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
Hi Sir/Madam:
I got an error when executing the new version "mri_glmfit-sim" correction for
multiple comparisons with permutation at the group level according to
FsFastTutorialV6.0.
This was the command I used: "mri_glmfit-sim --glmdir my-glm --p
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
External Email - Use Caution
Dear freesurfer experts,
I want to create an annot from the output of PALM, the vertexwise file
corrected by TFCE-FWEp. The values of this files are in 'p-values'.
However, the mri_surfcluster has some problems: it could not recognize the
fsaverage an
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
Hi,
Following previous discussions on the mailing list, I am using
mri_surfcluster to extract MNI (or Talairach) coordinates of a label using:
mri_surfcluster --in $SUBJECTS_DIR/fsaverage/surf/lh.area --clabel
lh.G_cingulate-Isthmus.label --sum ~/Desktop/pract3 --centroid --thmin 0
--hemi lh --su
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 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. I tried using tksurfer but it doesn't work so well on my
computer and I read that freeview does not allow to do that yet.
I'm now t
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
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_surfcluster does not prevent cluster to
growing outside the mas
Hi list,I'd like to perform mri_surfcluster on a group to eliminate cluster < 5
voxels from sig.nii.gz after FDR correction.I'm running mri_surfcluster --in
sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum summaryfile --ocn
ocnid
but --subject ... must be included.
How should do I d
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
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 contrast) or F-statistic (if two
lines of contrast), but not Z-sta
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
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 expect,
i.e., only clusters with a minimum vertex-wise p-value
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
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
fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum
area50.pos.cluster.summary --o area50.pos.
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
Dear FS experst,
I used the command mri_surfcluster. For one analysis, I obtained 6 clusters
with one huge of 473 cm2 which corresponds to several "sub-clusters" because it
was expanded through a large part of the cortex (covering several anatomical
regions). Is there a way to separate one appa
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
Dear Freesurfers,
I’m struggling with finding a way of getting a table of the cluster maxima of
FEAT functional data registered to (reg-feat2anat) and resampled to (feat2surf)
reconstructed surfaces. I want to extract cluster maxima for single subjects
but preferentially NOT in fsaverage group
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
Dear experts,
in one of the earlier posts there was a discussion about mri_surfcluster and
the -centroid option.
I'am using Freesurfer 5.1 (Linux) so I don't have the --centroid option
implemented. Is there a possibility to use it anyway (via a script)???
Thank you advance.
Best.
Christiane
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
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 know to get the FDR threshold from tksurfer, but I want to restrict the
clusters to a certain cluster size. Based on a previous thread (
ht
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
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 2009, but now
I am running into unexpected errors. I wonder if something happened along
the way of FreeSurfer and/or MNE stream upgrades and now mn
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
Dear freesurfers,
I would like to obtain the cluster size (in mm3) and coordinates of the
maxima of a cortical volume comparison using mri_surfcluster.
mri_surfcluster --in
$PATH/control_cronic_dones_right_volume/rh-Diff-control-cronic-Intercept-volume/sig.mgh
--hemi rh --subject fsaverage --thmi
Dear Freesurfers,
I know that Qdec outputs coordinates in a "Freesurfer specific space", rather
than in Talairach space, per this old thread
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-November/008878.html
However, I found that mri_surfcluster (Freesurfer v5.0) in its summary out
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 -
Hi,
I am trying to use an annotation file that was created from a parcellation
scheme developed in my lab with mri_surfcluster. However, it's unclear to
me how I can set the corresponding color table for this annotation file
either locally or globally. mri_surfcluster doesn't seem to have a --cta
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
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 cluster stats using min threshold of 3...
Found 9 clusters
Contrast: '
Hi all,
We're trying to create labels from a group level sig.mgh file. However,
after the labels are created and an annotation file/color table is made, we
try to view the sig.mgh file and the annotation file in tksurfer, but they
don't extactly overlap, even though they are both configured to the
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
Hi all,
We ran mri_surfcluster on our group data (we didn't do montecarlo
simulations), so we used our .mgh file. We used the -ocn flag to make an
output file so we could look at the specific clusters. When we looked at
the data of the ocn file using tksurfer, the most significant cluster
wasn't
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
Hello,
I would like to know if the output coordinates from the "mri_surfcluster"
command is on the MNI space or on the Talairach.
Thanks in advance.
Best, Kelly
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
dear freesurfer experts. i have another problem in generating output useing
mr_surfcluster command.
i was wondering how to generate an output with the significant clusters from my
qdec analysis i learnd that i have to use the mri_surfcluster command and use
the sig.mgh file from my qdec. howev
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
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
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free
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
Hi Everyone,
I'm having a bit of a problem with mri_surfcluster. I ran it alright
last week on the right hemisphere, and now am unable to get it to run
through with the left.
First I'm running mri_glmfit to get .csd files with 1 iterations
(split into 10 runs to speed things up), and then I'm r
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
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 negatively correlated with my independent
variable display a value in tksurfer of -1+CWP, and clusters that are
positivel
hi,
i am having a strange problem with mri_surfcluster.
i give it the following command line:
mri_surfcluster --in
/disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh
--subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6
--sum
/
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
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.glmdir mris_preproc.surface.lh.log
rh.sickle.thickness.10.mgh
FSGDstudy.txt lh.sickle.thicknes
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
Hi,
An oddity re: command syntax for mri_surfcluster.
The --ocp flag writes the file sig.cluster.mgh. However, when I also
include the --cwsig flag the file sig.cluster.mgh is not generated.
Currently I run the command twice, once to generate the sig.cluster.mgh,
and once to generate the cluster
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