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does it happen if you don't use --cache-in? Also, can you send the full
terminal output?
On 5/30/2023 6:46 PM, Akansha Mahesh Naraindas wrote:
External Email - Use Caution
Hi
I am attempting to create a group file using MRIS PREPROC
My com
External Email - Use Caution
Hi
I am attempting to create a group file using MRIS PREPROC
My command is as follows
mris_preproc --fsgd brainmorph.fsgd --cache-in thickness.fwhm10.fsaverage
--target fsaverage --hemi rh --out mripreproc-rh-thickness.mgh
But I am receiving the e
How did you create
/data/Psychiatrie/Meike_Hettwer/CTFreesurfer/WMC2_new_n4/rh.resilience_extra.volume.10.mgh
It apparently has 102 subjects in it, but the FSGD file specifies 105,
thus the mismatch
On 7/31/2020 3:19 AM, Meike Hettwer wrote:
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Dear freesur
External Email - Use Caution
Dear freesurfer experts
I got an error that I don't understand when running mri_glmfit on
cortical volume in the right hemisphere. I only have one group and one
covariate of interest (+ age and ICV).
ERROR: dimension mismatch between y and X. y has
External Email - Use Caution
Hello Freesurfers!
In regards to the link below:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36839.html
Is there a way to fix a dimension mismatch?
Thanks,
Ken
Sent with [ProtonMail](https://protonmail.com) Secure Email.__
You should only need those first two commands (+ the mri_mask). Use
--interp nearest with the ribbon
On 04/10/2017 12:27 PM, Maria Hakonen wrote:
>
> Hi Bruce,
>
>
> Thank you for the reply! I have now tried:
>
>
> mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh
> --tal -
Probably you'll want to use mri_vol2vol so that you can incorporate your
registration between the fMRI and the anatomical
On 04/10/2017 10:28 AM, Bruce Fischl wrote:
> Hi Maria
>
> are they in register? If so you can do:
>
> mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz
> mri_mask fmri_data.
Hi Bruce,
Thank you for the reply! I have now tried:
mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh
--tal --talres 2
mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh --tal
--talres 2
mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz
mri_mask m
Hi Maria
are they in register? If so you can do:
mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz
mri_mask fmri_data.mgh mask.mgz masked_fmri.mgz
cheers
Bruce
On Mon, 10 Apr 2017, Maria Hakonen
wrote:
Dear Freesurfer experts,
I have tried to mask fMRI data with grey matter mask as follo
Dear Freesurfer experts,
I have tried to mask fMRI data with grey matter mask as follows:
mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
However, I am getting an error " dimension mismatch between source and
mask".
Could someone please let me know how to solve this problem?
Best,
Maria
_
Hi Isabelle
when you say you reanalyzed it from scratch, did you actually delete the
subject dir and start over or just rerun autorecon1? If the latter, that
won't reanalyze from scratch but will keep existing edits and such.
Did you do anything out of the ordinary the first time you ran it?
T
Dear FreeSurfer experts,
After running the following command:
recon-all -autorecon2 -autorecon3 -subjid S08_FS
I get the following error:
/Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri
\n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n
threshold mask volume at 5
E
rom: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, July 30, 2015 12:19 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] selxavg3-sess error
>
> those look ok. Can
du]
> Sent: Tuesday, August 04, 2015 3:08 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Dimension mismatch between mask and run
>
> There is still a warning about "multiple formats". This means you have
> not deleted all the offending files.
>
>
-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 3:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Dimension mismatch between mask and run
There is still a warning about "multiple formats". This means you have
not
dRegression_Stable5_050514/Xtmp.mat
> XCond = 35.9364 (normalized)
> Computing compensation for resdual AR1 bias
> 1 -0.5 -0.507451(t=0.046548)
> 2 -0.25 -0.264(t=0.105696)
> 3 0 -0.0235997(t=0.137308)
> 4 0.25 0.211292(t=0.189719)
> 5 0.5 0.434363(t=0.2
rection M: 0.031657 1.0595
Computing contrast matrices
OLS Beta Pass
run 1t= 0.0
ERROR: dimension mismatch between mask and 1th run
>> --
ERROR: fast_selxavg3() failed\n
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mg
I'm not sure, but it may be that there are some files that are nii and
others that are nii.gz. Eg,
ls -tl /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/015/masks/
total 1248
-rw-rw 1 arodthom roffmagp 3579 Aug 3 18:06 brain.e3.nii.gz
-rw-rw 1 arodthom roffmagp 5383 Aug 3
Hi Freesurfer experts,
For a data set of n=100, selxavg3 is erroring out on 10 subjects (GDDA086, 88,
89, 91, 93, 94, 95, 96, 97, and 98). It says ERROR: dimension mismatch between
mask and 1th run. Do you know why freesurfer is having trouble with these
subjects in particular, and how I can a
for any suggestion !!
Tom
*Gesendet:* Mittwoch, 15. April 2015 um 15:14 Uhr
*Von:* "Douglas Greve"
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] dimension mismatch
I would think that going into the DTI space would make this worse
since the voxels are bigger (?). B
Greve"
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] dimension mismatch
I would think that going into the DTI space would make this worse since the voxels are bigger (?). But if that is what you want to do, use mri_label2vol to map the aparc+aseg.mgz into the DTI space, then
arvard.edu
*Betreff:* Re: [Freesurfer] dimension mismatch
Don't use the --inv flag on vol2vol
doug
On 4/14/15 10:03 AM, Thomas Potrusil wrote:
Dear FreeSurfers!
After successful registration using
dt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o
$outdir_dtirecon
etreff: Re: [Freesurfer] dimension mismatch
Don't use the --inv flag on vol2vol
doug
On 4/14/15 10:03 AM, Thomas Potrusil wrote:
Dear FreeSurfers!
After successful registration using
dt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o $outdir_dtirecon
I resampled the anat
Don't use the --inv flag on vol2vol
doug
On 4/14/15 10:03 AM, Thomas Potrusil wrote:
Dear FreeSurfers!
After successful registration using
dt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o $outdir_dtirecon
I resampled the anatomical into the functional space using (I´m
interested in ADC-
Dear FreeSurfers!
After successful registration using
dt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o $outdir_dtirecon
I resampled the anatomical into the functional space using (I´m interested in ADC-values)
mri_vol2vol --mov $dti_vol --reg $outdir_dtirecon/register.dat --fstarg --
Hi Cedric, try it with --noreshape. If you're using mgh format, then
reshaping is not necessary.
doug
On 01/22/2013 09:16 AM, Koolschijn, Cédric wrote:
> Hi Doug and other FS-experts,
>
> I succesfully applied the registration step of the Cortical Thickness of a
> Volume-defined ROI wiki:
> http:/
Hi Doug and other FS-experts,
I succesfully applied the registration step of the Cortical Thickness of a
Volume-defined ROI wiki:
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
However, I'm having troubles at the end.
3) Map the ROI-mask to the fsaverage surface, to create an
can you send the full terminal output?
doug
Greg Burgess wrote:
> I ran the surfaces a couple of weeks ago, and I ran all of the fsfast steps
> today. I used the -force flag for preproc-sess, mkanalysis-sess, and
> selxavg3-sess to make sure that all steps were run rather than leaving old
> fil
Greve
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dimension mismatch in fieldsign-sess
I ran the surfaces a couple of weeks ago, and I ran all of the fsfast steps
today. I used the -force flag for preproc-sess, mkanalysis-sess, and
selxavg3-sess to make sure that all steps were run
I ran the surfaces a couple of weeks ago, and I ran all of the fsfast steps
today. I used the -force flag for preproc-sess, mkanalysis-sess, and
selxavg3-sess to make sure that all steps were run rather than leaving old
files in place.
--Greg
On Mar 8, 2012, at 2:06 PM, Douglas N Greve wrote
Did you happen to change the surface for your subject between the time
you ran preprocessing and the time you ran fieldsign-sess? It looks like
the number of vertices changed.
doug
Greg Burgess wrote:
> Hi freesurfers,
>
> I'm getting an error that I don't know how to track down.
>
> Running th
Hi freesurfers,
I'm getting an error that I don't know how to track down.
Running the following command:
fieldsign-sess -a rtopy.self.lh -sphere -s CP10021_v5
I get the following error:
reading colortable from annotation file...
colortable with 36 entries read (originall
Hi Michell, you appear to have two FreeSurfer analysis for this subject:
/usr/local/freesurfer/subjects/ld12
/usr/local/freesurfer/subjects/retinotopy/sj12
Can you verify that these are *exactly* the same?
doug
Michelle Umali wrote:
> Hi Doug and Freesurfers,
> No matter what I try I am still
Hi Doug and Freesurfers,
No matter what I try I am still getting the Dimension mismatch error when
running fieldsign-sess. I even ran recon-all -s sj12 -make all.
I don't think it's a problem with the directories (below). The subjectname
file is correct, and when I run field-sign-sess it sees th
Can you check that the subjectname file is correct? In some cases, it
looks like it is using subject sj12, in others it looks like it is using
subject ld12.
doug
Michelle Umali wrote:
> Hi Doug,
> I re-ran from preproc-sess using the -force flag, and I still get the
> same dimension mismatch e
You can an asynchrony between your fmri data and the anatomical:
Anatomical: num vertices: 146530
fMRI: 158944 vertices
re-run the fMRI starting from preproc-sess. You will need to make sure that
preproc-sess actually re-runs at least the sample-to-surface. By default, it
just looks to see if th
Hi Doug,
I've attached the mri_info output on the eccen and polar images as well as
the mris_info on the lh.sphere surface
Thanks.
Michelle
On Mon, Oct 3, 2011 at 2:38 PM, Douglas N Greve
wrote:
> Can you send me the result of running mri_info on
> eccen/real.nii
> eccen/imag.nii
> polar/real
Hi Doug,
I've attached the output from running fieldsign-sess.
Thanks for all your help.
Michelle
On Mon, Oct 3, 2011 at 12:59 PM, Douglas N Greve
wrote:
> Michelle, before you do that, can you run the offending program with -debug
> and send me the (copious) terminal output? Your anat should no
Michelle, before you do that, can you run the offending program with
-debug and send me the (copious) terminal output? Your anat should not
have to be re-run.
doug
Michelle Umali wrote:
> Hi Bruce,
> Will this undo my wm and pial edits?
>
> Thanks.
> Michelle
>
> On Sat, Oct 1, 2011 at 3:37 PM,
no, it shouldn't, but make a backup of your data before running it for
sure
On Mon, 3 Oct 2011, Michelle Umali wrote:
Hi Bruce,
Will this undo my wm and pial edits?
Thanks.
Michelle
On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl
wrote:
try running
recon-all -s subject -make all
Hi Bruce,
Will this undo my wm and pial edits?
Thanks.
Michelle
On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl wrote:
> try running
>
>
> recon-all -s subject -make all
>
> and leave the -dontrun off. It should bring everything up to date
>
> Bruce
>
>
>
> On Sat, 1 Oct 2011, Michelle Umali wrote
try running
recon-all -s subject -make all
and leave the -dontrun off. It should bring everything up to date
Bruce
On Sat, 1 Oct 2011, Michelle Umali wrote:
Dear Freesurfers,
I'm still getting a MRISripZeros() and MRIScopyMRI Surf/src mismatch error
when running fieldsign-sess. You sugges
Dear Freesurfers,
I'm still getting a MRISripZeros() and MRIScopyMRI Surf/src mismatch error
when running fieldsign-sess. You suggested that this problem was due to the
surfaces being out of synch. When I ran recon-all -s subject -make all
-dontrun, I saw that several steps had not run. The dat
Hi all,
after running a group comparison using qdec I wanted to use mc-z
instead of FDR for multiple comparison correction
I tried to run mri_glmfit-sim-mc-z.abs.2
and got an error...
ERROR: dimension mismatch between X and contrast /Users//subjects/
qdec/Untitled/tmp.mri_glmfit-sim-5637/
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