Wassima
Sent: Tuesday, August 1, 2023 4:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory
External Email - Use Caution
Hello M.Yujing,
I’m using the HCP-A cohort (Human Connectome Project – Aging), where the
structural MRIs were
wondering how you created
/media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of MANSSOUR Wassima
Sent: Tuesday, August 1, 2023 2:52 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_preproc error
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That should be enough RAM. What is your command line? Can you send the
log file?
On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote:
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Hello FreeSurfer Developers,
I'm conducting the *Surface Based Group Analysis*
Did you specify a hemi? If you run it with --help it will give you docs.
You can also find them on line. You should also send the command line
On 2/17/2022 9:23 AM, Koustav Chatterjee wrote:
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Dear FreeSurfer experts,
I need your help.
I am trying to run
External Email - Use Caution
Dear FreeSurfer experts,
I need your help.
I am trying to run mris_preproc --fsgd in order to see the effect of
cortical volume on velocity, accounting for the effects of eTIV in the
analysis.
My .fsgd file looks like
GroupDescriptorFile 1
Title
, 2019 9:22 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error: dimension mismatch
If you have a volume and a registration file, you can run mris_preproc
with the --iv option. Eg, something like
mris_preproc --fsgd abc.fsgd --target fsaverage --hemi lh \
* --out abc
-
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Greve, Douglas
> N.,Ph.D.
> *Sent:* Friday, February 15, 2019 8:26 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mris_preproc error: dimension mismatch
> The subject s
, 2019 8:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error: dimension mismatch
The subject surface probably changed since the last time you ran qcache and now
has a different number of vertices. Try re-running qcache for those subjects.
On 2/15/19 2:58 AM, Peters
The subject surface probably changed since the last time you ran qcache and now
has a different number of vertices. Try re-running qcache for those subjects.
On 2/15/19 2:58 AM, Peters, Douglas G wrote:
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Hi Everyone,
I'm trying to prepare my Cerebral blood
External Email - Use Caution
Hi Everyone,
I'm trying to prepare my Cerebral blood flow surface data for mri_glmfit group
analysis (qdec doesn't allow you to choose your own subject surface files to
analyze, so I figured mri_glmfit is my only option). Quick summary of what I
you will also need to recreate
lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh
On 5/21/18 12:45 PM, Barletta, Valeria wrote:
> Hi Freesurfers,
> I sent this help request some days ago but had some problems in receiving the
> reply because of mailing list subscription issues...
Hi Freesurfers,
I sent this help request some days ago but had some problems in receiving the
reply because of mailing list subscription issues...
Sorry for submitting this request again:
I used the command mris_preproc to have all the surfaces of my cohort
concatenated in fs average and I
You probably need to regenerate this file:
/autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh
On 5/11/18 2:39 PM, Barletta, Valeria wrote:
> Hi Freesurfers,
> I used
Hi Freesurfers,
I used the command mris_preproc to have all the surfaces of my cohort
concatenated in fs average and I obtained this error message from several of my
subjects:
#@# 3/11 MS073_R01_05/Bay8_3T/fs/MS073_R01_05 Fri May 11 14:24:58 EDT 2018
--
---
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm baffled as
I've used all of my scripts and fsgd files before.
There are 2 groups with 3 covariates but I keep getting this error:
mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage
--target
Can you run it with --debug as the first argument and send the terminal
output?
doug
On 11/05/2014 04:21 PM, Cooke, Gillian wrote:
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm
baffled as I've used all of my scripts and fsgd files before.
There are 2
, November 05, 2014 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Can you run it with --debug as the first argument and send the terminal
output?
doug
On 11/05/2014 04:21 PM, Cooke, Gillian wrote:
Hi All,
I am getting a consistent error when I try to run
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Can you run it with --debug as the first argument and send
: [Freesurfer] mris_preproc error
run it like this
mris_preproc --debug --fsgd fsgd/HRR60.fsgd ...
doug
On 11/05/2014 05:32 PM, Cooke, Gillian wrote:
Unfortunately I'm getting this error in the terminal:
bash: --debug: command not found
From: freesurfer
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: Wednesday, November 05, 2014 4:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
run
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Hmm, still not sure what's up. Can you attach your fsgd file to an email?
doug
On 11/05/2014 05:48 PM, Cooke, Gillian wrote:
Thanks Doug - this is what it produces:
out mris_preproc/lh.HRR60.thickness.10.mgh
set echo = 1
-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Hmm, still not sure what's up. Can you attach
Doug,
thank you very much.
One subject result from mris_preproc only have partial brain data. this
caused error. But I dont know why this subject data failed in
mris_preproc.
my command is the following,
mris_preproc --target fsaverage --hemi $hemi --out sub1.mgh --paired-diff
--iv
oops. I pasted the original error message incorrectly. below is the error
with the corrected path.
Hi,
In anattempt to prepare to run a monte carlo cluster threshold simulation
with a group of subjects in stable3, I run into the following error using
mris_preproc:
[troy:retrievalnewest]
Hi,
In anattempt to prepare to run a monte carlo cluster threshold simulation
with a group of subjects in stable3, I run into the following error using
mris_preproc:
[troy:retrievalnewest] (nmr-stable3-env) mris_preproc --fsgd
SM2_glm_MC_controls.fsgd --target allsubavg --hemi lh --sf
Hi,
It looks like the error I was obtaining from mris_preproc looks like it
was due to a failure in stxgrinder-sess that I did not realize had
occurred. I have a feeling that once this problem is resolved mris_preproc
will run correctly, but help here would be much appreciated...The error is
There are a couple of problems here. You're specifying sh+smvsnh.mat as the
contrast, but it should not have a .mat extension, so it can't find the input.
This exposed a bug in mris_preproc, which I have just fixed. Even if you remove
the .mat, I think it still fails because there is no
That looks like a matlab problem. Maybe something in your startup.m file?
Cameron Ellis wrote:
Hi,
It looks like the error I was obtaining from mris_preproc looks like it
was due to a failure in stxgrinder-sess that I did not realize had
occurred. I have a feeling that once this problem is
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