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Hi Freesurfer team.
I made the following command:
#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
foreach smoothing (10)
foreach meas (volume)
mris_preproc --fsgd FSGD/{$study}.fsgd \
--cache-in {$meas}.fwhm{$smoothing}.
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Hi,
I am using mri_convert to change the orientation of an image in its native
space from LPS to PSR.
Ex. Mri_convert -out_orientation PSR input_file output_file
Sometime when I do this, I lose the last coronal slice(s) of the occipital lobe
when t
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Okay.
I tried the following file. HCA8133362_V1_MR.zip
ftp> put HCA8133362_V1_MR.zip
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.
ftp>
ftp> put HCA8133362_V1_MR.zip
200 PORT command successful. Consider u
Please compress the whole subject directory and upload it to the ftp
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On May 28, 2021, at 15:35, Daniel Davidson Callow
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Sure, what is the best way to share it with you? and which folders/files
should I send?
On Fri, May 28, 2021 at 3:28 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> wrote:
> It seems the linear registration is dying. Would you mind
Multiple subjects or all of them?
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
> On May 28, 2021, at 12:26, 林鈺庭 wrote:
>
>External Email - Use Caution
>
> Dear Dear FreeSurfer Developers,
>
> (We’re the message
It seems the linear registration is dying. Would you mind sharing the subject,
please?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On May 28, 2021, at 12:20, Daniel Davidson Callow
mailto:dcal...@umd.edu>> wrote:
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Greg,
Additional clarification.
Are these 2 options runs independently - i.e. separate tests?
For example, add CPs to brain.mgz and then rerun entire recon-all -all command?
Is the experts options file used with the CPs above in one run or separate
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Thanks Doug. Will try with difference distances. Where is the expert file
placed?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Thursday, May 27, 2021 5:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesu
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Dear Dear FreeSurfer Developers,
(We’re the message 3)
This happened to multiple subjects. Our computer got 16GB MHz DDR4 , We thought
it met the requirements to run the module based on the documentation on
freesurfer wiki , or didn’t it? :(
Best
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Hello Juan,
I am using data from the HCP aging dataset which has a T1 and a
high-resolution hippocampal scan (T2).
Yes, it does seem that the T2 and T1's are roughly aligned to each other.
It seems like it has something to do with the creation of the
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Dear Experts,
I have extracted subcortical vols corrected for intracranial vols using
asegstats2table and I ran mri_glmfit using the following command
mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C
groupdiff.mtx \--glmdir aseg.glm
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The specific volume to surface mapping we do in the HCP Pipelines minimizes the
partial volume effects.
Matt.
From: on behalf of Marina Fernández
Reply-To: Freesurfer support list
Date: Friday, May 28, 2021 at 10:06 AM
To: "freesurfer@nmr.mgh.har
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Hi Matt,
Thank you very much for the quick answer.
We have our data analyzed with another pipeline that also uses Freesurfer
functions. For this reason we prefer to calculate myelin maps outside of
the HCP Pipelines.
Do you think the way of calculati
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I would use the HCP Pipelines for this.
Matt.
From: on behalf of Marina Fernández
Reply-To: Freesurfer support list
Date: Friday, May 28, 2021 at 9:25 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] PVC to calculate myelin maps
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Dear experts,
I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
I saw that the correction of partial volume effects can be used to create
the maps (Shafee, Buckner & Fischl, 2015)*.
Can I use the PVC functions of PetSurfer for
Dear Daniel,
Are the T2s and T1s roughly aligned in RAS (physical coordinates)? In other
words: do they (roughly) overlap when you open them together in Freeview?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On May 28,
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Hi,
Thanks for this. Using mri_surf2vol as a QC hadn't occured to me and is a nice
solution. I feel again using --fillribbon is the best way to project the
surface to the volume for my case?
There is one other issue I had seen, but didn't know if it
Dear Josephine,
This is a bit weird, as the code was very close to finishing. Does this happen
for one or multiple subjects? Also: is it possible that you’re running out of
RAM memory? How much RAM does your computer have?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UC
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Hello,
I am running into errors when running
segmentHA_T2.sh ${subj}
/data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
Approximately 10% of my subjects are being processed but for some reason,
the majority fail to execute. Here is
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Hello,
I am running into errors when running
segmentHA_T2.sh ${subj}
/data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
Approximately 10% of my subjects are being processed but for some reason,
the majority fail to execute. Here is
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