You will need to add --mczsim-dir /path/to/your/tables
Or copy your tables into $FREESURFER/average/mult-comp-cor/fsaverage
On 10/25/2024 1:20 PM, Sujeevini Sujanthan wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I'm encountering an error when attempting to run mri_gl
Yes, all the 7.X versions will give the same answer unless you
explicitly use a new feature
On 3/20/2023 2:45 PM, mariangela asimina wrote:
External Email - Use Caution
I see now this is an issue addressed stable 7.2.0 version of FreeSurfer:
*MailScanner has detected a possible fraud
External Email - Use Caution
I see now this is an issue addressed stable 7.2.0 version of FreeSurfer:
https://secure-web.cisco.com/1_0nM8kQPAwlCZzUFPKYxFeyxAfrBfjVnMbuFBgpiLtOtAz0Rcg2ns0AHK0Z-UuAC0K-jylD0ZM1hP4emJWrKoCvyUwJv4VVaznUFGMKUwg5OuApejYTaxHdKuzNe5HOOGskw2aVkgC0HOeyCPniLzo
alf of Tarumi Takashi
>
> Sent: Thursday, January 20, 2022 7:59 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>
> External Email - Use Caution
>
> Dear Dr. Yendiki,
>
> Thank you so m
line.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Tarumi Takashi
Sent: Thursday, January 20, 2022 7:59 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
External Email - Use Caution
De
External Email - Use Caution
Dear Dr. Yendiki,
Thank you so much for your reply. Yes, the command can run without the
"--1d" flag. But, I thought that the flag is "required for any along-tract
analysis" as stated in your TraculaStatistics instruction and highlighted
in the release
Hi Taka - Does it work when you remove the "--1d" from the command line? I
think that must be an error in the documentation.
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Tarumi Takashi
Sent: Wednesday, January 12, 2022 7:04 PM
To: frees
This happens because the cached p-values were generated from a
simulation that only went up to 30mm FWHM of smoothing. lGI has lots of
internal smoothness which often pushes it over this level. You can try
not using any smoothing, or, even better, try using permutation instead.
https://surfer.n
ind
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm36/pos/th40/mc-z.csd
Regards,
Xiaoxu
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Wednesday, January 13, 2021 9:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer]
When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD
files as found in $FREESURFER_HOME/average/mult-comp-cor
On 1/5/2021 4:55 PM, Na, Xiaoxu wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I’ve all the subjects successfully done recon-all, lgi befo
External Email - Use Caution
Hi Doug,
Deleting the .csd files and re-running worked.
Thank you!
Meaghan
On Tue, Sep 15, 2020 at 11:30 AM Douglas N. Greve
wrote:
> *Message sent from a system outside of UConn.*
>
> Hmm, there should have been a lot more terminal output than that
Hmm, there should have been a lot more terminal output than that.
Try this, delete the CSD files:
rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd
Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files
On 9/14/2020 2:58 PM, Meaghan Perdue wrote:
Exter
External Email - Use Caution
Hi Doug,
Here is the command:
mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0 abs
--cwp 0.05 --2spaces --bg 4
And here is the output:
mri_glmfit simulation done 4.78645
mri_glmfit simulation done 4.806
mri_glmfit simulati
please send the full command line and terminal output
On 9/9/2020 3:19 PM, Meaghan Perdue wrote:
External Email - Use Caution
Hello Freesurfer experts,
We're receiving the following error message when trying to run
mri_glmfit-sim:
ERROR: CSDmerge: CSDs have same seed
This only occu
See this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
On 2/7/2020 9:52 PM, Kim, Gwang-Won wrote:
Hi there,
I ran “mri_glmfit-sim –glmdir g2v3.wls –2spaces –perm 1000 1.3 abs”.
But, there was error message as follow: “design matrix is not
orthogonal, c
External Email - Use Caution
Hi Freesurfer,
I am also experiencing the same problem and everything regarding FREESURFER
path looks ok just getting error that says:
Reading source surface
/storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white
MRISread(): could not open fil
On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Hi Douglas,
>
> Thanks a lot for your answers.
>
> 1) For the permutations, would you recommend using this for
> controlling for MC in cortical thickness analyses too?
Yes
> Why is it recommended to use permutation
External Email - Use Caution
Hi Douglas,
Thanks a lot for your answers.
1) For the permutations, would you recommend using this for controlling
for MC in cortical thickness analyses too? Why is it recommended to use
permutation simulation as opposed to Z Monte Carlo simulation
On 11/23/2018 11:26 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Dear Freesurfer Developers,
> I have a 2-part question:
> 1) I was advised to use permutation to control for multiple
> comparisons in an LGI analysis, would you mind elaborating how to do
> this in command line (in
External Email - Use Caution
Hi Douglas,
Yes, the file
(/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white)
exists, I can view it in Freeview and have read permissions.
I had recently tried downloading this patch:
https://surfer.nmr.mgh.harvard.edu/pub/dis
Can you verify that the followign file exists, that you have read permission,
and that you can successfully load it into freeview?
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
On 9/21/18 11:41 AM, C.P.E. Rollins wrote:
External Email - Use Caution
Hello Freesur
Is this for a volume analysis? If so, then you'll need to use the --grf
option instead of using the mcz simulations (those are just for surface)
On 07/08/2017 01:03 PM, Aly Negreira wrote:
> Hi Doug!
>
> Thank you for the reply! Re-ran w/ --debug as first option. Below is
> the output. Not sur
Hi Doug!
Thank you for the reply! Re-ran w/ --debug as first option. Below is the
output. Not sure if this is helpful, but when I cd to
/Applications/freesurfer/average/mult-comp-cor/fsaverage
there are only directories for lh and rh, nothing for mni.
Thanks for the help!
Aly
Alysons-iMac:~/an
Hi Aly, it is not creating the path correctly, not sure why. Can you run
it again with --debug as the first option and send me the terminal output?
doug
On 7/1/17 1:57 PM, Aly Negreira wrote:
Hi Freesurfer Community,
I'm using FsFast on my dissertation data and trying to run a monte
carlo
rojectoutputdata/rh.paired-diff.glmdir/y.fsgd dods
>> --surf fsaverage rh white
>> simbase
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>> FWHM = -nan
>> ERROR: input FWHM is NaN (not a number).
>> Check the mask
...@nmr.mgh.harvard.edu]
Sent: Monday, May 09, 2016 5:30 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error
It looks like over half your voxels have been pruned because they have
value identical to 0 in at least one subject
Found 149926 points in label.
Pruning voxels by thr
>Check the mask in the glm directory.
> Mon May 9 09:11:28 CDT 2016
> ERROR: cannot find any csd files
>
> -----------------
>
> Many thanks for helping me with this Doug.
>
> Regards
&
oun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 06, 2016 3:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error
something is going wrong because the FWHM is not-a-number (
44094.721767
>
> Thanks
> Koushik
>
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, May 06, 2016 10:46 AM
>
___
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 06, 2016 10:46 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error
The problem is with the
The problem is with the estimate of the FWHM for that run. Can you
re-run mri_glmfit and send me the command line and terminal output?
On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
> Dear FS experts,
>
> I ran into an error with one of my mri_glmfit-sim execution
> and was
Thanks
Xiaomin
On Tue, Sep 8, 2015 at 2:03 PM -0700, "Douglas N Greve"
wrote:
Use "abs" not ""
On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
> Hi,
>
> I got this error when run mri_glmfit-sim: missing name for redirect.
> I am running freesurfer 5.3. the command is: mri_glmfit --glmdir
> ces
Use "abs" not ""
On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
> Hi,
>
> I got this error when run mri_glmfit-sim: missing name for redirect.
> I am running freesurfer 5.3. the command is: mri_glmfit --glmdir
> ces.nii --cache 2 --sim-sign . The ces.nii was generated from
> group level analysis
gh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_glmfit-sim error
what is the error? I did not see anything in the log file.
On 10/24/2014 04:18 AM, wrz891...@163.com wrote:
>
> Dear Freesurfer Experts,
> I'm a new freesurfer, it comes some errors whendoing m
Thanks a lot ! It just stopped woking at the last line and it didn't
generate the results ,so I didn't konw how to deal whit it .
wrz891...@163.com
From: Douglas N Greve
Date: 2014-10-25 00:32
To: freesurfer
Subject: Re: [Freesurfer] mri_glmfit-sim error
what is the error?
what is the error? I did not see anything in the log file.
On 10/24/2014 04:18 AM, wrz891...@163.com wrote:
>
> Dear Freesurfer Experts,
> I'm a new freesurfer, it comes some errors whendoing mri_glmfit-sim
> analysis. I don't konw what is wrong about it ,it just never work when
> # doning at mr
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MRI_glmfit-sim error
I think that could be the problem. I don't think that qdec cleans up
after itself, so that is probably a contrast from another analysis. Try
rerunning qdec using a different output folder, or just delete that
contrast.
doug
On 07/29/2014
d.edu
> Subject: Re: [Freesurfer] MRI_glmfit-sim error
>
> I'm not sure how that could have happened. Did you run mri_glmfit
> multiple times by any chance?
>
> On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:
>>
>> I'm running a monte carlo sim and am getting an
] MRI_glmfit-sim error
I'm not sure how that could have happened. Did you run mri_glmfit
multiple times by any chance?
On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:
>
>
> I'm running a monte carlo sim and am getting an error:
>
>
> command line:
>
>
I'm not sure how that could have happened. Did you run mri_glmfit
multiple times by any chance?
On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:
>
>
> I'm running a monte carlo sim and am getting an error:
>
>
> command line:
>
>
> mri_glmfit-sim \
> --glmdir MTA_persistanceCP \
> --sim mc-z
thanks Doug.
just tried, but I still got no clusters.
below is the output of perm.abs.2.sig.cluster.summary.
# CreationTime 2013/06/05-18:52:23-GMT
# cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
GLM/osgm/perm.abs.2.sig.cluster.
try
mri_glmfit-sim --glmdir GLM --no-sim perm.abs.2
doug
On 06/05/2013 02:26 PM, Glen Lee wrote:
>
>
>
>
> On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> what was your original mri_glmfit-sim command?
>
> mri_glmfit-sim --glmdir GLM
>
>
>
On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve
wrote:
> what was your original mri_glmfit-sim command?
>
> mri_glmfit-sim --glmdir GLM --sim perm 2 2 perm.abs.2 --sim-sign abs
>> --overwrite
>>
>
>
> Then, I tried no-sim on the generated csd file with the following command:
>
> mri_
Doug --
Sorry for asking your help again as I can't seem to resolve this on my own.
I looked up the mri_glmfit-sim --help and added the path of csd file in the
argument, but it still fails to find .csd file.
Can you let me know once again what I did wrong? (see the command line
below).
mri_glmfit
--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info
doug
On 06/04/2013 09:11 AM, Glen Lee wrote:
> Hi Doug,
> I tried as you suggested, but i've got the following error:
> e.g.,cannot find any csd files.
> However, I can see them stored in csd folder as shown below:
>
>
Hi Doug,
I tried as you suggested, but i've got the following error: e.g.,cannot
find any csd files.
However, I can see them stored in csd folder as shown below:
/2D/results/LH/GLM/csd> ls
mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd
I'm guessing that I need to define the path for this
hi Glen, no cluster will show up if the p-value for all clusters is
above .05. You can change this with --cwpvalthresh to something like
.99. That should give you all the clusters. Also, you don't have to run
the full simulation again; you can use the --no-sim option and it will
use the simul
Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?
FYI, I use v5.1.0.
On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
wrote:
> You will need more like 1 iterations instead of 100.
> doug
>
> On 06/03/2013 04:49 PM, Glen Lee wrote:
> > Hello Fr
You will need more like 1 iterations instead of 100.
doug
On 06/03/2013 04:49 PM, Glen Lee wrote:
> Hello Freesurfer experts--
>
> I ran mri_glmfit-sim to validate the group level GLM result (which was
> already done using mri_glmfit), but I was not able to get any result
> out of it.
>
> E
Hi Sophie, the problem may be that you have used "0,001" instead of
"0.001".
doug
On 05/02/2013 10:40 AM, Sophie Maingault wrote:
> Dear experts,
>
> I have a error message when I use the command : mdi_glmfit-sim —glmdir
> X —cwpvalthresh 0,001 —cache 3 abs
>
> ERROR : cannot find
> /usr/local
Can you send your command line and terminal output?
On 05/14/2012 09:26 AM, Juke Cha wrote:
>
> Hi all,
>
> I've got an error while running mri_glmfit-sim. I ran this for several
> measures, and only for 'volume' and 'area' the function complained
> about missing CSD files stating "ERROR: cannot
Thank you very much!!
On Wed, Jan 4, 2012 at 11:55 PM, zhang mingxia
wrote:
> Hi, every one,
>
> I just run the flag mri_glmfit-sim for Surface-based Correction for
> Multiple Comparisons as below:
>
> mri_glmfit-sim \
> --glmdir lh.Chinese_fastreading_thickness.glmdir \
> --cache neg 1.3 \
> --c
Hi Mingxia, use
--cache 1.3 neg
you have it the other way around
doug
zhang mingxia wrote:
> Hi, every one,
>
> I just run the flag mri_glmfit-sim for Surface-based Correction for
> Multiple Comparisons as below:
>
> mri_glmfit-sim \
> --glmdir lh.Chinese_fastreading_thickness.glmdir \
>
Hi Joost, the precomputed tables only go up to 30mm FWHM. The 25 mm you
apply adds to some that is already there to cause it to be 31mm, so the
table does not exist. I would say that 25mm is a lot to smooth by. Do
you really need that much?
doug
j janssen wrote:
> Hi,
>
> - FS version: 5.1
> -
Can you tar up your glmdir and drop it to me?
doug
Yuko Yotsumoto wrote:
> Thank you Doug,
>
>> Hi Yuko, I think you must have an older version of glmfit-sim some how.
>> I've put a newer version here:
>
> I replaced the /bin/mri_glmfit-sim, but got the same error.
>
> [ERROR 1]
> In line 292:
>
Thank you Doug,
> Hi Yuko, I think you must have an older version of glmfit-sim some how.
> I've put a newer version here:
I replaced the /bin/mri_glmfit-sim, but got the same error.
[ERROR 1]
In line 292:
set csdCache =
$CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/
Hi Yuko, I think you must have an older version of glmfit-sim some how.
I've put a newer version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim-v5.0
copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the
name; and make a backup copy).
doug
yuko
You can make a soft link. Don't worry about that warning (it's not
important, and I've fixed it for the next version).
doug
GREGORY R KIRK wrote:
> hi folks,
>
> when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg
> i get an error message ERROR: cannot find
> /apps/x86_64
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