This might be related to a small bug in the previous longitudinal code, which
affected volume rescaling. It should be fixed now. You could try out the new
implementation: https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
Unfortunately, tensorflow and M1 don’t mix well at the moment. Not sure if
there is a universal fix yet.
Rob, do you remember where the mac-specific TF package can be installed from?
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Abdelkarim, Ahmed
Date: Tuesday, July
To mimic the original matlab implementation, segment_subregions saves stats as
*.txt files in the mri subdirectory of the subject.
But maybe we should just save things in the stats folder to be consistent.
Eugenio/Doug, what do you think?
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
o
Can you copy the attached trac-preproc into $FREESURFER/bin and try
again (after removing the link)?
On 7/22/2022 8:36 AM, kingwai@gmail.com wrote:
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Hi Anastasia,
Just downloaded FreeSurfer version 7.3 and trying out TRACULA.
Ran recon-all, segmentTha
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Hi Douglas,
�
Thank you for looking into this.
It gives the following error.
�
trac-preproc.sh -c config.file
intrareg: Undefined variable.
�
Thanks,
�
King-Wai
�
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Gr
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I am getting eerror: mri_segstats: could not open atlas transform file
/export01/local/freesurfer/subjects/sub-1221084/mri/transforms/talairach.xfm
The results do agree when Re running sclimbic.
it seems that when etiv differs a bit from the median, s
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Hi Anastasia
Thanks so much for the reply.
My trac-path worked until last step-it says dmric path done but it exited
without creating a merged_avg_16_syn_bbr and I also dont see pathoverall stat
etc for individual tracts
The error I get is:
fslmaths
are you sure the config file is right? it should be defining the
intrareg variable
On 7/25/2022 2:11 PM, kingwai@gmail.com wrote:
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Hi Douglas,
Thank you for looking into this.
It gives the following error.
trac-preproc.sh -c config.file
intrareg: Un
On 7/25/2022 2:45 PM, Miriam Taza wrote:
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I am getting eerror: mri_segstats: could not open atlas transform file
/export01/local/freesurfer/subjects/sub-1221084/mri/transforms/talairach.xfm
does
/export01/local/freesurfer/subjects/sub-1221084/mri/transform
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Hi Douglas,
�
According to
TRACULA tutorial
https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQN
I think the wiki is wrong. Try setting it to 3 in the config
On 7/25/2022 5:30 PM, kingwai@gmail.com wrote:
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Hi Douglas,
According to
TRACULA tutorial
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
htt
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I added it to the config file, then it complains
interreg: Undefined variable.
�
When I added interreg = 5, then it complains
subj: Undefined variable.
�
Should I continue fixing it until no more Undefined variable?
�
From: freesurfer-boun...
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Hi Freesurfer community,
I have run participants through an event-related fMRI task in which subjects
rate whether trait adjectives are descriptive of themselves or not, and
afterwards asked them to rate each trait word on emotional valence. Is it
po
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Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked
up after running ScLimbic. These are healthy adults and their scans look good.
Also, I noticed often when this occurs NAcc is also 0 or other regions.
I am concerned
I don't know; Anastasia is the author. She's busy today and tomorrow, I
was just trying to push it forward. Does it work with the given config
file in 7.2?
On 7/25/2022 5:46 PM, kingwai@gmail.com wrote:
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I added it to the config file, then it complains
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I reran sclimbic and I get the same result as the first time I ran sclimbic.
I also reran recon all on one subject. The etiv now differs from the original
recon all and the sclimbic output (although it is closer to sclimbic).
Here is the log for both
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Yes, my original config file works with 7.2
�
I really appreciate your help.
�
Thanks.
�
King-Wai
�
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Monday, July 25, 2022 9:23 PM
To: freesurfer@nmr.mgh.harva
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Andrew might have a better way to do this, but you could try the following.
Below you should substitute your base path to the freesurfer distribution for
where /Applications/freesurfer/dev is used.
1) Setup your freesurfer environment with FREESURFER_H
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