Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}
External Email - Use Caution
Hi Martin,
That was helpful! Thanks a lot =)!
Sincerely,
Guoyang
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez,
Eugenio
Sent: Tuesday, 30 October, 2018 3:42 PM
To: Freesurfer support list; Freesurfer support list
Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform
file {Disarmed}
[]
External Email - Use Caution
Hi Gouyang
There's no T2 longitudinal pipeline available at the moment.
In its absence, what you're doing is the way to go ;-)
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Chen Guoyang (IMH)
Sent: Tuesday, October 30, 2018 4:00:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform
file {Disarmed}
External Email - Use Caution
Hi Martin,
Thanks for the input! It worked perfectly.
A follow up question:
I understand that for T1 hippocampal subfield segmentation, Freesurfer has a
longitudinal module for it (segmentHA_T1.long.sh)
Does freesurfer have a longitudinal module for T1+T2 hippocampal segmentations?
If such a module is not available, will just like to consult you guys whether
are our current processing steps appropriate for longitudinal comparisons:
1. Run the longitudinal pipeline (FSv6.0) across all our subjects and
each of their timepoints, example:
recon-all –long Subject1_timepoint1 Subject1_base
recon-all –long Subject1_timepoint2 Subject1_base
2. Run segmentHA_T2.sh across each longitudinal scan of each of our
subjects, example:
segmentHA_T2.sh Subject1_timepoint1 Subject1_timepoint1.long.Subject1_base
Subject1_timepoint1_T2.nii T2 1
segmentHA_T2.sh Subject1_timepoint2 Subject1_timepoint2.long.Subject1_base
Subject1_timepoint2_T2.nii T2 1
Thanks!
Yours Sincerely,
Guoyang
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Saturday, 27 October, 2018 4:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform
file
Hi,
Looks like the input is a multi frame image. Should only be single frame.
Best Martin
On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
It seems like a problem with mri_robust_register.
Martin, any ideas?
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
MailScanner has detected a possible fraud attempt from
"imsva91-ctp.trendmicro.com:443" claiming to be
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From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Chen Guoyang (IMH)"
mailto:guoyang_c...@imh.com.sg>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 26 October 2018 at 11:35
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file
External Email - Use Caution
Dear Freesurfer experts,
I am currently attempting to include an additional T2 MRI scan in the
segmentation of our T1 scan. The freesurfer version that I'm using is the
freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).
However, I ran into this issue, ERROR: cannot find transform file. I've pasted
the output below.
Will like your advices for the this matter.
Thanks!
Sincerely,
Guoyang
OS Darwin
Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4
00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64
--
#
#@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib:
Registering norm.mgz to additional volume
/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single
frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.
/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz
--maskmov
/U
Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}
External Email - Use Caution
Hi Gouyang
There's no T2 longitudinal pipeline available at the moment.
In its absence, what you're doing is the way to go ;-)
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Chen Guoyang (IMH)
Sent: Tuesday, October 30, 2018 4:00:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform
file {Disarmed}
External Email - Use Caution
Hi Martin,
Thanks for the input! It worked perfectly.
A follow up question:
I understand that for T1 hippocampal subfield segmentation, Freesurfer has a
longitudinal module for it (segmentHA_T1.long.sh)
Does freesurfer have a longitudinal module for T1+T2 hippocampal segmentations?
If such a module is not available, will just like to consult you guys whether
are our current processing steps appropriate for longitudinal comparisons:
1. Run the longitudinal pipeline (FSv6.0) across all our subjects and
each of their timepoints, example:
recon-all –long Subject1_timepoint1 Subject1_base
recon-all –long Subject1_timepoint2 Subject1_base
2. Run segmentHA_T2.sh across each longitudinal scan of each of our
subjects, example:
segmentHA_T2.sh Subject1_timepoint1 Subject1_timepoint1.long.Subject1_base
Subject1_timepoint1_T2.nii T2 1
segmentHA_T2.sh Subject1_timepoint2 Subject1_timepoint2.long.Subject1_base
Subject1_timepoint2_T2.nii T2 1
Thanks!
Yours Sincerely,
Guoyang
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Saturday, 27 October, 2018 4:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform
file
Hi,
Looks like the input is a multi frame image. Should only be single frame.
Best Martin
On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio
mailto:e.igles...@ucl.ac.uk>> wrote:
It seems like a problem with mri_robust_register.
Martin, any ideas?
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedical Engineering
University College London
MailScanner has detected a possible fraud attempt from
"imsva91-ctp.trendmicro.com:443" claiming to be
http://www.jeiglesias.com<https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.jeiglesias.com=03F7EE2E-7932-1105-AA91-DA9BE547B048=6e3fe59570831a389716849e93b5d483c90c3fe4-dbc6e738e10a2646a86a99f0c9e164a3bdf6af7c>
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Chen Guoyang (IMH)"
mailto:guoyang_c...@imh.com.sg>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 26 October 2018 at 11:35
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file
External Email - Use Caution
Dear Freesurfer experts,
I am currently attempting to include an additional T2 MRI scan in the
segmentation of our T1 scan. The freesurfer version that I'm using is the
freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).
However, I ran into this issue, ERROR: cannot find transform file. I've pasted
the output below.
Will like your advices for the this matter.
Thanks!
Sincerely,
Guoyang
OS Darwin
Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4
00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64
--
#
#@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib:
Registering norm.mgz to additional volume
/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single
frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.
/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz
--maskmov
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz
--dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta
--noinit --cost NMI -nosym >/dev/null: Signal 127
ERROR: cannot find transform file
/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/
Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}
External Email - Use Caution Hi Martin, Thanks for the input! It worked perfectly. A follow up question: I understand that for T1 hippocampal subfield segmentation, Freesurfer has a longitudinal module for it (segmentHA_T1.long.sh) Does freesurfer have a longitudinal module for T1+T2 hippocampal segmentations? If such a module is not available, will just like to consult you guys whether are our current processing steps appropriate for longitudinal comparisons: 1. Run the longitudinal pipeline (FSv6.0) across all our subjects and each of their timepoints, example: recon-all -long Subject1_timepoint1 Subject1_base recon-all -long Subject1_timepoint2 Subject1_base 2. Run segmentHA_T2.sh across each longitudinal scan of each of our subjects, example: segmentHA_T2.sh Subject1_timepoint1 Subject1_timepoint1.long.Subject1_base Subject1_timepoint1_T2.nii T2 1 segmentHA_T2.sh Subject1_timepoint2 Subject1_timepoint2.long.Subject1_base Subject1_timepoint2_T2.nii T2 1 Thanks! Yours Sincerely, Guoyang From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter Sent: Saturday, 27 October, 2018 4:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file Hi, Looks like the input is a multi frame image. Should only be single frame. Best Martin On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: It seems like a problem with mri_robust_register. Martin, any ideas? -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com<https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.jeiglesias.com=03F7EE2E-7932-1105-AA91-DA9BE547B048=6e3fe59570831a389716849e93b5d483c90c3fe4-dbc6e738e10a2646a86a99f0c9e164a3bdf6af7c> From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Chen Guoyang (IMH)" mailto:guoyang_c...@imh.com.sg>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, 26 October 2018 at 11:35 To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file External Email - Use Caution Dear Freesurfer experts, I am currently attempting to include an additional T2 MRI scan in the segmentation of our T1 scan. The freesurfer version that I'm using is the freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version). However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below. Will like your advices for the this matter. Thanks! Sincerely, Guoyang OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 -- # #@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018 -- Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib: Registering norm.mgz to additional volume /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii. /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz --maskmov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta gunzip: can't stat: /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (l
Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file
Hi, Looks like the input is a multi frame image. Should only be single frame. Best Martin > On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio > wrote: > > It seems like a problem with mri_robust_register. > Martin, any ideas? > > -- > Juan Eugenio Iglesias > Centre for Medical Image Computing (CMIC) > Department of Medical Physics and Biomedical Engineering > University College London > http://www.jeiglesias.com <http://www.jeiglesias.com/> > > > > From: on behalf of "Chen Guoyang > (IMH)" > Reply-To: Freesurfer support list > Date: Friday, 26 October 2018 at 11:35 > To: "freesurfer@nmr.mgh.harvard.edu" > Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file > > External Email - Use Caution > > Dear Freesurfer experts, > > > > I am currently attempting to include an additional T2 MRI scan in the > segmentation of our T1 scan. The freesurfer version that I'm using is the > freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version). > > > > However, I ran into this issue, ERROR: cannot find transform file. I've > pasted the output below. > > > > Will like your advices for the this matter. > > > > Thanks! > > > > Sincerely, > > Guoyang > > > > OS Darwin > Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 > 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 > -- > > # > #@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018 > -- > Setting up environment variables > --- > DYLD_LIBRARY_PATH is > .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib: > Registering norm.mgz to additional volume > /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass > single frame MRI target > /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii. > > /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov > /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz > --maskmov > /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz > --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta > /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta > --noinit --cost NMI -nosym >/dev/null: Signal 127 > ERROR: cannot find transform file > /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta > gunzip: can't stat: > /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz > > (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz): > No such file or directory > ERROR: problem reading fname > SWITCH expression must be a scalar or string constant. > > Error in myMRIread>load_mgh (line 550) > > > > Error in myMRIread>myMRIread_aux (line 92) > > > > Error in myMRIread (line 63) > > > > Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207) > > > > MATLAB:badSwitchExpression > Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 > 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 > > T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file
External Email - Use Caution It seems like a problem with mri_robust_register. Martin, any ideas? -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com From: on behalf of "Chen Guoyang (IMH)" Reply-To: Freesurfer support list Date: Friday, 26 October 2018 at 11:35 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file External Email - Use Caution Dear Freesurfer experts, I am currently attempting to include an additional T2 MRI scan in the segmentation of our T1 scan. The freesurfer version that I'm using is the freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version). However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below. Will like your advices for the this matter. Thanks! Sincerely, Guoyang OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 -- # #@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018 -- Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib: Registering norm.mgz to additional volume /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii. /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz --maskmov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta gunzip: can't stat: /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207) MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file
External Email - Use Caution Dear Freesurfer experts, I am currently attempting to include an additional T2 MRI scan in the segmentation of our T1 scan. The freesurfer version that I'm using is the freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version). However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below. Will like your advices for the this matter. Thanks! Sincerely, Guoyang OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 -- # #@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018 -- Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib: Registering norm.mgz to additional volume /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii. /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz --maskmov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta gunzip: can't stat: /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 207) MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
