Dear Soichi,
Can you please double check that you’ve got writing permissions on your subject
directory?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Soichi Hayashi
Reply-To: Freesurfer support
There is no obvious error in the recon-all file, but it does terminate
just after creating a symbolic link. Are sym links possible in the
CentOS virtual machine in windows?
On 5/4/2020 5:14 AM, Frank Chau wrote:
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Dear Freesurfer experts,
I ran recon-all
I suspect that you passed it the name of a dicom directory, instead of a dicom
file.
Please see step 6 of tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
"If DICOM files are available, you just need to specify the first DICOM file in
the series that contains the DWIs,
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Hello!
Thank you for the tip!
As i understand it, -lGI has only one input which is pial surface. I am
running it without any other files in the subject directory, I only have
Subject- Name_-Surf- ?h.pial files when I attempt to execute the -lGI on
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Hello team,
I have encountered the following error while running the tracula pre-processing
command and was hoping you could help me understand how
to correct this.
#@# Image corrections Sat May 2 19:57:18 CDT 2020
mri_convert --bvec-voxel
Sorry, our interface is a little bit confusing on this. Use -T2 to
specify the T2 volume (eg, -T2 /path/to/T2.mgz). To apply the T2 to the
pial use -T2pial (without any arguments)
On 5/2/2020 7:55 PM, Octavian Lie wrote:
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Dear All,
I ran recon-all on the
On 5/2/2020 7:27 PM, Meike Hettwer wrote:
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>
> Hi doug, thanks for the quick response!
> I‘m not quite sure if I‘m getting the second part right- could you please
> elaborate a bit what you mean by
> „When there is only one numerator DOF, then the sig map
You have two classes and one variable. This means that you will have 4
parameters (betas) to estimate (an offset for each group and an age
slope for each group). But you only have four input subjects, so your
DOF is 0
On 5/2/2020 7:59 PM, jiahui wrote:
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Hello.
I am trying to run segmentHA_T1.sh right after successfully completing
recon-all -all
I have a freesurfer output directory under my currently working directory
inside ./output. So I ran this command.
$ segmentHA_T1.sh output .
When I do I
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If you replaced the lh.pial and rh.pial files with different ones generated in
another software, the vertex counts in these files will almost certainly not
match the number of vertices (and faces) of all the other surfaces generated by
FreeSurfer
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Dear all,
We have a PhD position available on imaging of the medial temporal lobe in
aging and dementia at Lund University, Sweden, with the Biofinder Group.
See here for more details and applying:
https://lu.varbi.com/en/what:job/jobID:331266
The
We are running a pilot, to try to analyze their epileptic monitoring unit
datasets using the Martinos tools (FreeSurfer and MNE)
The analysis was on an fMRI nii file, which I checked before running fsFast,
and it was LSA.
I wouldn't suspect anything is wrong unless I knew how the results should
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Hi Eugenio,
Another information: though script exited with errors, all the left
hemispheres generated hippoSFVolums and amydNucVolumes as outputs. Missing
right hemispheres for all.
Best,
Qi
On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E.
Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system
turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient's fMRI task dataset, which is
in LSA.
Any recommendation what should I do to make sure both
The actual orientation of the input should not matter as long as the
nominal orientation matches the true orientation -- FS automatically
handles the orientation correctly. When you ask whether the output will
be "in RAS", are you asking whether the left side is truly the left (and
right is
How was the nii created? Ie, how did it go from dicom to nii?
On 5/4/2020 1:56 PM, Peled, Noam wrote:
We are running a pilot, to try to analyze their epileptic monitoring
unit datasets using the Martinos tools (FreeSurfer and MNE)
The analysis was on an fMRI nii file, which I checked before
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Hi,
Terminal output is below:
/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c
Something else has gone wrong. wm.mgz should have been there in order to
get as far as it did. Is your SUBJECTS_DIR set properly?
On 5/4/2020 2:49 PM, Mason Wells wrote:
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Hi,
Terminal output is below:
Unfortunately, the log file does not indicate what went wrong. But it
does show that the error happened on the LH (so it is not just RH). Run
the command below and send all terminal output
cd
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
mris_anatomical_stats
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Thank you so much !
Best,
Qi
On Mon, May 4, 2020 at 12:44 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:
> Dear Qi,
>
> I’m really sorry you’re running into all these problem.
>
> We’ll look into it and get back to you
I'd need a lot more details. Where they using FreeSurfer? Sometimes the
data will go through several conversions and formats before analysis. If
the orientation info was lost or changed, then that could explain it
On 5/4/2020 1:22 PM, Peled, Noam wrote:
Thanks Doug!
Good to know that.
I
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Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c
../label/aparc.annot.DKTatlas40.ctab
Dear Qi,
I’m really sorry you’re running into all these problem.
We’ll look into it and get back to you asap
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Zeng, Qi"
Reply-To: Freesurfer
Thanks Doug!
Good to know that.
I realized I had a problem when I got activation on the wrong side (right
finger tapping shows activation on the right hemisphere)
The analysis was done in another hospital when I just helped them remotely.
They told me that their analysis software shows the
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Dear Freesurfer Developers,
How are you? We have been using Freesurfer Freeview for localizing
implanted electrodes for human brains, and the coordinate system of choice
was "Talairach". However, we are trying to utilize MNI152 coordinate system
for
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Dear Dr. Greve,
Thanks for your prompt response. That's good to know, and indeed I have
seen this page. The confusion came because the MNI coordinate I know have
an origin at anterior commisure, so the x value should range from neg 90
something,
This was a bug in FreeView. If you download version 7, you should see
reasonable numbers
On 5/4/2020 4:51 PM, Hye Bin Yoo wrote:
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Dear Dr. Greve,
Thanks for your prompt response. That's good to know, and indeed I
have seen this page. The confusion came
Uuummm interesting… thanks a lot! I’m still investigating this
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Zeng, Qi"
Reply-To: Freesurfer support list
Date: Monday, May 4, 2020 at 14:51
To: Freesurfer
I think the latest one, but maybe it'll a good idea to start with the original
dicoms and not with the nii.
Thanks!
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Monday, May 4, 2020 4:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer]
They are created during the -prior step (last step within -prep), which looks
like it didn't complete. You probably also ran out memory in that step and
didn't notice. Rerun -prior with increased memory and then try -path again.
From:
I have used that before and it seems to work. What version are you/they
using? I remember this kind of problem years ago when FSFAST was using
SPM to initialize the registration; at some point SPM changed the
interpretation of the coordinates which caused a left-right reversal.
On 5/4/2020
They are using dcm2niix of MRIcroGL
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Monday, May 4, 2020 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch
How was the nii created? Ie, how did it go from
The "RAS" in that image refers to scanner RAS (not MNI coords).
The "Talarairach" is actually MNI305 (it is called this in version 7 to
avoid this kind of confusion).
In case you have not seen it, here is a page that may answer more of
your questions.
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Hi FreeSurfer experts,
I ran developmental version of freesurfer to get the hippocampus subfields ROI
and volume. I can see in the hipposubfields.lh.T1.v21.stats and
lh.hippoSfVolumes-T1.v21.txt fils with separate information for the head and
tail
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Hi FS developers,
I have used mri_glmfit-sim to do multiple comparison like below:
mri_glmfit-sim --glmdir lh.thickness.0.glmdir --cache 3 abs --cwp 0.05
--2spaces
and in the lh.thickness.0.glmdir/group.diff directory, I got some output
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