Hi FS experts and users,
May I ask some questions about clusterwise correction for multiple comparisons?
1,In mri_glmfit-sim command, there is a --sim(--sim nulltype nsim threshold
csdbase) option. Choose the voxel/vertex-wise threshhold used to define
clusters. This will be -log10(p), where p is
Hi all,
I try to see the cluster wised result by typing "freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.ocn.annot",but
it feedback some error infomat
Dear Tracula Experts,
after careful checking we still cannot run trac-all -qa or dwri-motion as
the command always returns: could not open bvals but the same file is
flawlessy opened/retrieved in version 5.2.
[cat bvals is fine, trac-all -prep in 5.2. runs fine, trac-all -prep in 5.3
returns coul
Does the error in trac-all -prep with 5.3 occur when dmri_motion is run
or at a different step?
On Thu, 20 Feb 2014, Gerit Pfuhl wrote:
> Dear Tracula Experts,
> after careful checking we still cannot run trac-all -qa or dwri-motion as the
> command always returns: could not
> open bvals but t
Hi all,
I am having an topological defect error while running few of subjects. I have
gone through the freesurfer correcting topological defects wikipage. But I was
trying understand the log file. For an example, I got the following error for
one subject:
Correction of the Topology
Finding tru
Hi FreeSurfers,
I have trouble loading the .dat file into qdec, receiving the following
error message:
Verifying subject data.sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject 'DEM001.freesurfer'
> in
> SUBJECTS_DIR
My SUBJECTS_DIR is set correctly a
yes,
it happens at trac-all -qa after loading the *.nii file (see attachment) or
when run as
dmri_motion --dwi dwi_orig.nii.gz --mat dwi.ecclog --bval dmri/bvals --out
dwi_motion.txt immediately.
On 20 February 2014 17:08, Anastasia Yendiki
wrote:
>
> Does the error in trac-all -prep with 5.3
Dear FreeSurfers,
I have two discrete and binary factors (Dx: patients vs. controls; Sex: female
vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is
a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following
interpretation correct?
Red/yellow: In fem
yes, they are, though you don't need to do the positive and negative
contrasts because the sign is preserved
doug
On 02/20/2014 12:47 AM, charujing123 wrote:
> Hi FS experts and users,
> I am trying to implement independent sample t-test and correlation
> analysis.
> Here is my fsgdf design:
>
That subject appears to be out of synch. It was probably edited but then
not re-run all the way through. Try running
recon-all -s subject -make all
doug
On 02/20/2014 01:43 AM, charujing123 wrote:
> Hi FS experts,
> When I ran the mris_preproc, the left hemisphere completely done well,
> but t
On 02/20/2014 04:33 AM, charujing123 wrote:
> Hi FS experts and users,
> May I ask some questions about clusterwise correction for multiple
> comparisons?
> 1,In mri_glmfit-sim command, there is a --sim(--sim nulltype nsim
> threshold csdbase) option. Choose the voxel/vertex-wise threshhold
> u
Is the error preventing you from visualizing? Otherwise you can ignore
it (it will be fixed in the next version)
doug
On 02/20/2014 06:50 AM, charujing123 wrote:
> Hi all,
> I try to see the cluster wised result by typing "freeview -f
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=./Diff-C
Hi Siddharth, Bruce will have to answer this one. He's on vacation until
next week. Can you repost on monday?
doug
On 02/20/2014 11:21 AM, Ray, Siddharth wrote:
>
> Hi all,
>
> I am having an topological defect error while running few of subjects.
> I have gone through the freesurfer correcting
Can you send the qdec table?
doug
On 02/20/2014 11:45 AM, Miranka Wirth wrote:
> Hi FreeSurfers,
>
> I have trouble loading the .dat file into qdec, receiving the
> following error message:
> Verifying subject data.sh: 1: Syntax error: Bad fd number
> > ERROR: QdecProject::VerifySubjects: Couldn
It is not the dicom file but the rawavg.mgz that is the immediate problem.
As for the subject you sent, it is hard to say what is going wrong. It
looks like there might be a lot of WM pathology. Is that right? That
might be difficult for our intensity normalization. You can try placing
control
Definitely, I will repost this on Monday.
Thanks,
-Siddharth
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Thursday, February 20, 2014 1:46 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
The basic contrast is
(PM-PF)-(CM-CF)
If that is positive, then it will be red, otherwise blue
This opens up a lot of possibilities as to what is driving the
interaction, so it is hard to come up with a sentence like the one you
are trying to state
doug
On 02/20/2014 02:25 PM, Yang, Daniel w
Are you sure that this is an anatomical scan? It looks like it might be a
navigator of some sort as it only has 9 slices, and the direction info in the
file is messed up
Original Data has (0.9375, 0.9375, 11) mm size and (320, 320, 9)
doug
On 02/20/2014 04:37 AM, will brown wrote:
> Hi all,
>
Then it's no surprise that the error doesn't occur in 5.2, because 5.2
doesn't run dmri_motion at all.
When you run dmri_motion on the command line, do you use the same syntax
as the one you're showing below?
On Thu, 20 Feb 2014, Gerit Pfuhl wrote:
yes,
it happens at trac-all -qa after lo
tried adopted version of
dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals --out
output.txt
as well as trac-all -qa -c dmrirc_file with location of bval specified
and trac-all -prep -c, respectively
On 20 February 2014 21:16, Anastasia Yendiki
wrote:
>
> Then it's no surpr
If you upload these files for me, I can check what's going on:
yourDWIs.nii.gz
your.ecclog
your.bvals
You can upload them for me here:
https://gate.nmr.mgh.harvard.edu/filedrop2/
On Thu, 20 Feb 2014, Gerit Pfuhl wrote:
tried adopted version of
dmri_motion --d
Hi again,
When I convert a surface to .gii with mris_convert, it is shifted
compared to the original surface when loaded into freeview (see previous
mail). Does anyone know how to solve this?
Best,
Karen
On 02/18/2014 10:01 AM, Karen Marie Sandø Ambrosen wrote:
> Hi Freesurfer experts,
>
> I a
I think this is due to the fact that there is some geometry information
in our surface format that is probably not present in gii. Ruopeng, can
you verify?
doug
On 02/20/2014 05:11 PM, Karen Marie Sandø Ambrosen wrote:
> Hi again,
>
> When I convert a surface to .gii with mris_convert, it is sh
Hidoug and others,
Thanks doug.
I see.If I want to implement multiple regression, i.e. two EVs(score1 and
score2) explain pial thickness, what contrast I should design for this.
Thanks again.
All the best.
Rujing Zha
2014-02-21
charujing123
发件人：Douglas N Greve
发送时间：2014-02-21 03:39
主题：Re:
Hi doug,
Thanks doug.
I see.
All the best.
Rujing Zha
2014-02-21
charujing123
发件人：Douglas N Greve
发送时间：2014-02-21 03:43
主题：Re: [Freesurfer] questions of clusters defined and sign of the threshold in
simulation
收件人："freesurfer"
抄送：
On 02/20/2014 04:33 AM, charujing123 wrote:
> Hi FS expe
Hi doug,
It isnot.
Thanks.
All the best.
Rujing Zha
2014-02-21
charujing123
发件人：Douglas N Greve
发送时间：2014-02-21 03:45
主题：Re: [Freesurfer] viewing corrected result error
收件人："freesurfer"
抄送：
Is the error preventing you from visualizing? Otherwise you can ignore
it (it will be fixed in th
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