Dear professor,
I'm a postgraduate of neurosurgery. Recently, I'm interested in cortical
parcellation and subcortical segmentation using freesurfer. In my study, all
patients have brain tumors. So I begin to wonder if "recon-all" can still be
applied to these subjects, or in other word, is i
Dear Douglas N Greve, FreeSurfer Team,
Thank you for your clear explanation.
Best Wishes,
Han
On Wed, Jun 1, 2016 at 3:55 PM, Douglas N Greve
wrote:
> Column 5 is completely redundant with column 1 (and highly colinear with
> column 3). Column 6 is nearly identical to column 2 (and highly col
Column 5 is completely redundant with column 1 (and highly colinear with
column 3). Column 6 is nearly identical to column 2 (and highly colinear
with column 4). This is causing your matrix to be ill-conditioned
On 05/26/2016 02:12 PM, Hanbyul Cho wrote:
> Dear Douglas N Greve,
>
>
> I sent agai
Dear FreeSurfer Team,
I wonder you could not read an previous attached file.
Thank you,
Han
On Thu, May 26, 2016 at 12:12 PM, Hanbyul Cho
wrote:
> Dear Douglas N Greve,
>
>
> I sent again this design matrix (= Xg.dat) by attached.
>
> Thank you.
>
> Han.
>
> On Thu, May 26, 2016 at 11:59 AM, D
Are you using selxavg-sess or selxavg3-sess. you should be using
selxavg3-sess
On 06/01/2016 03:45 PM, Raney, Talia L. wrote:
> Okay, the thing is that when I remove the no-con flag I get this error
> "ERROR: the design type of this analysis is notask
>selxavg-sess can only be used to analys
This worked! Thanks very much for your help!
On 2016-05-23, at 11:25 AM, Douglas N Greve wrote:
> Try it without the --reshape option in mri_surf2surf
>
> On 05/20/2016 05:51 PM, Kari Parsons wrote:
>> Hi,
>>
>> I'm trying to get some cortical thickness volumes for an ROI that I
>> have
Okay, the thing is that when I remove the no-con flag I get this error "ERROR:
the design type of this analysis is notask
selxavg-sess can only be used to analyse event-related and blocked", which
means I have to change the analysis.info using mkanalysis-sess,correct? Which
flag would I use th
Hi FreeSurfer experts,
I have a question about two specific steps in my fc pipeline. Since my seed is
a single vertex, I convert the seed label to a mask, which I then smooth and
binarize, and then convert to a volume file for fcseed-sess.
1) Is there way to directly convert a label into a co
Don't include the -no-con-ok flag. For resting state, you don't need to
run mkcontrast-sess because a contrast will automatically be created for
you.
On 06/01/2016 02:24 PM, Raney, Talia L. wrote:
> Hi FreeSurfer users,
> I have some resting state data that I preprocessed and conducted first lev
Hi FreeSurfer users,
I have some resting state data that I preprocessed and conducted first level
analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is
createdcomes up because there is no contrast, I'm wondering if it's possible to
conduct functional ROI analyses with the data
Thanks, Anri. So the previous steps seem to have run fine. Are there any
.log files created in the stats/ folder, which is created by trac-all
-stat?
On Wed, 1 Jun 2016, Anri WATANABE wrote:
Hi Anastasia, This is a /scripts/trac-all.log of one subject of the
group.
Thanks,
Anri
*
Ok, sorry:
wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$
mri_glmfit \
> --glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir
ERROR: must specify an input X fil
Sorry about that. I attached the previous conversation below. Yes - I am
interested in applying the monte carlo sim to my own model fit. Doug can you
walk me through the steps I need to get this part done? When you say residuals,
I am assuming that I need to supply a vector file of residuals aft
Please include previous correspondence
On 06/01/2016 11:39 AM, Chung, Yoonho wrote:
>
> Yes - I am interested in applying the monte carlo sim to my own model
> fit. Doug can you walk me through the steps I need to get this part
> done? When you say residuals, I am assuming that I need to supply
Can you send me just the terminal output from mri_glmfit?
On 06/01/2016 12:45 PM, Hao wen wrote:
> Hi, thanks for your reply, here is the output of the terminal in txt
> file, hope to hear from you soon
> Merci
> Hao
>
> *De
Hi, thanks for your reply, here is the output of the terminal in txt file, hope
to hear from you soon
Merci
Hao
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Douglas Greve
Envoyé : mercredi 1 juin 2016 17:06:19
À : freesurfer@nmr.mgh.harvard.edu
Obj
Yes - I am interested in applying the monte carlo sim to my own model fit. Doug
can you walk me through the steps I need to get this part done? When you say
residuals, I am assuming that I need to supply a vector file of residuals after
I fit my model to the smoothed data (eg. using mri_surf2sur
You should first check your func-anat registration with tkregister-sess
On 6/1/16 11:20 AM, Martin Juneja wrote:
Hello FreeSurfer experts,
I am working on resting-state functional connectivity using freesurfer
by following the instructions from:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFast
I would not expect the glm to change much, but the activation might
shift around a little depending upon your new target.
On 6/1/16 11:18 AM, Makaretz, Sara Johanna wrote:
> Thank you! Does this mean that an older glm would have still used fsaverage
> for the "common surf" but then the output is
Hello FreeSurfer experts,
I am working on resting-state functional connectivity using freesurfer by
following the instructions from:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
I made sure that the seed region (for ever subject) I am using is at the
correct pl
Thank you! Does this mean that an older glm would have still used fsaverage for
the "common surf" but then the output is mapped to the target? Outputs from
older glms load no problem on the targets, and look "as expected"
Aka would you expect a major difference in glmfit outputs with old mris_pr
please send the terminal output that includes the error
On 6/1/16 8:10 AM, Hao wen wrote:
Hello, freesurfers:
I am doing group analysis, with two diff groups, so I want to know
that how to create my own Contrast and Design matrix, because that I
know in QDEC and CMline, in the freesurfer wik
1) You don't include sex as a covariate. Include it as a class (ie,
Class Male and Class Female rather than Class Main).
2) You need to include Minutes in your null hypothesis.
3) Include minutes as a covariate as you have done, then create the
proper contrast matrix. The contrast matrix will de
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Hi Bruce,
Thanks for your answer and all your help, I only want to look at cortical
thickness for now.
Best,
Marja
On Wed, Jun 1, 2016 at 11:11 PM, Bruce Fischl
wrote:
> Hi Marja
>
> yes, if you want to compare measures averaged over our predefined ROIs
> that is all you need to do. Note that
Hi Marja
yes, if you want to compare measures averaged over our predefined ROIs that
is all you need to do. Note that for volumes you probably want to include
ICT/eTIV as a regressor
cheers
Bruce
On Wed, 1 Jun 2016, Marja
Caverlé wrote:
Hi guys,
I just wanted to make sure I am underst
Dear list,
We have a question about the set up of the FSGD file.
We have 1 group, 2 continued covariates (age & mintues), 1 discontinued
covariate (sex)
GroupDescriptorFile 1
Title G1V3
Class Main
Variables Age Sex Minutes
Input subject1 Main 30 0 1200
Input subject2 Main 40 1 180
My qu
Hello, freesurfers:
I am doing group analysis, with two diff groups, so I want to know that how to
create my own Contrast and Design matrix, because that I know in QDEC and
CMline, in the freesurfer wiki, You just give the example for the DODS & DOSS,
but it is not so flexible!
I know that we
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