Hi Kilian,
Can you try adding '-careg'? Put it after "-autorecon2 -autorecon3".
Best,
Yujing
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Kilian M Pohl
Sent: Wednesday, December 7, 2022 10:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2
External Email - Use Caution
sorry listed wrong command line - after autrecon1 I run the following command
/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd
LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7
-autorecon2 -autorecon3 -no-isrunning -s
LAB_S01541_standard_20180307_4541_03072018 -no-fix-with-ga -rng-seed 1234
which is the one failing bc it cannot find transforms/talairach.m3z
#--------------------------------------
#@# SubCort Seg Tue Dec 6 17:58:54 UTC 2022
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz
transforms/talairach.m3z
/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca
aseg.auto_noCCseg.mgz
sysname Linux
hostname 3c46017221f4
machine x86_64
setenv SUBJECTS_DIR
/data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7
cd
/data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz
transforms/talairach.m3z
/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca
aseg.auto_noCCseg.mgz
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using
Gibbs prior factor = 0.500 renormalizing sequences with structure alignment,
equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
== Number of threads available to for OpenMP = 4 == reading 1 input volumes
reading classifier array from
/usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca
reading input volume from norm.mgz
average std[0] = 7.2
reading transform from transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
error: No such file or directory
error: transforms/talairach.m3z: could not open transform
Best,
Kilian
On 12/7/2022 10:37 AM, Huang, Yujing wrote:
> Hi Kilian,
>
> I'm wondering what were your initial recon-all commands for FS 5.3 and FS
> 7.1.1 because I'm not sure '-autorecon1' is making mri_ca_register call by
> default.
>
> But It looks like you can use '-careg' to turn on mri_ca_register call.
>
> Here is a description of recon-all steps:
> https://secure-web.cisco.com/1htG9ZyeR94R_NHNY2O3znkDPMKCM94AkH1H0RTut
> 4TvM_XNOMp0b5IpfWMN7VaDVEGT1aTGDBGyyZvW4Nj5L3Jb4Tp90UiTrCAvyd27dxmIE_X
> ROTE0gqoE38RdR4TKP6LuV7mtS1Z-CIqEVQbcWi8yu-PKAb0IwpB8IfntCbMCcVlRSbMfJ
> HKa1FDowaKA1unNg3oUyPiX8AYXRQHKTyuIt5xsfA7-sPU3N4BRDSQSOJ-FH0oNHnApsKU
> ytFLrwfuhXgCiF_erN1CzrSjUDJxHgWmdO50hq99m225g7BQmmhC7eWJbORDT4zpF-8osy
> /https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all
>
> Best,
>
> Yujing
>
> -----Original Message-----
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Kilian M Pohl
> Sent: Wednesday, December 7, 2022 12:53 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] ma_ca_register is not called anymore in version
> 7.3.2
>
> External Email - Use Caution
>
> Hi ,
>
> I have used the following call starting at Freesurfer 5.3
>
> /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd
> LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7
> -autorecon1 -noskullstrip -no-isrunning -s
> LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234
>
> It is still working with Freesurfer 7.1.1 but we now tried updating to
> 7.3 and it is failing (on the same case). Looking at the recon-all.log
> it seem that ma_ca_register is not called anymore so that I get the
> following error message
>
> ERROR: cannot find or read transforms/talairach.m3z
>
> (see attached recon-all .log)
>
> Do I have to add flags ? I need to run with -noskullstrip
>
> Best,
>
> Kilian
>
>
>
> --
> Kilian M. Pohl, Ph.D.
>
> Associate Professor
> Department of Psychiatry & Behavioral Sciences Stanford University
>
> 401 Quarry Road
> Stanford, CA 94305-5717
>
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--
Kilian M. Pohl, Ph.D.
Associate Professor
Department of Psychiatry & Behavioral Sciences Stanford University
401 Quarry Road
Stanford, CA 94305-5717
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