date:20240304

Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-04 Thread Stefano Delli Pizzi

External Email - Use Caution

Here -debug outputs

preproc-sess -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 
-fsd rest -per-run -sliceorder up -debug
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return

foreach grp ( $grpdefs )
foreach grp ( )

goto check_params ;
goto check_params

if ( $#SessList == 0 ) then
if ( 1 == 0 ) then

if ( $#SearchPathList == 0 ) then
if ( 0 == 0 ) then
set SearchPathList = "." ;
set SearchPathList = .
endif
endif

goto check_params_return ;
goto check_params_return


set UniqueList = ( ) ;
set UniqueList = ( )
foreach d ( $SearchPathList )
foreach d ( . )
if ( ! -e $d ) then
if ( ! -e . ) then

set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( . )
set UniqueList = ( . )
end
end

set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( . )

set errs = 0 ;
set errs = 0


set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( 091223sbj01m_tp1 )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( . )
set stst = $d/$sess
set stst = ./091223sbj01m_tp1
if ( -d $stst ) then
if ( -d ./091223sbj01m_tp1 ) then
if ( ! -r $stst ) then
if ( ! -r ./091223sbj01m_tp1 ) then
pushd $stst > /dev/null ;
pushd ./091223sbj01m_tp1
set tmp = ( $tmp `$PWDCMD` ) ;
set tmp = ( `$PWDCMD` )
pwd
popd > /dev/null ;
popd
endif
endif
end
end
set nfound = ( $#tmp ) ;
set nfound = ( 1 )
if ( $nfound == 0 ) then
if ( 1 == 0 ) then
if ( $nfound > 1 ) then
if ( 1 > 1 ) then
set SessPath = ( $SessPath $tmp ) ;
set SessPath = ( 
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
end
end


set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then

set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( 
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
endif
endif
end
end


echo $SessPath
echo /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1

exit $errs ;
exit 0
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return

goto check_params ;
goto check_params
if ( $#instem == 0 ) set instem = "f" ;
if ( 0 == 0 ) set instem = f
set instem = f

if ( $#fsd == 0 ) then
if ( 1 == 0 ) then

if ( $DoMC || $DoReg ) then
if ( 0 || 1 ) then
if ( $PerRun == 0 && $PerSess == 0 ) then
if ( 1 == 0 && 0 == 0 ) then
endif
endif

if ( $DoMC ) then
if ( 0 ) then

set mcoutstem = $instem ;
set mcoutstem = f
endif
endif

if ( $DoSTC ) then
if ( 1 ) then
if ( $#stcinstem == 0 ) set stcinstem = $mcoutstem
if ( 0 == 0 ) set stcinstem = f
set stcinstem = f
if ( $#stcoutstem == 0 ) then
if ( 0 == 0 ) then
if ( $#SliceOrder ) set stcoutstem = $stcinstem.$SliceOrder
if ( 1 ) set stcoutstem = f.up
set stcoutstem = f.up
if ( $#SliceDelayFile ) set stcoutstem = $stcinstem.sdf
if ( 0 ) set stcoutstem = f.sdf
endif
endif
else
else

if ( $ToSurf || $ToMNI305 || $ToCVS ) then
if ( 1 || 1 || 0 ) then
if ( $#fwhm == 0 ) then
if ( 1 == 0 ) then
set DoVolSmooth = 0 ;
set DoVolSmooth = 0
set DoSurfSmooth = 0 ;
set DoSurfSmooth = 0
set DoSmooth = 0 ;
set DoSmooth = 0
endif
endif

if ( $DoSmooth ) then
if ( 0 ) then

if ( $DoInorm && $#inormstem == 0 ) then
if ( 0 && 0 == 0 ) then

if ( ! $DoMC && ! $DoSTC && ! $DoSmooth && ! $DoMask && ! $DoTemplate ) then
if ( ! 0 && ! 1 && ! 0 && ! 1 && ! 1 ) then

if ( $#ProjFrac && $DoProjAvg ) then
if ( 0 && 0 ) then

if ( $UseB0DC && $#ProjFracExpKey ) then
if ( 0 && 0 ) then

if ( $#regfile == 0 ) then
if ( 0 == 0 ) then
if ( ! $UseB0DC ) set regfile = register.dof$RegDOF.lta
if ( ! 0 ) set regfile = register.dof6.lta
set regfile = register.dof6.lta
if ( $UseB0DC ) set regfile = register.dof$RegDOF.b0dc.lta
if ( 0 ) set regfile = register.dof6.b0dc.lta
endif
endif

if ( $#SliceDelayFile != 0 && $#SliceOrder != 0 ) then
if ( 0 != 0 && 1 != 0 ) then

goto check_params_return ;
goto check_params_return


if ( $nolog ) then
if ( 0 ) then

set logdir = log ;
set logdir = log
mkdir -p $logdir
mkdir -p log
if ( ! -e $logdir ) then
if ( ! -e log ) then

if ( $#SessList > 1 ) then
if ( 1 > 1 ) then

set sb = `basename $SessList`
set sb = `basename $SessList`
basename /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1
set LF = $logdir/preproc-sess.$sb.log
set LF = log/preproc-sess.091223sbj01m_tp1.log
endif
endif
if ( -e $LF ) mv $LF $LF.old
if ( -e log/preproc-sess.091223sbj01m_tp1.log ) mv 
log/preproc-sess.091223sbj01m_tp1.log log/preproc-sess.091223sbj01m_tp1.log.old
mv log/preproc-sess.091223sbj01m_tp1.log 
log/preproc-sess.091223sbj01m_tp1.log.old
endif
endif
endif
endif
echo

Re: [Freesurfer] recon-all-clinical synthseg error

2024-03-04 Thread Agata Wolna

External Email - Use Caution

Hi!

I've managed to debug the problem and it turns out that it was generated by
the mri_convert function - it produced a corrupted native.mgz image that
synthseg couldn't correctly read. I encounter this problem when pulling the
freesurfer:7.4.1 from dockerhub and when I was using a version downloaded
from the freesurfer website. Replacing the mri_convert script with a one
from a previous release (7.1.1) solved the problem, but I'm just letting
you know, in case that's a more general issue (and in all cases I was
running the script in a singularity containers).

Best wishes,
Agata

pon., 26 lut 2024 o 11:02 Agata Wolna  napisał(a):

> Hi!
>
> Thanks for getting back to me. I'm running it on CentOS Linux 7 in a
> singularity container. What I did is to pull the freesurfer container from
> the DockerHub 
> (https://secure-web.cisco.com/171ahSlRX4vDMQD6prCFbKOWLRaTb3TeYqaUPEw1RHNCsVe3tGhp2kLFzWK3DJBLSx-UgUbpykn2uadM_p35sDDmGGUu-97iv7xWk1uOF7fCA5zzinTnVGh-ThVdtMXCb9wrWbtVUluLHZqPDir9P61Y41lyQx6J8ExkHyMN3nDhsdJG3NKQ0YCbHpN6OXcbMXy6k6AGFamQP8CZo_1lxhCV5WCZD26w_wkehvkhvpWl7Dd8-79VHNEEopR-cjICmGSqmg7GHDHiBc1SkoGDf-Hrij5PrwTlD6yLqb5U83FrN3wzFoW9dq-kjChSC2PKLUxnb8MKiKmHqCpn6WhL36g/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Ffreesurfer%3A7.1.1)
>  and
> I replaced the /usr/local/freesurfer with this version:
> https://secure-web.cisco.com/1kTRkrixWgWU1iw8Qqe5X9q-Fz5Cs0dBxd03uelbVyK3aahbt-NDyUMFDpzSxsqPZKM2WUqoyOMnywfNkFMZP_5uzLcnYmhRlPJwt6eoOMbmo_-bFRvK9YV6H-tS6FGTlH7lZCDQw4Tr2_WlN4a-2ByEqPmRw_RHrKq8SU2Sk4aNDWHoS5lPwMqIs5td3Mpd2KWBbQCJ7f20xoIDdqxcxnMQ5K3m5nC2y5sS1QzfGMOTXHSLiC-7D-Dr218ggnoS6u3Eg-UqVFYGtZZm_ACvQ6OSAYJ7z7VdTRgX6PRuMv1mQLduPWJ1CXUv1RmUDCBI4mZKBJZd0GkBTpL_9yzF30w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
>  (build-stamp
> is freesurfer-linux-centos7_x86_64-dev-20240209-8d5b885).
>
> Do you think that this might be an issue related to the differences in
> dependencies for the 7.1.1 and the dev version that I replaced the 7.1.1
> with? Also, if you happen to have a containerized version of the newest dev
> version (or any version higher than 7.4, as I assume they would all support
> the recon-all-clinical function, right?) maybe I could just pull the entire
> container from somewhere and see if it solves the problem?
>
> Best wishes,
> Agata
>
> niedz., 25 lut 2024 o 21:56 fsbuild  napisał(a):
>
>>
>> It could help to know what OS version and what Freesurfer version you are
>> running.  From your path /usr/local/freesurfer it looks like you are
>> running a Freesurfer release, e.g.., 7.4.1.
>>
>> - R.
>>
>> On Feb 25, 2024, at 21:45, Agata Wolna  wrote:
>>
>> External Email - Use Caution
>>
>> Hi!
>>
>> I'm trying to run recon-all-clinical but I'm running into an error with
>> the SynthSeg at the very beginning. Do you have any hints what the problem
>> might be here? Here's the full error message:
>>
>> the following problem occured with image [mypath]/mri/native..mgz :
>> Traceback (most recent call last):
>>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in
>> predict
>> image, aff, h, im_res, shape, pad_idx, crop_idx =
>> preprocess(path_image=path_images[i],
>>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in
>> preprocess
>> im, _, aff, n_dims, n_channels, h, im_res =
>> get_volume_info(path_image, True)
>>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in
>> get_volume_info
>> im, aff, header = load_volume(path_volume, im_only=False)
>>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in
>> load_volume
>> x = nib.load(path_volume)
>>   File
>> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/loadsave.py",
>> line 110, in load
>> img = image_klass.from_filename(filename, **kwargs)
>>   File
>> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
>> line 503, in from_filename
>> return klass.from_file_map(file_map, mmap=mmap,
>> keep_file_open=keep_file_open)
>>   File
>> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
>> line 526, in from_file_map
>> header = klass.header_class.from_fileobj(mghf)
>>   File
>> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
>> line 171, in from_fileobj
>> + int(klass._data_type_codes.bytespervox[tp]) *
>> np.prod(hdr_str_to_np['dims'])
>> KeyError: 10
>>
>> resuming program execution
>>
>>
>> ERROR: some problems occured for the following inputs (see corresponding
>> errors above):
>> [mypath]/mri/native..mgz
>> Error in SynthSeg
>>
>> Best,
>> Agata
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>>

Re: [Freesurfer] Citing the bert dataset

2024-03-04 Thread Fischl, Bruce R.,PHD

I guess if nothing else you can cite the 2012 FreeSurfer paper

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Shounak Nandi
Sent: Monday, March 4, 2024 2:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Citing the bert dataset

External Email - Use Caution
Hi,

I have used the 
bert

 dataset in one of the scientific works and was curious how I cite it?

I am eager to know your thoughts.

Thanks,
Shounak Nandi

Radiology Trainee,
Department of Radiology and Radiological Science,
Division of Cancer Imaging Research,
Johns Hopkins School of Medicine,
Baltimore, MD
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Citing the bert dataset

2024-03-04 Thread Shounak Nandi

External Email - Use Caution

Hi,

I have used the 
bert
 

 dataset in one of the scientific works and was curious how I cite it?

I am eager to know your thoughts.

Thanks,
Shounak Nandi

Radiology Trainee,
Department of Radiology and Radiological Science,
Division of Cancer Imaging Research,
Johns Hopkins School of Medicine,
Baltimore, MD
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

2024-03-04 Thread Huang, Yujing

1. 'mris_convert' uses the metadata 'AnatomicalStructurePrimary' value in 
surface gii to determine the left/right hemi
grep -A 2 -B 1 'AnatomicalStructurePrimary' surf/lh.white.gii
 


 

2. I think the error that you get from 'mri_aparc2aseg' is because the .annot 
is for fsaverage not the individual subject surface. I think you can use 
mri_surf2surf to generate .annot in individual surface space - 
https://freesurfer.net/fswiki/mri_surf2surf

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 5:55 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi again and sorry for the very confusing questions...



I now (without really knowing what I did) managed to get

mris_convert --annot left.fsaverage_MY_PARC_2_164.label.gii 
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii 
lh.MY_PARC_164k_1.annot

to run without errors. However it creates an .annot file with a rh.lh -prefix, 
eg rh.lh.MY_PARC_164k_1.annot

I've checked multiple times that the .label.gii file used as input is really 
Left Hemisphere. I tried just renaming the .annot file but then

mri_aparc2aseg --old-ribbon --s subject --annot MY_PARC_164k_1 --o 
MY_PARC_164k_1.mgz

gives the following error


Loading lh annotations from ~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot
error: No such file or directory
error: # elements (163842) in 
~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot and # vertices (154818) 
don't match
ERROR: MRISreadAnnotation() failed 
~/subjects_dir/subject/label/lh.MY_PARC_164k_1.annot

best and thanks for the help

karin


From: 
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 support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

All these filenames are too similar. You mentioned at least 3 different files.

mris_info 
fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error)
mris_info 
fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii(ok)
mris_convert 
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii (error)
ls -lt   
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii  (ok)

Make sure the file exists and provide full path to mris_info/mris_convert 
command.

If you continue to have problems with mris_info/mris_convert, share the .gii 
and we will take a closer look.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi again this gives


ls -lt fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
-rw-rw-r-- 1 karin karin 4323015 feb 29 21:54 
fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
best

karin


From: 
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 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

It seems to me that it failed to open the .gii file.

Can you check if 
'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii' exists and you 
have the read permission?
'ls -lt fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Westin, Karin
Sent: Thursday, February 29, 2024 4:09 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?


External Email - Use Caution

Hi I realized that the error occurs only with the Lh- file, that also gives 
this error


mris_info fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
** failed to open GIFTI XML file 
'fs_R-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'
gifti_read_image() returned NULL

Is this a freesurfer error or is there something with the file?



thanks

Karin


From:

Re: [Freesurfer] lack of volume called 001.mgz

2024-03-04 Thread Huang, Yujing

I'm not sure what files you copied over. For the initial run of recon-all, you 
need to specify input files using '-i ' option. See recon-all wiki 
help page for detail: 
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: Saturday, March 2, 2024 1:37 PM
To: Freesurfer support list 
Subject: [Freesurfer] lack of volume called 001.mgz

External Email - Use Caution

Dear Yujing,

Thank you very much for your help, but I still have a problem. I copied the 
files to create another SUBJECTS_DIR inside my Linux...I get the following 
error when I run the recon-all -all -s command:

gcm@LAP-LKP:~$ recon-all -all -s NowakG
fs-check-version --s NowakG --o /tmp/tmp.W9nDpk Sat Mar  2 19:14:18 CET 2024

setenv SUBJECTS_DIR /subjects
cd /home/gcm
/usr/local/freesurfer/7.3.2/bin/fs-check-version --s NowakG --o /tmp/tmp.W9nDpk 
-rwxr-xr-x 1 root root 18565 Aug  4  2022 
/usr/local/freesurfer/7.3.2/bin/fs-check-version

freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
$Id$
Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux pid 2145 Current FS Version
freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
bstampfile exists /subjects/NowakG/scripts/build-stamp.txt
Subject FS Version: 
freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275
No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% 
fs-check-version match = 1 fs-check-version Done
INFO: SUBJECTS_DIR is /subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2
-rw-rw-r-- 1 gcm gcm 89354 Mar  2 18:42 /subjects/NowakG/scripts/recon-all.log
Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
#
#@# MotionCor Sat Mar  2 19:14:18 CET 2024
ERROR: no run data found in /subjects/NowakG/mri. Make sure to have a volume 
called 001.mgz in  /subjects/NowakG/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: 
http://secure-web.cisco.com/1tuieePwmpGJNz-se1po4eAte-Piv-L3dyFVwTAhmaZp1yuYYA6WDplZIn_eOMWSQ6XNWLWosRbbqgelF1dP6cwLzm49NGnC06aPYcm9dVEqiJHPlKBBJdCOCc5UpBZKFISeT2vAsKPmtPe5bSN1PtnI37qzrEzfKZy04iVyZ7gO9j5K9chOEjC-f8PIW5LZ1QreMBW2MF4XAAmUD9cfwmgL-W-Xp87kV3_MnP7BzXmeq7Jcd1g7syzCCfGmQTOgp8StEekKQqnO96-4yhVqPeMcxevRvfvieGQEmdvybuW2fdVKNNP-v_6GslOFvUscl9fCLKOFTtLXKsa3Hnw_gYg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FConversion
Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5
21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s NowakG exited with ERRORS at Sat Mar  2 19:14:18 CET 2024

For more details, see the log file
/subjects/NowakG/scripts/recon-all.log
To report a problem, see
http://secure-web.cisco.com/1ufOUDYmRZBZH5OvNEdAvUSqehiGigkQXoMoJ5I3aSHOfsc36kcTvYNgNB3aBZ4jVdHB0nuAnVNJWxdRwzvXmwEPI3gDUdU4QRXnZbUR1wcB5OQxntw7Z5gopDmzqs9na5EBTZln5BzgpoULJxgLdPUVbjXFh90-tX1tjhSxELnft_ckbwlGbLrRKwrBBCKMy_wZKQlYHCq_mwPmJG9BFcPayLVp7kVjiKDvmTBGdY6Zu5EuMOFDJ2P8ZQVDTueZfXLtA67Bvr353l_R5YXyreMeaC-ozgMEC92WM24o5BpFOk4M0MsW9VOofqZy5uFd7nnpikbOdTUnpE4XwkWOz8A/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Could you please give me advice what is wrong?

Best regards,
Joanna



W dniu 2024-01-08 23:25, fsbuild napisał(a):
> External Email - Use Caution
> 
>   Let me add that it will not work to use shared mount point from the 
> Windows filesystem as you list below,
> 
>> /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri
> 
> - for your SUBJECTS_DIR when running a recon-all command.  The command 
> will fail because the Windows file system does not support soft-links.
>   Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS 
> image running freesurfer.  You could however copy the files from that 
> mount point to create another SUBJECTS_DIR somewhere inside your Linux 
> image, e.g., under your home directory in linux.
> 
> ... in your linux terminal window ...
> 
> $ cd
> $ mkdir subjects
> $ export SUBJECTS_DIR=$HOME/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://secure-web.cisco.com/1BjMQpgiIYbM2liRLcu1lhuxV-DQbuX4Z-UYpPPpt
> MAbFi-NJiLZF1zFn86PASJOkrN6-GWw1d4D3OrHd1v-GqrcqNMoqsq_voJWaLftiEd-vak
> jsu5IvQ6kyUg5k7ghDpdCZU14EMBNDP8eYcsCjl1E5D5gNql2i-Y9Zu1Kpc6TuQh3odI2O
> ietrxyv5hM2H9YDVJ2J51cEZLa2CHRqUpe5QTE89g3k1kNK7jl8nNBK5kqYLoLEuZ-gJrr
> h_Ac2wDqYS5bIbjvKJN4lXnWjHzt6IJAq6spPNw_wAGm40hlLBAz-b5P1MtR3NajhBpUlp
> PBt-Yo9PLR0TwzBHrCLiHA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswi
> ki%2Frecon-all
> 
> Best,
> 
> Yujing
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  On Behalf Of Joanna Kidon
> Sent: Monday, January

Re: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects

2024-03-04 Thread Philip P

External Email - Use Caution

Thanks Malte, that is very helpful ! 

> On 01.03.2024, at 08:20, Hoffmann, Malte,PhD  
> wrote:
> 
> If you construct the non-linear template within the current rigid (or affine) 
> mid-space, then there are two things you can do.
> 
> (1) You can just replace the base image and run the remainder of the base and 
> longitudinal streams as is to transfer the results out to the TPs using the 
> rigid (or affine) LTAs. This is what we did in the abstract, showing 
> improvements with a better-quality base image that can lead to better 
> longitudinal initialization.
> 
> (2) On top of this, you can use the warps to initialize the longitudinal TPs 
> as you suggest. Unfortunately, we found that this does not always improve 
> things. For example, volumetric warps are often not that great around the 
> cortex, and initializing the longitudinal surfaces with warps instead of the 
> LTAs turned out to be detrimental when I looked into this.
> 
> In principle, we adapted the steps of the longitudinal stream to accept warps 
> but it’s been several years and I’ve not kept track of changes. If you’re up 
> for the challenge, mri_warp_convert --outmgzwarp/--outm3z can be helpful 
> depending on how you estimate your warps.
> 
> 
> From: Philip P mailto:philip.pruck...@gmail.com>>
> Sent: Wednesday, February 28, 2024 20:41
> To: Hoffmann, Malte,PhD
> Cc: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: [Freesurfer] Longitudinal Freesurfer in the presence of large 
> tissue defects
> 
>External Email - Use Caution
> 
> Hi Malte,
> 
> Thanks for the response, it’s encouraging to hear you think the longitudinal 
> pipeline will still provide benefits, even in the absence of a non-linear 
> template!
> 
> However out of interest: I was able to generate a non-linear unbiased session 
> template without moving tissue from outside into the resection area. If I’d 
> want to use this template for the analysis, is there any modifications I’d 
> have to make to the existing workflow except for 1) using the non-linear 
> template as norm_template.mgz and 2) running all commands that make use of 
> the session_to_template.lta transforms with the appropriate non-linear warps?
> 
> Thanks for your help, its greatly appreciated !
> 
> Best,
> Philip
> 
> 
>> On 27.02.2024, at 08:42, Hoffmann, Malte,PhD  
>> wrote:
>> 
>> Hi Philip,
>> 
>> The deformable template was most beneficial when differences between time 
>> points (TPs) were largest. While this is perhaps not surprising, it meant 
>> that the long registration time of 8h/TP in the abstract was not time well 
>> spent since we were already certain of group differences.
>> 
>> We generally recommend the longitudinal stream for longitudinal data since 
>> much information is shared between the TPs. The median rigid template is 
>> typically a robust starting point for the processing of the individual TPs, 
>> sometimes even for developmental studies where you see the size of the brain 
>> increase.
>> 
>> In your specific case, non-linear registration (using an image-intensity 
>> objective like in the abstract) might be detrimental. The algorithm will 
>> likely move tissue from outside the resected area into this area since the 
>> scan before resection will have matching intensities there, but this won’t 
>> necessarily make for a good template.
>> 
>> Malte
>> 
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Philip P 
>> 
>> Sent: Sunday, February 4, 2024 01:48
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: [Freesurfer] Longitudinal Freesurfer in the presence of large  
>> tissue defects
>> 
>>   External Email - Use Caution
>> 
>> Dear Freesurfer Developers,
>> 
>> I am currently running the Longitudinal Pipeline on a cohort with 
>> significant portions of brain tissue removed. The obtained base templates 
>> overall look reasonable, however, when overlaying the transformed session 
>> T1ws and flicking between them, there still are noticeable residual 
>> differences. This is not surprising, given the inevitable brain shift after 
>> tissue removal, which rigid registration cannot account for. In my search 
>> for a non-linear base template option I came across the "Longitudinal 
>> FreeSurfer with non-linear subject-specific template improves sensitivity to 
>> cortical thinning” ISMRM abstract (MailScanner has detected a possible fraud 
>> attempt from "secure-web.cisco.com " claiming 
>> to be 
>>

Re: [Freesurfer] if: Expression Syntax - preproc-sess

Re: [Freesurfer] recon-all-clinical synthseg error

Re: [Freesurfer] Citing the bert dataset

[Freesurfer] Citing the bert dataset

Re: [Freesurfer] [ext] Re: mris_convert reading surf.gii files?

Re: [Freesurfer] lack of volume called 001.mgz

Re: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects

7 matches

Site Navigation

Mail list logo

Footer information