I'm trying to understand the issues related to mri_convert.
It looks like you did the following:
1. mri_convert aparc.DKTatlas+aseg.deep.mgz aparc.DKTatlas+aseg.deep.nii.gz
2. saved the manually edited as aparc.DKTatlas+aseg.deep.edited.nii.gz
3. mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz
There is an error in your first 'recon-all -autorecon1 -noskullstrip' attempt:
"
\n
ERROR! FOV=302.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
\n
"
You can't
Here is the wiki help page to setup and config your FreeSurfer:
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Christine Farrugia
Sent: Tuesday, May 7, 2024 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
, with the current source code of
git repo. Should I try the source code of 7.4.1? which works well with its x64
binaries on my intel-based cluster, but I'm not sure whether the problem can be
solved on this aarch64 cpu.
Sincerely,
Tianxiang Lyu
Graduate School of Medicine,
Juntendo University
Huang
Your recon-all should have generated the following label files in your
subject’s label directory:
label/?h.FG1.mpm.vpnl.label
label/?h.FG2.mpm.vpnl.label
label/?h.FG3.mpm.vpnl.label
label/?h.FG4.mpm.vpnl.label
label/?h.hOc1.mpm.vpnl.label
label/?h.hOc2.mpm.vpnl.label
label/?h.hOc3v.mpm.vpnl.label
$SUBJECTS_DIR/fsaverage should be symbolic link to
$FREESURFER_HOME/subjects/fsaverage.
Can you check if it exists?
There should be lh.FG1.mpm.vpnl. label and rh.FG1.mpm.vpnl. label in
$SUBJECTS_DIR/fsaverage/label/ directory.
What is your command? Running the command by itself will show the
Is your Freesurfer Environment sourced correctly? Here is the wiki help
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Gregory Book
Sent: Tuesday, April 23, 2024 9:21 AM
To: freesurfer
Subject:
It looks like mris_transform interface changed since Freesurfer 5.3.
In Freesurfer 7.4.1, I believe you need to specify both --trx-src <> and
--trx-dst <> if you are giving mris_transform the transform in xfm format. Or,
you can use lta_convert to convert xfm to lta.
Best,
Yujing
From:
h.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems
Can you try 'mri_i
rd.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: Monday, April 15, 2024 4:44 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview problems
Can you try 'mri_info --voxel 0 0 0'? Just wanted to make sure
Can you try 'mri_info --voxel 0 0 0'? Just wanted to make sure
the license file is read properly.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Savoia, Alice (Stud. FPN)
Sent: Monday, April 15, 2024 10:42 AM
To: Freesurfer support list
Subject: Re: [Freesurfer]
These three TAGs (TAG_SURF_DATASPACE, TAG_SURF_MATRIXDATA,
TAG_SURF_TRANSFORMEDSPACE) are available in the surface files if they are
output from Freesurfer dev version.
They are the same as the metadata DataSpace/MatrixData/TransformedSpace in
GIFTI. You can use the information to convert [x,
It looks like mris_fix_topology for lh hemisphere core dumped. This is from
your recon-all.log:
“
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see
There is a space in your path
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.
Rename the directory name and try again.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
Sent: Sunday, March 31, 2024 11:18 PM
To:
Hi Yilei,
I think "nu_correct: Command not found. FREESURFER: Undefined variable." is
unrelated to your recon-all didn't finish. That error happens in the beginning
of recon-all and recon-all uses ANTS N4BiasFieldCorrection for nu correct
instead. We have addressed this error in our dev
The recon-all ‘WM/GM Contrast’ step is skipped for longitudinal base
processing. So, I’m not sure that ‘-qcache’ option can be used in base
processing.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Dan Levitas
Sent: Thursday, March 21, 2024 11:56 AM
To:
T1s?
Thank you,
Melody
On Thu, Mar 21, 2024 at 4:51 AM Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>> wrote:
Are you trying to preserve previous recon-all output and re-run using different
version of Freesurfer?
If not, ‘recon-all -all -s ’ will re-run recon-all from the beginning.
Y
...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, March 21, 2024 6:11 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard
It looks like Freesurfer can't find minc toolkit binaries on your system.
Did your recon-all finish fine? I think FS 7.2 recon-all is configured to use
ANTS N4BiasFieldCorrection for nu correct by default.
This is from your log:
"mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz
Are you trying to preserve previous recon-all output and re-run using different
version of Freesurfer?
If not, ‘recon-all -all -s ’ will re-run recon-all from the beginning.
You can find the original input to recon-all in mri/orig/00x.mgz. You can also
construct new subject directory structure
Hi Letitia,
Can you send the full command lines that you ran and the output?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Schneider, Letitia Maria
Sent: Thursday, March 14, 2024 10:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_label2vol
[Folder icon]
https://partnershealthcare-my.sharepoint.com/:f:/g/personal/yhuang43_mgh_harvard_edu/EpPzvvFe_jJFvpRs1gHUEwcB_z1zoKX_V0KktTrtGvHklw?email=taylor.ariko%40miami.edu=nQS1oZ
I uploaded those two binaries to OneDrive. Let me know if you can access them.
From: Huang, Yujing
Sent
umped)"
[cid:image001.png@01DA7077.5F9EC230]
I think before you asked which free surfer version, which is here:
[cid:image002.png@01DA7077.5F9EC230]
On Wed, Mar 6, 2024 at 4:51 PM Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>> wrote:
It is hard to tell without the data. Is there a
ian
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March 6, 2024 at 11:05 AM
To: Freesurfer sup
and rh.area for your review.
Many thanks,
Taylor
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, March
Sorry, just recognized it. The option to pass label file is ‘-l’. It looks
like you have ‘-1’ instead.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Wednesday, March 6, 2024 10:57 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] ascii: bad interpreter
I’m not sure which version of Freesurfer you are using. But it seems the
command line options are not in the right order. Here is the wiki help -
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Kavanaugh, Brian
rd.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not
establish read a
Hi Taylor,
I don't understand how you could get that error. It seems to me that
read_signa() is for reading .signa files.
Can you try 'mris_calc -o rh.area.mid rh.area add rh.area.pial' directly? Pass
full path to your rh.area and rh.area.pial.
What does 'mri_info rh.area' report?
Best,
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:59:50 PM
To: Freesurfer suppor
E/subjects
> $ cd $SUBJECTS_DIR
> $ cp -p -f -R /mnt/c/Users/GCM/Desktop/subjects/NowakG .
>
> - R.
>
> On Jan 8, 2024, at 16:10, Huang, Yujing
> wrote:
> You need to specify the input files to process. Here is the wiki page
> for recon-all -
> https://se
Hi Rosie,
Are you trying to combine all volume files (.nii.gz) into one single volume by
stacking all frames? Maybe you should use Freesurfer mri_concat instead of
mrcalc?
Here are the help pages for mri_concat and mri_vol2surf:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_concat
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:29:25
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, February 29, 2024 10:05:36 PM
To: Frees
It looks like if you don't specify a subject (--target subject) as common
space, it will default to 'fsaverage'. See
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc
The input to -surfreg <> is the surface registration to the common space. I
think it should be a surface file not in .mgh
ard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: Monday, February 26, 2024 4:21:01 PM
To: Freesurfer support list
Subject: [ext] Re: [Freesurfer] mris_convert reading surf.gii files?
Your mris_convert command l
Your mris_convert command looks correct. I'm able to do the conversion like
this with dev version:
mris_convert --annot label/rh.aparc.annot.gii surf/rh.white.gii rh.aparc.annot
I'm wondering which Freesurfer you are running. If you do 'mris_info surf.gii',
what does it report?
Best,
Yujing
Do you run ‘recon-all -parallel’ or ‘recon-all –threads ’?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Horn, Mitchell Jacob
Sent: Friday, February 23, 2024 12:28 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline
Bottom line is
k freesurfer has such
an output.
In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity
measure. I want to know how I can measure the intensities for the grey matter
regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>> wrote:
Recon-a
Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg
volume.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Tuesday,
There is an error before the 'multiple frames error':
"
Found 384 DICOM file(s)
load Image
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855821.dcm,
size 114688
Warning: Unable to determine slice direction: please check whether slices are
flipped
Warning:
, 2024 5:09 AM
To: Freesurfer support list ; Huang, Yujing
Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
External Email - Use Caution
Many thanks for the answer! Sorry, there seems to be some context missing. I
was replying to an old post from the archives
Hi Stefano,
I looked at the log files that you sent in a separate email. I see 2 problems
here:
1. when running preproc-sess with -nomc option, rawfunc2surf-sess couldn't
find file fmcpr.up or fmcpr.even in the directory
2. I think the 'if: Expression Syntax' error is from stem2fname
To
I'm not familiar with the logic. The program is calling
Remesher::removeCollapsedTrias() from remesher.cpp in loops. The program will
get out of loop when Remesher::removeCollapsedTrias() returns -1.
I can take a closer look if I have access to the data.
Best,
Yujing
From:
I think mri_segstats –i option will do that -
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Wednesday, February 7, 2024 8:12 AM
To: Freesurfer support list
Subject: [Freesurfer] Calculation
If you run recon-all, ?h.pial will appear as symbolic links to ?h.pial.T1.
Here is the list of symbolic links you should find in your subject/surf
directory:
rh.pial -> rh.pial.T1
lh.pial -> lh.pial.T1
rh.fsaverage.sphere.reg -> rh.sphere.reg
lh.fsaverage.sphere.reg -> lh.sphere.reg
rh.white.K
I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the
script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”?
I’m hoping it will give some hints.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Sven Kühn
Sent: Sunday,
Not sure where this happened. Does it produce any log files that you can share?
Maybe both logs with and without the -nomc option.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Stefano Delli Pizzi
Sent: Saturday, February 3, 2024 2:33 PM
To:
It looks like your recon-all was killed. Is it possible that your recon-all ran
out of the job limit (time, memory, ...).
I also noticed you have these options to recon-all '-3T -no-isrunning'. Make
sure you don't have other instance of recon-all running on the same subject.
Best,
Yujing
Just checked mris_euler_number, holes are calculated from euler number: holes
= 1-eno/2
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, February 1, 2024 10:27 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Euler number calculation
le]
It seems that there is no problem with converting the pial surface to gii, but
there is an issue with converting functional surface data to gii.
Best,
zhiwei
Date: Fri, 26 Jan 2024 13:29:24 +
From: "Huang, Yujing"
mailto:yhuan...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] conve
How does your command line look like? To convert functional file, use ‘-f
’. You also need to specify surface file.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of wangzhiwei3233
Sent: Friday, January 26, 2024 4:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
Your recon-all command doesn't have the directive to tell it what to run - add
option '-all' to your command.
See this wiki page for detail
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Weisholtz, Daniel S.,MD
. Just reads in the data as
is
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list
m
Not sure what kind of server you are running. Maybe your IT can help with the
file extension issue.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of James Bartolotti
Sent: Monday, January 22, 2024 6:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] File extension
I'm not sure about the MATLAB codes. When the C codes read in images, no
automatically transformation is done.
I think you can verify it by checking several [c, r, s] locations of both
images loaded with MRIread(). I think c and r are reversed in MATLAB. And the
index starts from 1.
Best,
oun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all canno
After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.
1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the
execute permissions?
2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission
Best,
Yujing
From:
mri_brainvol_stats reads the following files:
mri/aseg.mgz
surf/lh.white
surf/rh.white
surf/lh.pial
surf/rh.pial
mri/brainmask.mgz
mri/transforms/talairach.xfm
$FREESURFER_HOME/ASegStatsLUT.txt
Can you check if they all exist for your subjects?
Any errors if you run 'mri_brainvol_stats ' at
Can you attach recon-all.log of a failing subject?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Carly McIntyre-Wood
Sent: Tuesday, January 16, 2024 4:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Issue with mri_brainvol_stats for only some participants
Can you try the troubleshooting methods from this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Sunniva Fenn-Moltu
Sent: Monday, January 15, 2024 6:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Freesurfer .annot saves the annotation value at each vertex . The annotation is
calculated from RGB in label file. Any labels with same RGB assigned will have
the same annotations. They will appear to be the same label in .annot file.
Fix the label table in .gii, re-run mris_convert.
If you
rfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
Sent: 12 January 2024 14:24
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure
Your recon-all command
Here is an explanation of etiv calculation in Freesurfer -
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
etiv is not obtained via direct segmentation of all structures within the skull
boundaries. Rather, its estimation depends on the linear transform between the
T1 image and a T1w
Your recon-all command doesn't have the directive to tell it what to run. You
also need to specify input files for your initial run. See this wiki page for
detail https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
The recon-all.log attached contains runs between 2009 and 2010 on subject
You need to specify the input files to process. Here is the wiki page for
recon-all - https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Best,
Yujing
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Joanna Kidon
Sent: Monday, January 8, 2024 3:33 PM
To:
This is from your recon-all.log
"
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz
mri_convert: extra argument
It looks like there are some extra characters before '-flo_seg' flag. The
command line is split into 2 lines.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of r04458...@ntu.edu.tw
Sent: Wednesday, December 27, 2023 4:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
This is from Freesurfer wiki - MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be
This is from Freesurfer wiki -
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ
Q. I have already skull-stripped data. Can I submit it to recon-all?
A: If your skull-stripped volume does not have the cerebellum, then no. If it
does, then yes, however you will have to run the data
edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Huang, Yujing
Sent: Monday, December 18, 2023 8:55 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] aparcstats2table - append option
I would like to confirm that this is wha
I would like to confirm that this is what you have in mind:
1. the new '-append' flag will work with '--tablefile=OUTPUTFILE'
2. when same OUTPUTFILE is specified, new stats output will be appended to
the end of file
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf
The conversions between tkrRas and scannerRAS are as following in Freesurfer:
tkrRAS = tkrvox2ras * inv(vox2ras) * scannerRAS
scannerRAS = vox2ras * inv(tkrvox2ras) * tkrRAS
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Eric Tsang
Sent: Thursday, December 14, 2023
Your recon-all was killed – “Command terminated by signal 9”.
Was your VM VirtualBox up and running the whole time?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fargol Rezayaraghi
Sent: Friday, December 15, 2023 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
Can you try ‘mri_segstats’? It will compute statistics on segmented volumes -
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats
Yujing
From: Ahsan Ali
Sent: Friday, December 15, 2023 10:57 AM
To: Freesurfer support list ; Huang, Yujing
; Fischl, Bruce R.,PHD
Subject: Re: [Freesurfer
Hi Ahsan,
Can you specify the commands that you have tried?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ahsan Ali
Sent: Thursday, December 14, 2023 11:02 PM
To: Fischl, Bruce R.,PHD ;
freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Statistical Characteristics
Freesurfer only handles nifty-1 now.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Patricia Pais Roldan
Sent: Thursday, December 14, 2023 8:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] cannot read nifti-2 files in freesurfer - files ok in AFNI
Can you check if you have any extra empty lines after your last ‘Input’?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Laura Willers de Souza
Sent: Thursday, December 14, 2023 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aparcstats2table - IndexError
rd.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Huang, Yujing
Sent: vrijdag 24 november 2023 16:33
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Automatic prompt reply for freesurfer subsegmentations
I think you need to specify ‘--src_type curv’ and ‘--trg_type curv’ to read
thickness files.
It looks like you passed ‘thickness’ to the wrong flag. Use ‘—srcsurfval’ and
‘—trgsurfval’ instead.
Here is wiki help page - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2surf
Best,
Yujing
Hi Jakob,
I believe we fixed the bug in FS 7.4 release. Can you give it a try?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Litsch, Jakob Benjamin
Sent: Wednesday, December 6, 2023 10:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segmentation error
Hi,
‘mri_binarize –replace v1 v2’ performs transitive replacements if multiple
‘–replace’ args are specified. This has been the behavior since May 25, 2021
commit.
Now, new mri_binarize option '--no-transitive-replace' is introduced to turn
off the transitive replacements. Let me know if this
for correct conversion to reg.lta?
Thank you!
M
On Wed, Nov 29, 2023 at 3:40 PM Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>> wrote:
Try to specify –src <> and –trg <>
--src
specify src image geometry (mov volume for TKREG/register.dat)
--trg
specify trg ima
/dtrecon/COR-.info
ERROR readREG: cannot read src MRI
Mirsols-MacBook-Pro:dtrecon mirsolchoi$
Is there an additional file I need to complete this process?
Thank you so much for your time.
Mirsol
On Wed, Nov 29, 2023 at 3:24 PM Huang, Yujing
mailto:yhuan...@mgh.harvard.edu>>
You can try lta_convert.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mirsol Choi
Sent: Wednesday, November 29, 2023 5:19 PM
To: Freesurfer support list
Subject: [Freesurfer] Converting register.dat file to reg.lta
External Email - Use Caution
Hello there,
Hi Yunus,
‘fsaverage’ is an average subject comes with Freesurfer distribution in
$FREESURFER_HOME/subjects/. fsaverage is a template brain based on a
combination of 40 MRI scans of real brains. It can be used as a common space
for group comparison.
What is your SUBJECTS_DIR? You should not
Freesurfer distributes ‘fsaverage’ under $FREESURFER_HOME/subjects directory.
recon-all should create symbolic link to $FREESURFER_HOME/subjects/fsaverage
under $SUBJECTS_DIR.
This is from your recon-all.log
“
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME
‘mri_aparc2aseg’ adjusts Yeo’s 17 Network segmentation value to 1000+ for lh,
and 2000+ for rh. I don’t think you can use Freeview with
‘1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt’,
which labels from 1-114.
You may find it helpful
of Anatomy & Neurosciences, Amsterdam UMC Location VUmc
Van:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
namens Huang, Yujing
mailto:yhuan...@mgh.harvard
It looks like "imageDump.mgz" is copied to the directory during segmentation.
Can you check your 'umask'?
>umask
I think "mode 0444 (r--r--r--)" is caused by the umask setting to 0222. Try to
change your umask to 0002 in .bashrc or .profile - add a line 'umask 0002'.
Best,
Yujing
From:
oreach subject (your-list-of-subjects)
recon-all -s $subject -all ...
end
On 11/21/2023 12:04 PM, Dunia A Alhamad wrote:
External Email - Use Caution
But this will take long time because I had another group with 300 patients
On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing
mailto
cellation>
Thanks,
Kei
差出人:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
が Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
の代理で送信
送信日?: 2023年11月21日 10:52
宛先
NaNs are in your original input image. They are replaced with 0 in the output
mri/orig/001.mgz.
Doug mentioned “Sometimes SPM will put NaNs in the image to indicate a mask.”.
Is that your case?
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Carlos Alcocer
Sent: Tuesday,
Hi Kei,
Here is my calculation:
198 aparc.a2005s+aseg.mgz
192 aparc.a2009s+aseg.mgz
114 aparc+aseg.mgz
I can't find aparc.DKTatlas+aseg.mgz in Freesurfer distribution directory. Is
it the same as aparc+aseg.mgz?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of
Your ‘recon-all -autorecon2-wm -autorecon3’ finished without errors.
‘unknown-args.txt’ is created to filter out arguments not in recon-config.yaml.
It doesn’t mean those flags are not recognized.
I don’t know why new surfaces are not created after your editing of wm.mgz. Can
you re-send your
Hi Atena,
Can you check if you have environment variable FS_LICENSE set?
>echo $FS_LICENSE
Set FS_LICENSE to your license file in 7.4.1,
>export FS_LICENSE=
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Atena Akbari
Sent: Friday, November 17, 2023 6:06 PM
To:
Hi Carlos,
Can you attach recon-all.log?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Carlos Alcocer
Sent: Thursday, November 16, 2023 4:57 PM
To: Freesurfer support list
Subject: [Freesurfer] recon-all error
External Email - Use Caution
Hi,
For some of
Hi Peter,
Here is an example to convert from native space to MNI305 (fsaverage) in
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2vol
mri_vol2vol --mov orig.mgz
--targ $FREESURFER_HOME/average/mni305.cor.mgz
--xfm transforms/talairach.xfm
--o orig-in-mni305.mgz
In your
Hi Peter,
mri_label2label can only read MGH format label files.
lh.JulichBrainAtlas_3.0.3.label.gii looks like an annotation file. I think
mri_surf2surf should be used instead
https://freesurfer.net/fswiki/mri_surf2surf.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf
Sorry, I take my suggestion back. Annotation values are saved in .annot file,
not the label id. Different colortable won't work.
Yujing
From: Huang, Yujing
Sent: Tuesday, November 14, 2023 9:24 AM
To: Freesurfer support list
Subject: RE: Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer
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