote:
Dear List
I'm wondering about the proper way to set up an
Dear List
I'm wondering about the proper way to set up an analysis that includes site
as a regressor, and whether this is possible in qdec?
My qdec.table.dat file looks like this.
fsidgroup site
1 grp1 1
2 grp2 2
3 grp2 2
4 grp1 3
and so on
Hi Doug,
I just wanted to double check on what you mean. I want to run statistical
models without the interaction term. When I ran a test using DOSS and
co-varying for sex, age, and ICV, I chose two discrete factors (study,
sex), 1 covariate (age), and 1 nuisance factor (ICV). The results I got
Hi Shannon, there is not a way in QDEC or with an FSGD file. You'll have
to create a design matrix and feed that into mri_glmfit with the --X
option. Let me know if you need any more assistance.
doug
On 9/10/12 5:43 PM, Shannon Kogachi wrote:
Hi Doug,
I just wanted to double check on what
I am trying to use the generate stats data tables feature in qdec but am
getting the error message below. So based on the error message I know that
the trouble subject is SZ0020 and I looked in his file and found the
attached aseg.stats file, which looks okay. I reven tried rerunning the
segstats
Hi,
I was wondering if there is a way to run statistical tests, such as a
2-way ANCOVA, on QDEC but without the interaction effect. I ran a 2-way
ANCOVA for thickness measures for a longitudinal study, and no interaction
effect was found. Therefore, I would like to run the same test but without
Hello,
I went on the FS course in Amsterdam recently. I have run a QDEC analysis to
see whether cortical thickness differs between my two groups. I have two
questions:
1. I put in the lh_bankssts_thickness as my continuous variable. The display
outputs results for whether average thickness
Hi Clare,
On 08/10/2012 06:19 AM, Gibbard, Clare wrote:
Hello,
I went on the FS course in Amsterdam recently. I have run a QDEC
analysis to see whether cortical thickness differs between my two
groups. I have two questions:
1. I put in the lh_bankssts_thickness as my continuous
Hi Carolina, the FWHM is the full-width/half-maximum and indicates how
much smoothing you have. This is surface-based smoothing, not volume
based, and it can be difficult to compare to volume based smoothing as
is done in fMRI. The surface-based smoothing can be larger because you
don't have
Does
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
exist and do you have read permission?
doug
On 07/10/2012 09:20 AM, Natalia h wrote:
Dear expert,
I got an error while clicking the Monte Carlo simulation in qdec.
I am using Mac 10.6 and qdec
Dear list,
Sorry to repost it again, but i had rechecked it and found that all the
directories have no permission problems, but qdec could not load this CSD
file. Not sure why it is like this.
Thank you for the help again!
natalia
On Tue, Jul 10, 2012 at 3:20 PM, Natalia h
Carolina,
It means its smoothing on the surface with a kernel of 10mm full-width
half-max. Smoothing on the surface can generally be larger than in a
volume. See these slides for a description of the difference:
http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt
you can
Dear expert,
I got an error while clicking the Monte Carlo simulation in qdec.
I am using Mac 10.6 and qdec version 1.4, freesufer 5.1
Have no clue why it always gives this error in the terminal:
mri_surfcluster --in
Hello,
In the qdec analysis the default smoothing factor is 10. What does it mean? For other technics such as fMRI we generally use a lower smoothing factor (~3 or lower). What would happen if I low down the FWHM?
Thank you, Carolina
___
Freesurfer
Hi.
I would like to test the effect of a covariate that interact with a factor.
Eg. I have group (XX and XY) as fixed factors, and a ROI thickness (L Fusiform)
as covariate.
Now I would like to calculate the correlation LFusiform for XX - correlation
LFusiform for XY.
Is this possible by
Yes, you just need to set up qdec with your two groups and one
covariate. After you run the analysis, one of the statements should be
something like Does the slope differ between groups XX and XY .
doug
On 7/4/12 10:24 AM, Emilia Lentini wrote:
Hi.
I would like to test the effect of a
Hello FreeSurfers,
I have a similar problem as described in an old thread
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12357.html)
- qdec doesn't read my factor.levels properly.
I have checked the files with gedit and can't see any control
characters, which might have caused the
Anne,
It looks like the diagnosis.levels file has 'MApsychosis' as a level but
the error message says 'Psychosis', so they would need to match.
Nick
On Tue, 2012-07-03 at 15:51 +0200, Anne Uhlmann wrote:
Hello FreeSurfers,
I have a similar problem as described in an old thread
Freesurfers-
When running analysis in qdec is it possible to use each individual
subjects brain volume (white matter + gray matter) as a covariate? If so,
what would be the easiest way to go about getting this information.
Best-
Michael
--
Michael D. Kruepke
PhD - University of Illinois at
I got an error beginning with this.
Thanks for any help
Error in analyze: command failed: mri_glmfit --y
/mypath/qdec/LH_insula_thick/y.mgh --fsgd
**
Electronic Mail is not secure, may not be read every day, and should not be
used for
Hi everyone,
I got the error I just mentioned. Terminal window says no contrasts specified.
I am trying to use timepoint (1-4) as a discrete factor to look at thickness
across time. I guess I will have to resort to longitudinal processing?
Thanks for the help
-Anson
Hi,
I am in the testing process of Freesurfer on a 64-bit Ubuntu installed
personal computer.
However when I run the qdec command as suggested in the testing stages I
receive the following error.
qdec.bin: error while loading shared libraries: libXss.so.1: cannot open
shared object file: No
Hi Jenny, Martin will be the best person to answer your question.
Unfortunately, he is in China now. I think he's back next week.
doug
On 06/20/2012 01:37 AM, Jenny Liu wrote:
Hello,
I am attempting to use the Qdec Analysis for longitudinal data.
Specifically, each subject has two
Freesurfers-
For pre-smoothing subject surfaces for qdec using:
recon-all -s subjid -qcache
Is it necessary to have all the variations of smoothing done (ie - fwhm
0,5,10,15,20,25) or is it possible to run with only a subsection of these?
Best-
Michael
--
Michael D. Kruepke
PhD - University
Perfect that should make things a bit easier on me, also according to this
post
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12406.html
it is not possible to run multiple subjects with this set up (recon-all -s
(subjectid) -qcache -fwhm 10, however this was from 2009, so not
HI
I believe that recon-all -s subjid -qcache
will pre-cache smoothing from 0 through 25 fwhm. You can howevere select
a small subjection of this by issuing recon-all
-s subjid -qcache -fwhm desired smoothing.
-measure surfmeas can follow -qcache, where surfmeas is one of:
thickness,
curv,
nope, can't run multiple subjects
On 06/20/2012 01:43 PM, mdkrue...@uwalumni.com wrote:
Perfect that should make things a bit easier on me, also according to
this post
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12406.html
it is not possible to run multiple subjects with
Message -
From: mdkrue...@uwalumni.com
To: Douglas N Greve gr...@nmr.mgh.harvard.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, June 20, 2012 1:43:28 PM
Subject: Re: [Freesurfer] qdec analysis sequence
Perfect that should make things a bit easier on me, also according
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, June 20, 2012 1:43:28 PM
Subject: Re: [Freesurfer] qdec analysis sequence
Perfect that should make things a bit easier on me, also according to this
post
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12406.html
@nmr.mgh.harvard.edu
Sent: Wednesday, June 20, 2012 1:43:28 PM
Subject: Re: [Freesurfer] qdec analysis sequence
Perfect that should make things a bit easier on me, also according
to this post
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12406.html
thickness
-fwhm 10; done
hope this helps
kk
- Original Message -
From: mdkrue...@uwalumni.com
To: Kushal Kapse kka...@mail.med.upenn.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, June 20, 2012 2:57:30 PM
Subject: Re: [Freesurfer] qdec analysis sequence
Kushal
Hello
I am using the Qdec Analysis.The long and base directories are created
already, and I am at the first stage of post-processing.
For the long_mri_slopes command, there seems to be some difficulty for Qdec
to find the appropriate folder.
As background, in my qdec table, I have the fsid and
501 - 600 of 984 matches
Mail list logo
