Good afternoon,
Quick question about unpacking:
The instructions I have from a previous staff member said to do this:
In folder where files are going, type: unpacksdcmdir -src
-targ . -scanonly scanout.txt
So what I submit is:
unpacksdcmdir -src
/cluster/archive/338/siemens/Prisma_fit-67026-202
not sure what is going on. It received a kill signal (the 9 mentioned at
the end). This often means that it was killed externally. Does this
happen repeatedly? Does this happen on other subjects? How much memory
did you allocate to your virtual box?
On 9/23/2022 1:04 AM, Ahmad Khan wrote:
Sam way as with unpacksdcmdir, ie, by specifying -run run subdir format
stemname
Another way it to use the -auto-runseq format , eg -auto-runseq mgz
this will output all the runs preprending the run number and protocol name
If you are using 7.3.X, then you can also add --dcm2niix which will
spe
yes, it is ok
On 9/22/2022 8:36 AM, Alexandra Brouillard wrote:
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Hi
I ran recon-all on an external server using the version 6. I recently
downloaded the v6 on my Mac v12.6. I was able to set a home directory
but get a ‘*permission denied*’ error when typi
On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote:
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Would providing better manual segmentations of those structures of
interest help you in building better solutions?
I can work with the segmentation that is produced now, but I am
interested in improving the res
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Sorry if this is a repeat email from last night, but signal 9 can mean you ran
out of memory. You should try allocating more memory to the VM..
You could also try running the latest freesufer version = 7.3.2 which is
compiled for Ubuntu 20 and you ca
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Hi Freesufer's,
I need to run a group analysis but I don't know how to do it, the error
always appears (print below). There are 3 groups ( risk_group) that I would
like to insert as a class (LR = level 1, HR = level 2 and MDD = level 3)
and I would like
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Dear Freesurfer experts,
We appreciate any advice or guidance from your community of professionals
and experts in the field about the issue below.
Thank you for your kindness.
Dear Freesurfer experts,
In order to normalize white matter intensity of T1
Hi JamesB
there is T2/FLAIR normalization in recon-all if you process it through there.
You can look for "nonmax_suppress" if you want to find the command line
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of James Brown
Sent: Friday, Se
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Dear Dr Bruce,
Thank you very much for your guidance.
I ran recon-all on a subject "test" using Freesurfer V6.0 and the following
command line is reported in the "recon-all.log":
/usr/local/freesurfer/6.0/bin/recon-all -all -qcache -i T1.nii.gz -flair
I think you need to add something like -FLAIRpial or -T2pial so it uses it (in
which case it will first normalize it), but hopefully someone else can confirm
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of James Brown
Sent: Friday, Septe
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Hi all,
I am receiving this error when trying to run sclimbic module.
mri_sclimbic_seg --i /Users/mdbargen/Documents/control-T1 --o
/Users/mdbargen/Documents/control-limbic --conform
Segmenting image 1/68
Loaded input image from
/Users/barisgen
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