Did you create the "my-glm" folder? If so, what was your command? Can
you send a link to the exact wiki page?
On 11/6/19 2:49 AM, 王如雪 wrote:
>
> External Email - Use Caution
>
>
> Hi Sir/Madam:
>
> I got an error when executing the new version "mri_glmfit-sim"
> correction for multiple c
External Email - Use Caution
Yes, the file ($SUBJECTS_DIR/fsaverage/surf/rh.white) exists and I can open
it with freeview. The mri_surfcluster worked well in the past. However, I
recently downloaded the fspalm and the mri_surfcluster attached for the
fspalm. I do not know if it cou
The "locale" error is probably not a problem. Does
/media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white exist? What operating
system are you using?
On 4/24/2019 6:41 AM, Javier Navas wrote:
External Email - Use Caution
Dear freesurfer experts,
I want to create an annot from the out
It turns out that setting --min to 0 causes a problem. Try setting it to
something close to 0, eg 1e-6
On 03/09/2017 03:10 AM, Ladan Shahshahani wrote:
> Hi,
>
> Following previous discussions on the mailing list, I am using
> mri_surfcluster to extract MNI (or Talairach) coordinates of a label
use this program
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr
On 7/6/16 9:22 AM, tom parker wrote:
Dear Freesurfers,
I ran a comparison between different groups using mri_glmfit.
Now I would like to correct the results in sig.mgh by multiple
comparisons using FDR.
Dear Doug,
thank you for the clarification.
So to make sure, do you use this group_avg_area for each vertex also for
building null distribution of maximal cluster size? The area values in .csd
files are values of group_avg_area of cluster with maximal group_avg_area in
each simulation step?
Loo
It is quite confusing and took us some time to understand ourselves.
When we create an average subject like fsaverage, we have to create a
triangular mesh just like we do with any subject. This means that we
have to assign an xyz to each coordinate. When trying to represent a
group, this is not
Dear Doug,
thank you very much for the support.
I am quite confused by this info about correcting of area of fsaverage
clusters. Could you please clarify to me the following:
How exactly the values of lh.area, lh.white.avg.area.mgh of fsaverage were
computed?
How the cluster area inside mri_s
On 04/11/2016 04:46 PM, Antonin Skoch wrote:
> Dear FreeSurfer experts,
>
> I am using mri_surfcluster to compare results from PALM and FreeSurfer
> cluster extent inference.
>
> I came across several issues in mri_surfcluster I cannot cope with.
>
> 1.
> I observed that --mask option in mri_sur
Thanks! The F.mgh works well, and it also increases precision as
converting from the exponent itself is less precise.
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
On 11/9/15, 10:57 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas Greve" wrote
There should be a t.mgh file there (or maybe F.mgh). You can just pull
the value out of the vertex out of that.
On 11/9/15 6:46 PM, Yang, Daniel wrote:
> Hi Doug,
>
> Got it! Sorry that I keep forgetting this. So it’s an exponent statistic.
>
> The reviewers asked for a statistic and df. I think
Hi Doug,
Got it! Sorry that I keep forgetting this. So it’s an exponent statistic.
The reviewers asked for a statistic and df. I think I can convert it to a
Z-statistic so it’s more “conventional”.
I also noticed that qdec provides a df when I set up the model. It is
valid to use that df to deri
On 11/09/2015 10:51 AM, Yang, Daniel wrote:
> Dear FreeSurfer experts,
>
> In the output mri_surfcluster (e.g.,
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary),
>
> what is the statistics behind the Max?
>
> Is it either t-statistic (if only 1 line of contra
On 02/26/2015 01:46 PM, Janosch Linkersdörfer wrote:
> Hi all,
>
> I experimented with the different flags for mri_surfcluster and have 2 issues
> that I don't understand, it would be great if somebody could enlighten me:
>
> 1) When I set --thmin (or --fdr) with --thsign abs, I get what I would
Works fine! Thanks alot!
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this
try now
On 12/22/2014 04:59 PM, Philipp Heimbeck wrote:
> Dear Doug,
>
> I face the same problem (
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36985.html ),
> but the current mri_surfcluster-version with the "--centroid" capability
> can't be found at
> ftp://surfer.nmr.mgh.ha
Dear Doug,
I face the same problem (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36985.html ),
but the current mri_surfcluster-version with the "--centroid" capability
can't be found at
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster
any more.
It cannot read the .w file as input. There is no need to use .w files
(despite what it might say).
On 12/03/2014 12:22 AM, wangzhiwei3233 wrote:
> *The command I used is* /mri_surfcluster --in sig.w --subject
> fsaverage --hemi lh --annot aparc --sign pos --minarea 30 --sum
> area100.pos.cluste
The command I used is mri_surfcluster --in sig.w --subject fsaverage --hemi lh
--annot aparc --sign pos --minarea 30 --sum area100.pos.cluster.summary --o
area100.pos.cluster.w --thmin 1.3
Teriminal output is
thsign = pos, id = 1
version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 g
That is the right command line. What is the terminal output?
On 12/2/14 8:01 AM, wangzhiwei3233 wrote:
Hi Freesurfer experts,
I just want to try cluster level threshold by cluster size, but
not by mc simulation.
So I tried the command like : mri_surfcluster --in sig.nii.gz
--subject f
There is not an explicit program to do this. You can re-run
mri_surfcluster with a lower threshold and mask to the big cluster to
force all the results to be within that cluster.
doug
On 11/06/2014 04:29 AM, Sophie Maingault wrote:
> Dear FS experst,
>
> I used the command mri_surfcluster. For
It is possible but not easy. You'll have to start almost from scratch.
Motion correct your time series. Then run mri_vol2surf to sample the
time series on the surface (use nifti output). Smooth on the surface.
Run FEAT using this as the input. Turn off spatial smoothing and
prewhitening and ma
Dear Doug,
thanks for your helpful comments according to the reading out fMRI cluster peak
vertices!
Actually, I'm able now to read out cluster peak vertices (see bottom). I
applied the mri_surfcluster command for resampled and surface smoothed Feat
stats on smoothwm surface with projfrac 0.5
mri_surfcluster will probably do what you need though there are some
caveats:
- You will not be able to get the results corrected for multiple comparisons
- If you are looking at the z-score, then this will not be as powerful
as it could be because you applied no smoothing (unless you applied
Try this version (for linux)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster
On 07/16/2014 09:55 AM, Jockwitz, Christiane wrote:
>
> Dear experts,
>
> in one of the earlier posts there was a discussion about
> mri_surfcluster and the –centroid option.
>
>
>
> I
there are lots of output. You can create an annotation (--oannot),
labels (--olab), copy the input and set nonclusters to 0 (--o), map of
corrected voxel-wise significances (--vwsig), or map of cluster-wise
significances (--cwsig). Of course you can get a simple table of the
output too (--sum
Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR
threshold from tksurfer and will use that as my -thmin.
One last thing, how would I view the results of mri_surfclluster in
tksurfer? Would I load the ocn.mgh file? If so, I can't seem to find it.
On Thu, Jan 23, 2014 at 2:02 PM
just add "--subject fsaverage_sym"
btw, that command does not perform FDR
doug
On 01/23/2014 01:41 PM, krista kelly wrote:
> Hi all,
>
> I have obtained laterality indices using xhemi analyses and would like
> to use FDR instead of the mri_glmfit-sim suggested in the xhemi
> instructions. I kn
Oops - my bad, on this last round I mixed one filename dash with a dot.
Works now - so (just to remind myself) the new feature is to use
mri_surf2surf to convert from w to mgz before running mri_surfcluster.
Thanks Doug! :) -Tommi
> It looks like that file does not exist:
> ls /autofs/cluster/scr
It looks like that file does not exist:
ls /autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz
ls: /autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz: No such file
or directory
r...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> I am still receiving a similar error. mri_surf2surf inputes the w fi
Hi Doug,
I am still receiving a similar error. mri_surf2surf inputes the w file
and writes out a mgz file and exits apparently ok. However, mri_volcluster
still exits with
"could not read test-lh.mgz as type"
Details:
mri_surf2surf \
--srcsubject Wyss_000 \
--trgsubject Wyss_000 \
--hemi lh \
-
Hi Tommi, convert the w file to an mgz with mri_surf2surf. Specify the
source format with --sfmt w
doug
r...@nmr.mgh.harvard.edu wrote:
> Hi Doug and Matti,
>
> I am using mri_surfcluster to threshold and extract ROIs from MEG/EEG
> source analysis data. The same code used to work fine in Jan 200
Yolanda, don't run mris_anatomical_stats on fsaverage. You should map
the label to each individual with mri_label2label, then use
mris_anatomical_stats. Sorry for not being clearer eariler.
doug
Yolanda Vives wrote:
> Hi Bruce,
>
> That's the error:
>
> limiting computations to label
> fsaverag
Hi Bruce,
That's the error:
limiting computations to label
fsaverage/label/grouplabel_concro_rh-0001.label.
reading volume
/nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz...
ERROR: cannot find
/nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz
mris_anatomi
Hi Yolanda,
you need to email us the screen output with the error so we can diagnose
it.
cheers
Bruce
On Thu, 28 Jul 2011, Yolanda Vives wrote:
> Thank you Douglas for your suggestions!
>
> If I use mris_anatomical_stats, would I perform the following procedure?
>
> - To run "mri_label2label"
Thank you Douglas for your suggestions!
If I use mris_anatomical_stats, would I perform the following procedure?
- To run "mri_label2label" to all the subjects of my comparison
- To run mris_anatomical_stats. I would obtain the volume of the labels in
each subject
- Mean volume of all the subject
Hi Yolanda, don't use thmax (it will exclude everything with a sig>7 --
not what you want I assume). That command otherwise looks right, but it
won't correct for multiple comparisons. You can run
mris_anatomical_stats on the output label to give you the stats you want.
doug
Yolanda Vives wrot
Hi Chris, mri_surfcluster should output coordinates in "Talairach" space
(The newer 5.1 version uses MNI305 space). Internally, we always use
MNI305 space. To report "Talairach" coordinates, we then apply a
transform (http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html) to give
particular values
Hi Elisa, how was the slt file created? Can you send it and the summary
file to me (don't send to the group).
doug
Elisa Golfinopoulos wrote:
> Hi all,
>
> I wanted to follow-up on my previous e-mail, which may have been a bit
> too vague.
>
> I am using the command:
>
> mri_surfcluster --in ./o
Hi,
I apologize for spamming the list, but for future reference this problem was
resolved when I opened the color table and annotation file on the average
brain in tksurfer and then exported the annotation file with a new name.
Using the new annotation file with mri_surfcluster, the color table wa
Hi all,
I wanted to follow-up on my previous e-mail, which may have been a bit too
vague.
I am using the command:
mri_surfcluster --in ./osgm/sig.mgh --subject average --surf inflated
--annot slt --sign abs --csd ../csd/mc-z.abs-osgm.csd --sum
./osgm/summaryfile.txt --o ./osgm/cluster_peaks.o -
Don't use --thmax.
doug
Fernanda Palhano wrote:
> Hello,
>
> I'm running a cortical thickness analysis using Qdec. When I do Find
> Clusters and Go to Max, I obtain 9 clusters (min threshold 3, max
> threshold 5):
>
> Generating cluste
The value of the vertcies in the OCN is the the cluster number, not a
significance. If you are trying to set all non-clusters to 0 (and keep
the image the same otherwise), then use the output from the --o flag.
doug
Mandy Nagy wrote:
> Hi all,
>
> We ran mri_surfcluster on our group data (we di
Kelly,
I believe they are in Talairach space. Information on how to get them in
MNI space is located here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10038.html
Allison
--
On Fri, 19 Mar 2010, Kelly Silva wrote:
Hello,
I would like to know if the output coordinates
If you want p-values for the clusters, then you need to run a simulation
(mri_glmfit-sim). I think QDEC creates a script to do it.
doug
Rosa Steimke wrote:
> dear freesurfer experts. i have another problem in generating output useing
> mr_surfcluster command.
>
> i was wondering how to generat
by default it uses the 1st time point. If you want to change it, spec
--frame.
d
Yigal Agam wrote:
Hi,
When I run mri_surfcluster on a surface with 12 timepoints, how do I
know when each of the reported clusters occurred?
Thanks,
Yigal
___
Freesu
Looks like it's working again!
Thanks for fixing it, Doug, and for pointing out that it was fixed, Pratap!
-Lauren
On Fri, Jan 9, 2009 at 3:54 PM, Kara Dyckman wrote:
> Thanks Pratap,
> I'll try it again.
> Kara
>
> Pratap Kunwar wrote:
>>
>> Kara and Lauren,
>>
>> I think Doug has fixed this pr
Thanks Pratap,
I'll try it again.
Kara
Pratap Kunwar wrote:
Kara and Lauren,
I think Doug has fixed this problem. i had similar problem but it is
working now.
pratap
Hi Lauren (and Doug),
I'm having the same issue. I ran montecarlo simulations on Friday and
then
tried to use the re
Kara and Lauren,
I think Doug has fixed this problem. i had similar problem but it is
working now.
pratap
> Hi Lauren (and Doug),
>> I'm having the same issue. I ran montecarlo simulations on Friday and
>> then
>> tried to use the results in mri_surfcluster. It ran, but I also got the
>> same
Hi Lauren (and Doug),
I'm having the same issue. I ran montecarlo simulations on Friday and then
tried to use the results in mri_surfcluster. It ran, but I also got the
same CWP values (-0.1) for each cluster in the sum file.
Also, when it runs, it gives a CEPHES ERROR. Here is what I get
Yep. That would explain it. Thanks!
-
Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota
Doug Greve wrote:
The values in the mgh file should be -log10(abs(CWP)). Would that
explain the discrepancy?
James N Porter wrote:
Hello-
When I
The values in the mgh file should be -log10(abs(CWP)). Would that
explain the discrepancy?
James N Porter wrote:
Hello-
When I look at the CWP results of mri_surfcluster in the
sig.cluster.sum versus the resultant sig.cluster.mgh, the results are
different. Specifically, all clusters negati
You need to tell it the subject with --subject
On Tue, 10 Apr 2007, Kirk, Gregory wrote:
running freesurfer-v3.0
SUBJECTS_DIR=/home/gkirk/freesurfer-v3.0/freesurfer/subjects/sickle_cell
glm is at /home/gkirk/freesurfer-v3.0/freesurfer/subjects/sickle_cell
and contains
age.mat lh.sickle.g
That's very wierd. Do you want to try the latest version and see if you
get the same thing? I've copied it to:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster
doug
[EMAIL PROTECTED] wrote:
Hi,
An oddity re: command syntax for mri_surfcluster.
The --ocp flag wr
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